Starting phenix.real_space_refine on Sat Oct 11 16:22:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jg1_22309/10_2025/7jg1_22309_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jg1_22309/10_2025/7jg1_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 { model { file = "/net/cci-nas-00/data/ceres_data/7jg1_22309/10_2025/7jg1_22309_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jg1_22309/10_2025/7jg1_22309_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jg1_22309/10_2025/7jg1_22309.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jg1_22309/10_2025/7jg1_22309.map" } 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-2.0-5842/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: 4.58, per 1000 atoms: 0.29 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: 1.83 Conformation dependent library (CDL) restraints added in 488.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.54 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: 3.81 Time building geometry restraints manager: 2.37 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: 3.440 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: 0.110 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.690 Find NCS groups from input model: 0.250 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.190 ------------------------------------------------------------------------------- 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 aren 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 : 0.440 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: 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: 0.7405 (mt-10) cc_final: 0.7154 (mt-10) REVERT: D 407 LEU cc_start: 0.7431 (mt) cc_final: 0.7231 (mt) 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: 0.2390 time to fit residues: 83.2583 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 : 0.328 ------------------------------------------------------------------------------- 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: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 J 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.239149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.200531 restraints weight = 25311.030| |-----------------------------------------------------------------------------| r_work (start): 0.4391 rms_B_bonded: 3.14 r_work: 0.4225 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.4072 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.4072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 8197 Z= 0.159 Angle : 0.706 6.687 11205 Z= 0.372 Chirality : 0.048 0.416 1320 Planarity : 0.006 0.050 1441 Dihedral : 6.908 52.958 1191 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.55 % Favored : 95.26 % Rotamer: Outliers : 2.39 % Allowed : 11.10 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.25), residues: 1033 helix: -2.22 (0.41), residues: 102 sheet: 0.80 (0.24), residues: 426 loop : -1.05 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 245 TYR 0.015 0.001 TYR A 390 PHE 0.017 0.002 PHE B 316 TRP 0.015 0.001 TRP D 276 HIS 0.003 0.001 HIS J 63 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 8173) covalent geometry : angle 0.69627 (11155) SS BOND : bond 0.00435 ( 19) SS BOND : angle 1.40413 ( 38) hydrogen bonds : bond 0.05287 ( 289) hydrogen bonds : angle 6.14241 ( 939) Misc. bond : bond 0.00497 ( 1) link_BETA1-4 : bond 0.00316 ( 1) link_BETA1-4 : angle 1.63952 ( 3) link_NAG-ASN : bond 0.00588 ( 3) link_NAG-ASN : angle 3.32681 ( 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: 22 poor density : 160 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 VAL cc_start: 0.8389 (t) cc_final: 0.8177 (t) REVERT: B 292 ASN cc_start: 0.6461 (m-40) cc_final: 0.6244 (m-40) REVERT: C 244 GLN cc_start: 0.6535 (tp40) cc_final: 0.5999 (mp10) REVERT: C 317 LYS cc_start: 0.6431 (mptt) cc_final: 0.5634 (tptt) REVERT: D 296 CYS cc_start: 0.5971 (m) cc_final: 0.5572 (m) REVERT: J 21 ILE cc_start: 0.7943 (mm) cc_final: 0.7609 (tp) outliers start: 22 outliers final: 16 residues processed: 177 average time/residue: 0.1884 time to fit residues: 46.7176 Evaluate side-chains 148 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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 B residue 439 THR Chi-restraints excluded: chain B residue 456 SER 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 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: 1.