Starting phenix.real_space_refine on Wed Mar 4 19:45:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jg1_22309/03_2026/7jg1_22309_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jg1_22309/03_2026/7jg1_22309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jg1_22309/03_2026/7jg1_22309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jg1_22309/03_2026/7jg1_22309.map" model { file = "/net/cci-nas-00/data/ceres_data/7jg1_22309/03_2026/7jg1_22309_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jg1_22309/03_2026/7jg1_22309_trim.cif" } resolution = 3.3 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= 0.000 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 58 5.16 5 C 5014 2.51 5 N 1341 2.21 5 O 1590 1.98 5 H 7808 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15811 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3471 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 213} Chain: "B" Number of atoms: 3374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3374 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 17, 'TRANS': 206} Chain: "C" Number of atoms: 3457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3457 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 213} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3404 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 17, 'TRANS': 210} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 2049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2049 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 10, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.98, per 1000 atoms: 0.19 Number of scatterers: 15811 At special positions: 0 Unit cell: (154.66, 85.272, 131.252, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 O 1590 8.00 N 1341 7.00 C 5014 6.00 H 7808 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 237 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS A 261 " - pdb=" SG CYS A 318 " distance=2.04 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS B 294 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 427 " distance=2.04 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS J 68 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 261 " - pdb=" SG CYS B 318 " distance=2.04 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 427 " distance=2.04 Simple disulfide: pdb=" SG CYS C 237 " - pdb=" SG CYS C 296 " distance=2.03 Simple disulfide: pdb=" SG CYS C 261 " - pdb=" SG CYS C 318 " distance=2.03 Simple disulfide: pdb=" SG CYS C 294 " - pdb=" SG CYS D 294 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 427 " distance=2.04 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS J 14 " distance=2.04 Simple disulfide: pdb=" SG CYS D 237 " - pdb=" SG CYS D 296 " distance=2.03 Simple disulfide: pdb=" SG CYS D 261 " - pdb=" SG CYS D 318 " distance=2.03 Simple disulfide: pdb=" SG CYS D 364 " - pdb=" SG CYS D 427 " distance=2.04 Simple disulfide: pdb=" SG CYS J 12 " - pdb=" SG CYS J 101 " distance=2.03 Simple disulfide: pdb=" SG CYS J 71 " - pdb=" SG CYS J 91 " distance=2.05 Simple disulfide: pdb=" SG CYS J 109 " - pdb=" SG CYS J 134 " 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=1, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG B 501 " - " ASN B 452 " " NAG D 501 " - " ASN D 452 " " NAG E 1 " - " ASN J 48 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 495.1 milliseconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 25 sheets defined 11.7% alpha, 46.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 350 through 355 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'B' and resid 247 through 252 removed outlier: 3.677A pdb=" N LEU B 251 " --> pdb=" O ALA B 247 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 247 through 252' Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 350 through 355 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'C' and resid 247 through 253 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 386 through 388 No H-bonds generated for 'chain 'C' and resid 386 through 388' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'D' and resid 248 through 253 Processing helix chain 'D' and resid 306 through 313 Processing helix chain 'D' and resid 350 through 356 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 415 through 422 Processing helix chain 'J' and resid 64 through 68 Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 244 Processing sheet with id=AA2, first strand: chain 'A' and resid 240 through 244 Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 276 Processing sheet with id=AA4, first strand: chain 'A' and resid 343 through 347 removed outlier: 3.524A pdb=" N THR A 363 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR A 406 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 343 through 347 removed outlier: 3.524A pdb=" N THR A 363 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N TYR A 406 " --> pdb=" O ALA A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 375 through 379 removed outlier: 3.635A pdb=" N SER A 426 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N PHE A 438 " --> pdb=" O ALA J 128 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 453 through 460 removed outlier: 7.091A pdb=" N VAL A 453 " --> pdb=" O SER B 454 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N SER B 456 " --> pdb=" O VAL A 453 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A 455 " --> pdb=" O SER B 456 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ILE B 458 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL A 457 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N SER B 460 " --> pdb=" O VAL A 457 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET A 459 " --> pdb=" O SER B 460 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N PHE J 60 " --> pdb=" O SER A 454 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N SER A 456 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N TYR J 62 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE A 458 " --> pdb=" O TYR J 62 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.756A pdb=" N THR B 260 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR B 297 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 244 removed outlier: 3.756A pdb=" N THR B 260 " --> pdb=" O GLN B 244 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR B 297 " --> pdb=" O GLY B 265 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 276 Processing sheet with id=AB2, first strand: chain 'B' and resid 343 through 347 removed outlier: 3.711A pdb=" N THR B 363 " --> pdb=" O LEU B 347 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N TYR B 406 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU B 407 " --> pdb=" O PRO B 395 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 409 " --> pdb=" O PHE B 393 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 383 through 384 Processing sheet with id=AB4, first strand: chain 'C' and resid 240 through 244 removed outlier: 5.645A pdb=" N THR C 260 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 303 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR C 262 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N SER C 301 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN C 264 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 299 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 240 through 244 removed outlier: 5.645A pdb=" N THR C 260 " --> pdb=" O LEU C 303 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N LEU C 303 " --> pdb=" O THR C 260 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR C 262 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N SER C 301 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASN C 264 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL C 299 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 273 through 276 Processing sheet with id=AB7, first strand: chain 'C' and resid 343 through 347 Processing sheet with id=AB8, first strand: chain 'C' and resid 343 through 347 Processing sheet with id=AB9, first strand: chain 'C' and resid 383 through 384 removed outlier: 3.629A pdb=" N LEU C 375 " --> pdb=" O GLY C 430 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE C 438 " --> pdb=" O THR J 86 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU J 78 " --> pdb=" O GLN J 81 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 454 through 458 removed outlier: 3.760A pdb=" N THR J 18 " --> pdb=" O ASN J 36 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG J 16 " --> pdb=" O ARG J 38 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA J 8 " --> pdb=" O VAL J 17 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N SER J 19 " --> pdb=" O ILE J 6 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE J 6 " --> pdb=" O SER J 19 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 465 through 466 Processing sheet with id=AC3, first strand: chain 'D' and resid 240 through 244 removed outlier: 3.538A pdb=" N SER D 240 " --> pdb=" O ASN D 264 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N THR D 260 " --> pdb=" O LEU D 303 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N LEU D 303 " --> pdb=" O THR D 260 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR D 262 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N SER D 301 " --> pdb=" O THR D 262 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASN D 264 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL D 299 " --> pdb=" O ASN D 264 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 273 through 276 removed outlier: 4.217A pdb=" N VAL D 273 " --> pdb=" O THR D 321 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR D 321 " --> pdb=" O VAL D 273 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 319 " --> pdb=" O THR D 275 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 343 through 347 removed outlier: 3.521A pdb=" N GLN D 343 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 343 through 347 removed outlier: 3.521A pdb=" N GLN D 343 " --> pdb=" O ARG D 367 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 383 through 384 362 hydrogen bonds defined for protein. 939 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: 3.29 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 7804 1.02 - 1.22: 6 1.22 - 1.42: 3251 1.42 - 1.63: 4845 1.63 - 1.83: 75 Bond restraints: 15981 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" C2 NAG E 1 " ideal model delta sigma weight residual 1.532 1.652 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN A 268 " pdb="HD22 ASN A 268 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN A 268 " pdb="HD21 ASN A 268 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" ND2 ASN J 48 " pdb="HD21 ASN J 48 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" N ALA A 272 " pdb=" CA ALA A 272 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.30e-02 5.92e+03 7.63e+00 ... (remaining 15976 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.49: 28982 6.49 - 12.99: 11 12.99 - 19.48: 2 19.48 - 25.97: 1 25.97 - 32.46: 2 Bond angle restraints: 28998 Sorted by residual: angle pdb=" CB MET B 428 " pdb=" CG MET B 428 " pdb=" HG3 MET B 428 " ideal model delta sigma weight residual 109.00 76.54 32.46 3.00e+00 1.11e-01 1.17e+02 angle pdb=" SD MET B 428 " pdb=" CG MET B 428 " pdb=" HG3 MET B 428 " ideal model delta sigma weight residual 108.00 76.57 31.43 3.00e+00 1.11e-01 1.10e+02 angle pdb=" C2 NAG E 1 " pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 110.06 88.39 21.67 3.00e+00 1.11e-01 5.22e+01 angle pdb=" C MET B 428 " pdb=" CA MET B 428 " pdb=" HA MET B 428 " ideal model delta sigma weight residual 110.00 91.03 18.97 3.00e+00 1.11e-01 4.00e+01 angle pdb=" CB GLN B 440 " pdb=" CG GLN B 440 " pdb=" HG2 GLN B 440 " ideal model delta sigma weight residual 109.00 92.79 16.21 3.00e+00 1.11e-01 2.92e+01 ... (remaining 28993 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 7154 17.70 - 35.40: 385 35.40 - 53.11: 125 53.11 - 70.81: 43 70.81 - 88.51: 13 Dihedral angle restraints: 7720 sinusoidal: 4335 harmonic: 3385 Sorted by residual: dihedral pdb=" CB CYS C 237 " pdb=" SG CYS C 237 " pdb=" SG CYS C 296 " pdb=" CB CYS C 296 " ideal model delta sinusoidal sigma weight residual 93.00 170.77 -77.77 1 1.00e+01 1.00e-02 7.57e+01 dihedral pdb=" CB CYS C 466 " pdb=" SG CYS C 466 " pdb=" SG CYS J 14 " pdb=" CB CYS J 14 " ideal model delta sinusoidal sigma weight residual 93.00 167.27 -74.27 1 1.00e+01 1.00e-02 7.00e+01 dihedral pdb=" CB CYS A 294 " pdb=" SG CYS A 294 " pdb=" SG CYS B 294 " pdb=" CB CYS B 294 " ideal model delta sinusoidal sigma weight residual -86.00 -36.18 -49.82 1 1.00e+01 1.00e-02 3.41e+01 ... (remaining 7717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 1316 0.203 - 0.405: 2 0.405 - 0.608: 0 0.608 - 0.811: 0 0.811 - 1.013: 2 Chirality restraints: 1320 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN J 48 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -3.41 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 452 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -1.53 -0.87 2.00e-01 2.50e+01 1.89e+01 ... (remaining 1317 not shown) Planarity restraints: 2405 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 268 " -0.114 2.00e-02 2.50e+03 1.12e-01 1.88e+02 pdb=" CG ASN A 268 " 0.009 2.00e-02 2.50e+03 pdb=" OD1 ASN A 268 " 0.108 2.00e-02 2.50e+03 pdb=" ND2 ASN A 268 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 268 " -0.160 2.00e-02 2.50e+03 pdb="HD22 ASN A 268 " 0.157 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 435 " 0.020 2.00e-02 2.50e+03 4.02e-02 1.62e+01 pdb=" N MET B 436 " -0.069 2.00e-02 2.50e+03 pdb=" CA MET B 436 " 0.017 2.00e-02 2.50e+03 pdb=" H MET B 436 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 438 " -0.019 2.00e-02 2.50e+03 3.50e-02 1.22e+01 pdb=" N THR B 439 " 0.060 2.00e-02 2.50e+03 pdb=" CA THR B 439 " -0.015 2.00e-02 2.50e+03 pdb=" H THR B 439 " -0.027 2.00e-02 2.50e+03 ... (remaining 2402 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.04: 179 2.04 - 2.68: 23828 2.68 - 3.32: 44713 3.32 - 3.96: 58066 3.96 - 4.60: 87487 Nonbonded interactions: 214273 Sorted by model distance: nonbonded pdb=" HB2 GLU J 47 " pdb=" HG SER J 54 " model vdw 1.406 2.270 nonbonded pdb=" O PRO D 278 " pdb=" HG SER D 279 " model vdw 1.532 2.450 nonbonded pdb=" OE2 GLU C 353 " pdb="HH12 ARG C 413 " model vdw 1.561 2.450 nonbonded pdb=" OG SER J 50 " pdb=" C1 NAG E 1 " model vdw 1.584 3.100 nonbonded pdb=" HB2 MET B 428 " pdb=" HG3 MET B 428 " model vdw 1.598 1.952 ... (remaining 214268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 237 through 371 or (resid 372 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 373 through 405 or (r \ esid 406 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 407 through 427 or (resid 428 and (name N or name CA or name C o \ r name O or name CB or name CG or name SD or name CE or name H or name HA or nam \ e HB2 or name HB3 or name HG3 or name HE1 or name HE2 or name HE3)) or resid 429 \ through 433 or (resid 434 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name H or name HA or name HB2 or name HB3 \ or name HG or name HD11 or name HD13 or name HD21 or name HD22 or name HD23)) o \ r resid 435 through 439 or (resid 440 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name OE1 or name NE2 or name H or name HA o \ r name HB2 or name HB3 or name HG2 or name HG3)) or resid 441 through 451 or (re \ sid 452 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or \ resid 453 through 460)) selection = (chain 'B' and (resid 237 through 371 or (resid 372 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 373 through 405 or (r \ esid 406 and (name N or name CA or name C or name O or name CB or name H or name \ HA )) or resid 407 through 460)) selection = (chain 'C' and (resid 237 through 371 or (resid 372 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 373 through 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB or name CG or nam \ e SD or name CE or name H or name HA or name HB2 or name HB3 or name HG3 or name \ HE1 or name HE2 or name HE3)) or resid 429 through 433 or (resid 434 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 o \ r name H or name HA or name HB2 or name HB3 or name HG or name HD11 or name HD13 \ or name HD21 or name HD22 or name HD23)) or resid 435 through 439 or (resid 440 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or \ name HG3)) or resid 441 through 451 or (resid 452 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 453 through 460)) selection = (chain 'D' and (resid 237 through 405 or (resid 406 and (name N or name CA or na \ me C or name O or name CB or name H or name HA )) or resid 407 through 427 or (r \ esid 428 and (name N or name CA or name C or