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 79 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 85 optimal weight: 0.0980 chunk 87 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4727 r_free = 0.4727 target = 0.235867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.196942 restraints weight = 25357.160| |-----------------------------------------------------------------------------| r_work (start): 0.4378 rms_B_bonded: 3.10 r_work: 0.4199 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8197 Z= 0.132 Angle : 0.622 5.377 11205 Z= 0.320 Chirality : 0.045 0.364 1320 Planarity : 0.005 0.053 1441 Dihedral : 6.248 47.116 1191 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.29 % Rotamer: Outliers : 2.72 % Allowed : 12.40 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.26), residues: 1033 helix: -1.42 (0.48), residues: 103 sheet: 1.05 (0.25), residues: 400 loop : -0.71 (0.27), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.011 0.001 TYR A 390 PHE 0.016 0.002 PHE C 340 TRP 0.011 0.001 TRP D 276 HIS 0.002 0.001 HIS J 63 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8173) covalent geometry : angle 0.61561 (11155) SS BOND : bond 0.00248 ( 19) SS BOND : angle 0.76404 ( 38) hydrogen bonds : bond 0.04305 ( 289) hydrogen bonds : angle 5.53476 ( 939) Misc. bond : bond 0.00173 ( 1) link_BETA1-4 : bond 0.00788 ( 1) link_BETA1-4 : angle 1.97975 ( 3) link_NAG-ASN : bond 0.00604 ( 3) link_NAG-ASN : angle 2.83562 ( 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 167 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 142 time to evaluate : 0.428 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 411 VAL cc_start: 0.8534 (t) cc_final: 0.8308 (t) REVERT: B 384 GLU cc_start: 0.6752 (pp20) cc_final: 0.6475 (tm-30) REVERT: C 244 GLN cc_start: 0.6347 (tp40) cc_final: 0.5693 (mp10) REVERT: C 317 LYS cc_start: 0.6388 (mptt) cc_final: 0.5597 (tptt) REVERT: C 373 GLU cc_start: 0.7540 (pm20) cc_final: 0.7050 (mp0) REVERT: C 405 THR cc_start: 0.6835 (p) cc_final: 0.6604 (p) REVERT: D 296 CYS cc_start: 0.6182 (m) cc_final: 0.5214 (m) REVERT: J 13 MET cc_start: 0.7823 (OUTLIER) cc_final: 0.7409 (ptp) REVERT: J 21 ILE cc_start: 0.7932 (mm) cc_final: 0.7579 (tp) REVERT: J 78 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5985 (mp) REVERT: J 113 MET cc_start: 0.7628 (mmt) cc_final: 0.7356 (mmp) outliers start: 25 outliers final: 20 residues processed: 158 average time/residue: 0.1942 time to fit residues: 42.9665 Evaluate side-chains 152 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU 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 C residue 259 ILE Chi-restraints excluded: chain C residue 260 THR 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: 0.7980 chunk 83 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 98 optimal weight: 3.9990 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: 0.5980 chunk 5 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 322 HIS J 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.231390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.191641 restraints weight = 25076.835| |-----------------------------------------------------------------------------| r_work (start): 0.4308 rms_B_bonded: 3.06 r_work: 0.4143 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3990 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.4883 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= 0.137 Angle : 0.610 9.109 11205 Z= 0.315 Chirality : 0.045 0.298 1320 Planarity : 0.005 0.060 1441 Dihedral : 5.611 34.630 1185 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.55 % Favored : 95.16 % Rotamer: Outliers : 3.05 % Allowed : 13.38 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.26), residues: 1033 helix: -1.23 (0.49), residues: 104 sheet: 1.01 (0.25), residues: 400 loop : -0.68 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 309 TYR 0.009 0.001 TYR A 390 PHE 0.012 0.002 PHE B 369 TRP 0.010 0.001 TRP D 276 HIS 0.003 0.001 HIS J 63 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8173) covalent geometry : angle 0.59952 (11155) SS BOND : bond 0.00340 ( 19) SS BOND : angle 1.67391 ( 38) hydrogen bonds : bond 0.03968 ( 289) hydrogen bonds : angle 5.24019 ( 939) Misc. bond : bond 0.00171 ( 1) link_BETA1-4 : bond 0.00419 ( 1) link_BETA1-4 : angle 1.32141 ( 3) link_NAG-ASN : bond 0.00382 ( 3) link_NAG-ASN : angle 2.27478 ( 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 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 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: B 384 GLU cc_start: 0.6931 (pp20) cc_final: 0.6607 (tm-30) REVERT: C 244 GLN cc_start: 0.6520 (tp40) cc_final: 0.5869 (mp10) REVERT: C 317 LYS cc_start: 0.6509 (mptt) cc_final: 0.5740 (tptt) REVERT: C 405 THR cc_start: 0.7018 (p) cc_final: 0.6713 (p) REVERT: C 420 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8282 (ttmm) REVERT: D 296 CYS cc_start: 0.6299 (m) cc_final: 0.6053 (m) REVERT: J 13 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.7526 (ptp) REVERT: J 21 ILE cc_start: 0.8044 (mm) cc_final: 0.7742 (tp) outliers start: 28 outliers final: 20 residues processed: 157 average time/residue: 0.2070 time to fit residues: 44.6087 Evaluate side-chains 141 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU 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 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 431 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 26 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 92 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.223427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.182548 restraints weight = 25132.261| |-----------------------------------------------------------------------------| r_work (start): 0.4276 rms_B_bonded: 3.05 r_work: 0.4100 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3946 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8197 Z= 0.133 Angle : 0.600 10.187 11205 Z= 0.308 Chirality : 0.045 0.274 1320 Planarity : 0.005 0.055 1441 Dihedral : 5.388 34.328 1185 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.23 % Favored : 94.39 % 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 : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.26), residues: 1033 helix: -1.10 (0.50), residues: 104 sheet: 1.09 (0.25), residues: 400 loop : -0.57 (0.27), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 309 TYR 0.013 0.001 TYR J 135 PHE 0.008 0.001 PHE B 316 TRP 0.009 0.001 TRP D 276 HIS 0.003 0.001 HIS C 322 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 8173) covalent geometry : angle 0.59241 (11155) SS BOND : bond 0.00533 ( 19) SS BOND : angle 1.39900 ( 38) hydrogen bonds : bond 0.03802 ( 289) hydrogen bonds : angle 4.98968 ( 939) Misc. bond : bond 0.00145 ( 1) link_BETA1-4 : bond 0.00462 ( 1) link_BETA1-4 : angle 1.26907 ( 3) link_NAG-ASN : bond 0.00390 ( 3) link_NAG-ASN : angle 1.95212 ( 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 153 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.300 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: A 317 LYS cc_start: 0.6648 (ttmt) cc_final: 0.6107 (tttt) REVERT: B 309 ARG cc_start: 0.5801 (mtp-110) cc_final: 0.4633 (ttm-80) REVERT: B 384 GLU cc_start: 0.7018 (pp20) cc_final: 0.6482 (tm-30) REVERT: C 244 GLN cc_start: 0.6540 (tp40) cc_final: 0.5970 (mp10) REVERT: C 317 LYS cc_start: 0.6571 (mptt) cc_final: 0.5889 (tptt) REVERT: C 373 GLU cc_start: 0.7834 (pm20) cc_final: 0.7444 (mp0) REVERT: C 405 THR cc_start: 0.7242 (p) cc_final: 0.7004 (p) REVERT: C 420 LYS cc_start: 0.8772 (mmmt) cc_final: 0.8342 (ttmm) REVERT: D 296 CYS cc_start: 0.6568 (m) cc_final: 0.6047 (m) REVERT: J 13 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.7473 (ptp) REVERT: J 21 ILE cc_start: 0.8015 (mm) cc_final: 0.7752 (tp) REVERT: J 78 LEU cc_start: 0.6562 (OUTLIER) cc_final: 0.6223 (mp) outliers start: 25 outliers final: 17 residues processed: 146 average time/residue: 0.2000 time to fit residues: 40.3927 Evaluate side-chains 131 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 443 ILE 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 13 MET Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 59 ASN Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 87 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 19 optimal weight: 0.5980 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 83 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 36 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN J 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.221509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.180092 restraints weight = 25059.865| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.03 r_work: 0.4060 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.5780 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= 0.130 Angle : 0.589 11.818 11205 Z= 0.300 Chirality : 0.044 0.239 1320 Planarity : 0.005 0.054 1441 Dihedral : 5.235 33.814 1185 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.55 % Favored : 95.16 % Rotamer: Outliers : 2.61 % Allowed : 15.23 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.26), residues: 1033 helix: -0.98 (0.51), residues: 104 sheet: 1.14 (0.26), residues: 396 loop : -0.53 (0.27), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 245 TYR 0.011 0.002 TYR A 297 PHE 0.007 0.001 PHE C 369 TRP 0.008 0.001 TRP D 276 HIS 0.006 0.001 HIS J 119 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8173) covalent geometry : angle 0.58499 (11155) SS BOND : bond 0.00330 ( 19) SS BOND : angle 1.04182 ( 38) hydrogen bonds : bond 0.03632 ( 289) hydrogen bonds : angle 4.81264 ( 939) Misc. bond : bond 0.00143 ( 1) link_BETA1-4 : bond 0.00233 ( 1) link_BETA1-4 : angle 1.14746 ( 