name O or name CB or name CG or nam \ e SD or name CE or name H or name HA or name HB2 or name HB3 or name HG3 or name \ HE1 or name HE2 or name HE3)) or resid 429 through 433 or (resid 434 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 o \ r name H or name HA or name HB2 or name HB3 or name HG or name HD11 or name HD13 \ or name HD21 or name HD22 or name HD23)) or resid 435 through 439 or (resid 440 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2 or name H or name HA or name HB2 or name HB3 or name HG2 or \ name HG3)) or resid 441 through 460)) } 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: 3.290 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: 0.090 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.810 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 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 0.261 8197 Z= 0.345 Angle : 0.808 21.674 11205 Z= 0.415 Chirality : 0.059 1.013 1320 Planarity : 0.005 0.054 1441 Dihedral : 12.870 88.510 3074 Min Nonbonded Distance : 1.584 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.33 % Allowed : 5.33 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.24), residues: 1033 helix: -3.51 (0.29), residues: 100 sheet: 0.91 (0.25), residues: 391 loop : -1.38 (0.24), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 377 TYR 0.019 0.001 TYR A 390 PHE 0.014 0.002 PHE B 369 TRP 0.012 0.002 TRP D 276 HIS 0.005 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8173) covalent geometry : angle 0.76405 (11155) SS BOND : bond 0.00530 ( 19) SS BOND : angle 1.03076 ( 38) hydrogen bonds : bond 0.13748 ( 289) hydrogen bonds : angle 7.80894 ( 939) Misc. bond : bond 0.26142 ( 1) link_BETA1-4 : bond 0.03775 ( 1) link_BETA1-4 : angle 6.96527 ( 3) link_NAG-ASN : bond 0.04911 ( 3) link_NAG-ASN : angle 8.32403 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 268 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 265 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 VAL cc_start: 0.7883 (t) cc_final: 0.7648 (t) REVERT: B 292 ASN cc_start: 0.6560 (m-40) cc_final: 0.6173 (m-40) REVERT: C 244 GLN cc_start: 0.6727 (tp40) cc_final: 0.6220 (mp10) REVERT: C 451 THR cc_start: 0.7009 (m) cc_final: 0.6630 (m) REVERT: D 296 CYS cc_start: 0.5507 (m) cc_final: 0.4715 (m) REVERT: D 398 GLU cc_start: 0.7404 (mt-10) cc_final: 0.7153 (mt-10) REVERT: J 21 ILE cc_start: 0.7732 (mm) cc_final: 0.6667 (mm) REVERT: J 57 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.7299 (ttt-90) outliers start: 3 outliers final: 1 residues processed: 267 average time/residue: 0.2222 time to fit residues: 77.2603 Evaluate side-chains 154 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 152 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain J residue 57 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 0.1980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 382 ASN D 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.240591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.202261 restraints weight = 25367.163| |-----------------------------------------------------------------------------| r_work (start): 0.4411 rms_B_bonded: 3.15 r_work: 0.4248 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4094 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8197 Z= 0.154 Angle : 0.704 6.559 11205 Z= 0.371 Chirality : 0.048 0.436 1320 Planarity : 0.006 0.048 1441 Dihedral : 6.910 54.105 1191 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.84 % Favored : 94.97 % Rotamer: Outliers : 2.07 % Allowed : 11.32 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1033 helix: -2.30 (0.40), residues: 102 sheet: 0.82 (0.24), residues: 426 loop : -1.06 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 245 TYR 0.016 0.001 TYR A 390 PHE 0.017 0.002 PHE B 316 TRP 0.017 0.001 TRP D 276 HIS 0.002 0.001 HIS B 322 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8173) covalent geometry : angle 0.69447 (11155) SS BOND : bond 0.00258 ( 19) SS BOND : angle 1.17432 ( 38) hydrogen bonds : bond 0.05382 ( 289) hydrogen bonds : angle 6.22978 ( 939) Misc. bond : bond 0.00128 ( 1) link_BETA1-4 : bond 0.00122 ( 1) link_BETA1-4 : angle 1.80975 ( 3) link_NAG-ASN : bond 0.00431 ( 3) link_NAG-ASN : angle 3.55771 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 287 LYS cc_start: 0.6451 (mttt) cc_final: 0.5775 (mmtt) REVERT: A 411 VAL cc_start: 0.8310 (t) cc_final: 0.8089 (t) REVERT: C 244 GLN cc_start: 0.6512 (tp40) cc_final: 0.5967 (mp10) REVERT: C 291 GLN cc_start: 0.7423 (mt0) cc_final: 0.7062 (mt0) REVERT: C 317 LYS cc_start: 0.6384 (mptt) cc_final: 0.5612 (tptt) REVERT: D 294 CYS cc_start: 0.4283 (OUTLIER) cc_final: 0.4072 (t) REVERT: D 296 CYS cc_start: 0.5941 (m) cc_final: 0.4470 (m) REVERT: J 18 THR cc_start: 0.7483 (p) cc_final: 0.7141 (p) REVERT: J 21 ILE cc_start: 0.7918 (mm) cc_final: 0.7551 (tp) outliers start: 19 outliers final: 14 residues processed: 178 average time/residue: 0.1652 time to fit residues: 41.4020 Evaluate side-chains 151 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 278 PRO Chi-restraints excluded: chain D residue 294 CYS Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 431 HIS Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 57 ARG Chi-restraints excluded: chain J residue 59 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 60 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 ASN J 89 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.232988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.194646 restraints weight = 25283.437| |-----------------------------------------------------------------------------| r_work (start): 0.4360 rms_B_bonded: 3.05 r_work: 0.4170 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8197 Z= 0.160 Angle : 0.658 7.420 11205 Z= 0.340 Chirality : 0.046 0.359 1320 Planarity : 0.005 0.056 1441 Dihedral : 6.437 47.116 1191 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.71 % Favored : 94.19 % Rotamer: Outliers : 3.48 % Allowed : 11.86 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.25), residues: 1033 helix: -1.47 (0.48), residues: 102 sheet: 0.97 (0.25), residues: 400 loop : -0.90 (0.26), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 245 TYR 0.018 0.002 TYR J 110 PHE 0.013 0.002 PHE C 340 TRP 0.012 0.001 TRP D 276 HIS 0.004 0.001 HIS J 63 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8173) covalent geometry : angle 0.64753 (11155) SS BOND : bond 0.00346 ( 19) SS BOND : angle 1.60242 ( 38) hydrogen bonds : bond 0.04427 ( 289) hydrogen bonds : angle 5.58085 ( 939) Misc. bond : bond 0.00214 ( 1) link_BETA1-4 : bond 0.00605 ( 1) link_BETA1-4 : angle 1.79600 ( 3) link_NAG-ASN : bond 0.00633 ( 3) link_NAG-ASN : angle 2.86532 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 179 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 VAL cc_start: 0.8665 (t) cc_final: 0.8457 (t) REVERT: B 384 GLU cc_start: 0.6761 (pp20) cc_final: 0.6469 (tm-30) REVERT: C 244 GLN cc_start: 0.6444 (tp40) cc_final: 0.5774 (mp10) REVERT: C 317 LYS cc_start: 0.6441 (mptt) cc_final: 0.5661 (tptt) REVERT: C 405 THR cc_start: 0.6921 (p) cc_final: 0.6678 (p) REVERT: C 420 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8408 (mmmm) REVERT: D 294 CYS cc_start: 0.4608 (t) cc_final: 0.4375 (t) REVERT: D 296 CYS cc_start: 0.6174 (m) cc_final: 0.5601 (m) REVERT: D 428 MET cc_start: 0.7089 (tpt) cc_final: 0.6712 (tpt) REVERT: J 13 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7402 (ptp) REVERT: J 21 ILE cc_start: 0.7958 (mm) cc_final: 0.7609 (tp) REVERT: J 78 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.6112 (mp) outliers start: 32 outliers final: 23 residues processed: 166 average time/residue: 0.1762 time to fit residues: 40.8396 Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 404 THR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 6 ILE Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 6 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 26 optimal weight: 10.0000 chunk 98 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 HIS J 63 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.225260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.183989 restraints weight = 25140.651| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 3.23 r_work: 0.4057 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3901 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8197 Z= 0.184 Angle : 0.657 6.143 11205 Z= 0.341 Chirality : 0.046 0.285 1320 Planarity : 0.006 0.062 1441 Dihedral : 5.754 38.449 1185 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.74 % Favored : 94.97 % Rotamer: Outliers : 3.48 % Allowed : 13.93 % Favored : 82.59 % 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 are not related in a simple way. whole: -0.31 (0.25), residues: 1033 helix: -1.43 (0.47), residues: 104 sheet: 0.97 (0.26), residues: 396 loop : -0.86 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 445 TYR 0.007 0.001 TYR D 425 PHE 0.011 0.002 PHE C 340 TRP 0.010 0.001 TRP D 276 HIS 0.005 0.001 HIS J 63 Details of bonding type rmsd covalent geometry : bond 0.00443 ( 8173) covalent geometry : angle 0.65270 (11155) SS BOND : bond 0.00400 ( 19) SS BOND : angle 1.05939 ( 38) hydrogen bonds : bond 0.04167 ( 289) hydrogen bonds : angle 5.27904 ( 939) Misc. bond : bond 0.00166 ( 1) link_BETA1-4 : bond 0.00472 ( 1) link_BETA1-4 : angle 1.23493 ( 3) link_NAG-ASN : bond 0.00389 ( 3) link_NAG-ASN : angle 2.19438 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 266 LEU cc_start: 0.7558 (mt) cc_final: 0.6942 (mt) REVERT: B 384 GLU cc_start: 0.7020 (pp20) cc_final: 0.6701 (tm-30) REVERT: C 244 GLN cc_start: 0.6661 (tp40) cc_final: 0.5997 (mp10) REVERT: C 317 LYS cc_start: 0.6649 (mptt) cc_final: 0.5724 (tppt) REVERT: C 405 THR cc_start: 0.7265 (p) cc_final: 0.7004 (p) REVERT: C 420 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8417 (ttmm) REVERT: D 296 CYS cc_start: 0.6395 (m) cc_final: 0.5926 (m) REVERT: J 13 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7446 (ptp) REVERT: J 21 ILE cc_start: 0.8026 (mm) cc_final: 0.7745 (tp) outliers start: 32 outliers final: 22 residues processed: 151 average time/residue: 0.1831 time to fit residues: 37.8510 Evaluate side-chains 134 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 87 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 0.0570 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 0.0470 chunk 91 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN D 291 GLN J 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4645 r_free = 0.4645 target = 0.226180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.185215 restraints weight = 25341.981| |-----------------------------------------------------------------------------| r_work (start): 0.4244 rms_B_bonded: 3.04 r_work: 0.4077 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8197 Z= 0.121 Angle : 0.600 9.256 11205 Z= 0.304 Chirality : 0.044 0.278 1320 Planarity : 0.005 0.057 1441 Dihedral : 5.424 37.738 1185 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.74 % Favored : 94.97 % Rotamer: Outliers : 2.18 % Allowed : 15.13 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.26), residues: 1033 helix: -1.16 (0.50), residues: 104 sheet: 1.05 (0.26), residues: 396 loop : -0.68 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 309 TYR 0.009 0.001 TYR A 297 PHE 0.011 0.001 PHE C 340 TRP 0.009 0.001 TRP D 276 HIS 0.004 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 8173) covalent geometry : angle 0.59473 (11155) SS BOND : bond 0.00706 ( 19) SS BOND : angle 1.16553 ( 38) hydrogen bonds : bond 0.03759 ( 289) hydrogen bonds : angle 5.01184 ( 939) Misc. bond : bond 0.00146 ( 1) link_BETA1-4 : bond 0.00881 ( 1) link_BETA1-4 : angle 1.45854 ( 3) link_NAG-ASN : bond 0.00425 ( 3) link_NAG-ASN : angle 1.99577 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6722 (ttmt) cc_final: 0.6177 (tttt) REVERT: B 309 ARG cc_start: 0.5771 (mtp-110) cc_final: 0.4648 (ttm-80) REVERT: B 384 GLU cc_start: 0.7004 (pp20) cc_final: 0.6764 (tm-30) REVERT: C 244 GLN cc_start: 0.6606 (tp40) cc_final: 0.5964 (mp10) REVERT: C 317 LYS cc_start: 0.6631 (mptt) cc_final: 0.5749 (tppt) REVERT: C 373 GLU cc_start: 0.8097 (pm20) cc_final: 0.7694 (mp0) REVERT: C 405 THR cc_start: 0.7232 (p) cc_final: 0.6973 (p) REVERT: C 420 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8394 (ttmm) REVERT: D 296 CYS cc_start: 0.6614 (m) cc_final: 0.5666 (m) REVERT: J 13 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.7451 (ptp) REVERT: J 21 ILE cc_start: 0.8089 (mm) cc_final: 0.7820 (tp) outliers start: 20 outliers final: 18 residues processed: 134 average time/residue: 0.1582 time to fit residues: 30.2232 Evaluate side-chains 130 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 83 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 78 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 380 HIS B 421 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.220612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.179280 restraints weight = 25125.387| |-----------------------------------------------------------------------------| r_work (start): 0.4250 rms_B_bonded: 3.02 r_work: 0.4074 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3923 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.5911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8197 Z= 0.123 Angle : 0.587 9.373 11205 Z= 0.298 Chirality : 0.044 0.247 1320 Planarity : 0.005 0.057 1441 Dihedral : 5.337 36.035 1185 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.42 % Favored : 94.29 % Rotamer: Outliers : 2.72 % Allowed : 15.13 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.26), residues: 1033 helix: -1.23 (0.49), residues: 104 sheet: 1.08 (0.26), residues: 400 loop : -0.63 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 309 TYR 0.011 0.001 TYR J 118 PHE 0.009 0.001 PHE C 340 TRP 0.008 0.001 TRP D 276 HIS 0.003 0.001 HIS J 63 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8173) covalent geometry : angle 0.57697 (11155) SS BOND : bond 0.00702 ( 19) SS BOND : angle 1.78986 ( 38) hydrogen bonds : bond 0.03705 ( 289) hydrogen bonds : angle 4.83578 ( 939) Misc. bond : bond 0.00136 ( 1) link_BETA1-4 : bond 0.00241 ( 1) link_BETA1-4 : angle 1.17474 ( 3) link_NAG-ASN : bond 0.00325 ( 3) link_NAG-ASN : angle 1.71845 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6707 (ttmt) cc_final: 0.6164 (tttt) REVERT: B 384 GLU cc_start: 0.7047 (pp20) cc_final: 0.6798 (tm-30) REVERT: C 244 GLN cc_start: 0.6575 (tp40) cc_final: 0.5912 (mp10) REVERT: C 317 LYS cc_start: 0.6628 (mptt) cc_final: 0.5753 (tppt) REVERT: C 405 THR cc_start: 0.7365 (p) cc_final: 0.7104 (p) REVERT: C 420 LYS cc_start: 0.8823 (mmmt) cc_final: 0.8435 (ttmm) REVERT: D 296 CYS cc_start: 0.6471 (m) cc_final: 0.5954 (m) REVERT: D 309 ARG cc_start: 0.7010 (mtp180) cc_final: 0.6780 (mtp85) REVERT: J 13 MET cc_start: 0.7622 (mtm) cc_final: 0.7402 (ptp) REVERT: J 21 ILE cc_start: 0.8101 (mm) cc_final: 0.7853 (tp) outliers start: 25 outliers final: 20 residues processed: 130 average time/residue: 0.1601 time to fit residues: 29.8581 Evaluate side-chains 130 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain C residue 396 LEU Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 380 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.216338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.174417 restraints weight = 24949.107| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.98 r_work: 0.4057 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3903 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.6301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8197 Z= 0.142 Angle : 0.586 10.118 11205 Z= 0.297 Chirality : 0.044 0.217 1320 Planarity : 0.005 0.055 1441 Dihedral : 5.201 36.436 1185 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.42 % Favored : 94.29 % Rotamer: Outliers : 2.94 % Allowed : 15.02 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.26), residues: 1033 helix: -1.12 (0.49), residues: 104 sheet: 1.03 (0.26), residues: 402 loop : -0.64 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 309 TYR 0.007 0.001 TYR J 118 PHE 0.009 0.001 PHE C 340 TRP 0.008 0.001 TRP D 276 HIS 0.005 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8173) covalent geometry : angle 0.57591 (11155) SS BOND : bond 0.00299 ( 19) SS BOND : angle 1.80595 ( 38) hydrogen bonds : bond 0.03690 ( 289) hydrogen bonds : angle 4.73918 ( 939) Misc. bond : bond 0.00142 ( 1) link_BETA1-4 : bond 0.00580 ( 1) link_BETA1-4 : angle 1.17545 ( 3) link_NAG-ASN : bond 0.00319 ( 3) link_NAG-ASN : angle 1.42880 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6815 (ttmt) cc_final: 0.6540 (ttmm) REVERT: A 394 GLU cc_start: 0.8171 (tt0) cc_final: 0.7942 (tp30) REVERT: A 432 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7066 (pt0) REVERT: B 291 GLN cc_start: 0.6543 (pp30) cc_final: 0.6217 (pp30) REVERT: B 384 GLU cc_start: 0.7177 (pp20) cc_final: 0.6913 (tm-30) REVERT: B 401 GLU cc_start: 0.6067 (tp30) cc_final: 0.5789 (tp30) REVERT: C 244 GLN cc_start: 0.6744 (tp40) cc_final: 0.6066 (mp10) REVERT: C 317 LYS cc_start: 0.6758 (mptt) cc_final: 0.5935 (tppt) REVERT: C 405 THR cc_start: 0.7658 (p) cc_final: 0.7415 (p) REVERT: C 420 LYS cc_start: 0.8847 (mmmt) cc_final: 0.8488 (ttmm) REVERT: D 296 CYS cc_start: 0.6537 (m) cc_final: 0.5994 (m) REVERT: J 3 GLU cc_start: 0.5243 (pt0) cc_final: 0.4744 (mm-30) REVERT: J 110 TYR cc_start: 0.7612 (m-80) cc_final: 0.7303 (m-80) outliers start: 27 outliers final: 22 residues processed: 142 average time/residue: 0.1769 time to fit residues: 35.2191 Evaluate side-chains 135 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 112 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 432 GLU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 76 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 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 244 GLN B 380 HIS ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.194433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.150049 restraints weight = 27307.292| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 3.43 r_work: 0.3782 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3644 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8197 Z= 0.137 Angle : 0.582 5.182 11205 Z= 0.296 Chirality : 0.044 0.206 1320 Planarity : 0.005 0.054 1441 Dihedral : 5.162 37.119 1185 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.71 % Favored : 94.00 % Rotamer: Outliers : 2.83 % Allowed : 15.45 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.26), residues: 1033 helix: -1.02 (0.50), residues: 103 sheet: 1.07 (0.26), residues: 398 loop : -0.64 (0.27), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 309 TYR 0.022 0.001 TYR B 425 PHE 0.009 0.001 PHE B 369 TRP 0.009 0.001 TRP D 276 HIS 0.019 0.002 HIS B 380 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8173) covalent geometry : angle 0.57884 (11155) SS BOND : bond 0.00302 ( 19) SS BOND : angle 0.98358 ( 38) hydrogen bonds : bond 0.03627 ( 289) hydrogen bonds : angle 4.66140 ( 939) Misc. bond : bond 0.00157 ( 1) link_BETA1-4 : bond 0.00299 ( 1) link_BETA1-4 : angle 1.09418 ( 3) link_NAG-ASN : bond 0.00322 ( 3) link_NAG-ASN : angle 1.36864 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 143 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6851 (ttmt) cc_final: 0.6591 (ttmm) REVERT: A 405 THR cc_start: 0.7845 (p) cc_final: 0.7584 (p) REVERT: B 291 GLN cc_start: 0.6660 (pp30) cc_final: 0.6305 (pp30) REVERT: B 384 GLU cc_start: 0.7177 (pp20) cc_final: 0.6942 (tm-30) REVERT: B 401 GLU cc_start: 0.6020 (tp30) cc_final: 0.5726 (tp30) REVERT: C 244 GLN cc_start: 0.6935 (tp40) cc_final: 0.6288 (mp10) REVERT: C 253 LEU cc_start: 0.8319 (tt) cc_final: 0.8001 (tp) REVERT: C 291 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7311 (mm-40) REVERT: C 317 LYS cc_start: 0.6778 (mptt) cc_final: 0.6012 (tppt) REVERT: C 405 THR cc_start: 0.7731 (p) cc_final: 0.7486 (p) REVERT: C 420 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8520 (ttmm) REVERT: D 296 CYS cc_start: 0.6754 (m) cc_final: 0.6221 (m) REVERT: J 3 GLU cc_start: 0.5217 (pt0) cc_final: 0.4730 (mm-30) outliers start: 26 outliers final: 24 residues processed: 136 average time/residue: 0.1710 time to fit residues: 32.1475 Evaluate side-chains 137 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 291 GLN Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 434 LEU Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 119 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 29 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 380 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.189456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.147532 restraints weight = 26469.219| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 3.07 r_work: 0.3751 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.6817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8197 Z= 0.166 Angle : 0.596 5.962 11205 Z= 0.305 Chirality : 0.044 0.194 1320 Planarity : 0.005 0.058 1441 Dihedral : 5.204 38.284 1185 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.23 % Favored : 94.39 % Rotamer: Outliers : 2.83 % Allowed : 15.67 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.26), residues: 1033 helix: -0.96 (0.51), residues: 98 sheet: 1.00 (0.26), residues: 398 loop : -0.67 (0.26), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 309 TYR 0.010 0.001 TYR C 425 PHE 0.010 0.002 PHE C 369 TRP 0.009 0.001 TRP D 276 HIS 0.013 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 8173) covalent geometry : angle 0.59337 (11155) SS BOND : bond 0.00298 ( 19) SS BOND : angle 0.94628 ( 38) hydrogen bonds : bond 0.03714 ( 289) hydrogen bonds : angle 4.69026 ( 939) Misc. bond : bond 0.00164 ( 1) link_BETA1-4 : bond 0.00240 ( 1) link_BETA1-4 : angle 1.06049 ( 3) link_NAG-ASN : bond 0.00338 ( 3) link_NAG-ASN : angle 1.33143 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6927 (ttmt) cc_final: 0.6666 (ttmm) REVERT: A 405 THR cc_start: 0.7875 (p) cc_final: 0.7630 (p) REVERT: B 291 GLN cc_start: 0.6711 (pp30) cc_final: 0.6370 (pp30) REVERT: B 384 GLU cc_start: 0.7146 (pp20) cc_final: 0.6863 (tm-30) REVERT: B 401 GLU cc_start: 0.6049 (tp30) cc_final: 0.5771 (tp30) REVERT: C 244 GLN cc_start: 0.6963 (tp40) cc_final: 0.6302 (mp10) REVERT: C 253 LEU cc_start: 0.8242 (tt) cc_final: 0.7956 (tp) REVERT: C 317 LYS cc_start: 0.6853 (mptt) cc_final: 0.6120 (tppt) REVERT: C 405 THR cc_start: 0.7733 (p) cc_final: 0.7514 (p) REVERT: C 420 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8553 (ttmm) REVERT: D 296 CYS cc_start: 0.6798 (m) cc_final: 0.6274 (m) REVERT: J 3 GLU cc_start: 0.5313 (pt0) cc_final: 0.4944 (mm-30) outliers start: 26 outliers final: 22 residues processed: 135 average time/residue: 0.1832 time to fit residues: 34.5908 Evaluate side-chains 132 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 380 HIS Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Chi-restraints excluded: chain J residue 125 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 92 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 30 optimal weight: 10.0000 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 380 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.192997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.149030 restraints weight = 27104.176| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 3.40 r_work: 0.3759 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8197 Z= 0.118 Angle : 0.568 4.564 11205 Z= 0.290 Chirality : 0.044 0.188 1320 Planarity : 0.005 0.057 1441 Dihedral : 5.093 38.433 1185 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.23 % Favored : 94.39 % Rotamer: Outliers : 2.29 % Allowed : 16.32 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.26), residues: 1033 helix: -0.77 (0.53), residues: 97 sheet: 1.07 (0.26), residues: 400 loop : -0.64 (0.27), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 309 TYR 0.012 0.001 TYR C 297 PHE 0.009 0.001 PHE C 340 TRP 0.010 0.001 TRP D 276 HIS 0.009 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8173) covalent geometry : angle 0.56611 (11155) SS BOND : bond 0.00264 ( 19) SS BOND : angle 0.78849 ( 38) hydrogen bonds : bond 0.03492 ( 289) hydrogen bonds : angle 4.58753 ( 939) Misc. bond : bond 0.00124 ( 1) link_BETA1-4 : bond 0.00268 ( 1) link_BETA1-4 : angle 1.16491 ( 3) link_NAG-ASN : bond 0.00332 ( 3) link_NAG-ASN : angle 1.27321 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 434 is missing expected H atoms. Skipping. Residue TYR 406 is missing expected H atoms. Skipping. Residue LYS 372 is missing expected H atoms. Skipping. Residue SER 50 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 317 LYS cc_start: 0.6932 (ttmt) cc_final: 0.6680 (ttmm) REVERT: A 405 THR cc_start: 0.7851 (p) cc_final: 0.7588 (p) REVERT: B 291 GLN cc_start: 0.6683 (pp30) cc_final: 0.6353 (pp30) REVERT: B 384 GLU cc_start: 0.7160 (pp20) cc_final: 0.6914 (tm-30) REVERT: B 401 GLU cc_start: 0.6022 (tp30) cc_final: 0.5745 (tp30) REVERT: C 244 GLN cc_start: 0.6874 (tp40) cc_final: 0.6215 (mp10) REVERT: C 253 LEU cc_start: 0.8297 (tt) cc_final: 0.8002 (tp) REVERT: C 274 PHE cc_start: 0.4970 (m-80) cc_final: 0.4621 (m-80) REVERT: C 297 TYR cc_start: 0.5880 (m-80) cc_final: 0.5679 (m-80) REVERT: C 317 LYS cc_start: 0.6807 (mptt) cc_final: 0.6075 (tppt) REVERT: C 405 THR cc_start: 0.7749 (p) cc_final: 0.7528 (p) REVERT: C 420 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8544 (ttmm) REVERT: D 296 CYS cc_start: 0.6803 (m) cc_final: 0.6277 (m) REVERT: J 3 GLU cc_start: 0.5339 (pt0) cc_final: 0.4942 (mm-30) outliers start: 21 outliers final: 20 residues processed: 129 average time/residue: 0.1847 time to fit residues: 33.3104 Evaluate side-chains 130 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 456 SER Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 373 GLU Chi-restraints excluded: chain C residue 390 TYR Chi-restraints excluded: chain D residue 256 ASP Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 405 THR Chi-restraints excluded: chain D residue 446 LEU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 87 GLN Chi-restraints excluded: chain J residue 119 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 36 optimal weight: 0.7980 chunk 102 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 82 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 17 optimal weight: 0.3980 chunk 89 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 0.0040 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.193797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.149969 restraints weight = 27115.395| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 3.44 r_work: 0.3771 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.7107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8197 Z= 0.108 Angle : 0.554 4.648 11205 Z= 0.280 Chirality : 0.043 0.183 1320 Planarity : 0.005 0.056 1441 Dihedral : 4.955 36.621 1185 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.32 % Favored : 94.29 % Rotamer: Outliers : 2.50 % Allowed : 16.43 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.26), residues: 1033 helix: -0.67 (0.53), residues: 97 sheet: 1.06 (0.26), residues: 405 loop : -0.54 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 413 TYR 0.009 0.001 TYR C 425 PHE 0.008 0.001 PHE C 340 TRP 0.010 0.001 TRP D 276 HIS 0.008 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8173) covalent geometry : angle 0.55230 (11155) SS BOND : bond 0.00242 ( 19) SS BOND : angle 0.72277 ( 38) hydrogen bonds : bond 0.03365 ( 289) hydrogen bonds : angle 4.49754 ( 939) Misc. bond : bond 0.00122 ( 1) link_BETA1-4 : bond 0.00173 ( 1) link_BETA1-4 : angle 1.14912 ( 3) link_NAG-ASN : bond 0.00310 ( 3) link_NAG-ASN : angle 1.25223 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4997.29 seconds wall clock time: 85 minutes 4.63 seconds (5104.63 seconds total)