3) link_NAG-ASN : bond 0.00324 ( 3) link_NAG-ASN : angle 1.65320 ( 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 146 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.450 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: 0.6715 (ttmt) cc_final: 0.6156 (tttt) REVERT: B 384 GLU cc_start: 0.7125 (pp20) cc_final: 0.6885 (tm-30) REVERT: C 244 GLN cc_start: 0.6665 (tp40) cc_final: 0.6078 (mp10) REVERT: C 317 LYS cc_start: 0.6652 (mptt) cc_final: 0.5809 (tppt) REVERT: C 373 GLU cc_start: 0.7910 (pm20) cc_final: 0.7540 (mp0) REVERT: C 405 THR cc_start: 0.7400 (p) cc_final: 0.7171 (p) REVERT: C 420 LYS cc_start: 0.8792 (mmmt) cc_final: 0.8392 (ttmm) REVERT: D 296 CYS cc_start: 0.6516 (m) cc_final: 0.6028 (m) REVERT: J 21 ILE cc_start: 0.8086 (mm) cc_final: 0.7828 (tp) outliers start: 24 outliers final: 21 residues processed: 139 average time/residue: 0.1724 time to fit residues: 34.1753 Evaluate side-chains 136 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 338 ASN 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 434 LEU Chi-restraints excluded: chain D residue 446 LEU 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 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: 2.9990 chunk 2 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 39 optimal weight: 0.3980 chunk 1 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN J 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4592 r_free = 0.4592 target = 0.219723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.178244 restraints weight = 25010.971| |-----------------------------------------------------------------------------| r_work (start): 0.4222 rms_B_bonded: 3.00 r_work: 0.4045 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3892 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8197 Z= 0.128 Angle : 0.578 6.062 11205 Z= 0.293 Chirality : 0.044 0.219 1320 Planarity : 0.005 0.059 1441 Dihedral : 5.120 33.957 1185 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.13 % Favored : 94.58 % Rotamer: Outliers : 3.05 % Allowed : 14.80 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.26), residues: 1033 helix: -0.99 (0.51), residues: 104 sheet: 1.12 (0.26), residues: 402 loop : -0.50 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.024 0.002 TYR J 135 PHE 0.008 0.001 PHE B 369 TRP 0.008 0.001 TRP D 276 HIS 0.003 0.001 HIS D 322 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8173) covalent geometry : angle 0.57487 (11155) SS BOND : bond 0.00365 ( 19) SS BOND : angle 0.85897 ( 38) hydrogen bonds : bond 0.03526 ( 289) hydrogen bonds : angle 4.68327 ( 939) Misc. bond : bond 0.00138 ( 1) link_BETA1-4 : bond 0.00266 ( 1) link_BETA1-4 : angle 1.17165 ( 3) link_NAG-ASN : bond 0.00327 ( 3) link_NAG-ASN : angle 1.44061 ( 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 149 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.353 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: 0.6742 (ttmt) cc_final: 0.6191 (tttt) REVERT: B 384 GLU cc_start: 0.7158 (pp20) cc_final: 0.6950 (tm-30) REVERT: C 244 GLN cc_start: 0.6714 (tp40) cc_final: 0.6123 (mp10) REVERT: C 253 LEU cc_start: 0.8324 (tt) cc_final: 0.7926 (tp) REVERT: C 274 PHE cc_start: 0.4640 (m-80) cc_final: 0.4374 (m-80) REVERT: C 317 LYS cc_start: 0.6716 (mptt) cc_final: 0.5887 (tppt) REVERT: C 405 THR cc_start: 0.7526 (p) cc_final: 0.7289 (p) REVERT: C 420 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8436 (ttmm) REVERT: D 296 CYS cc_start: 0.6505 (m) cc_final: 0.6019 (m) REVERT: J 21 ILE cc_start: 0.8073 (mm) cc_final: 0.7829 (tp) outliers start: 28 outliers final: 24 residues processed: 141 average time/residue: 0.1707 time to fit residues: 34.6330 Evaluate side-chains 146 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 443 ILE Chi-restraints excluded: chain A residue 446 LEU 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 296 CYS 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 431 HIS 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 50 SER 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: 0.7980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN C 380 HIS D 291 GLN J 63 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.216273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.177309 restraints weight = 25951.943| |-----------------------------------------------------------------------------| r_work (start): 0.4186 rms_B_bonded: 2.80 r_work: 0.4009 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3871 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.6627 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= 0.159 Angle : 0.607 6.559 11205 Z= 0.310 Chirality : 0.045 0.193 1320 Planarity : 0.005 0.058 1441 Dihedral : 5.200 35.808 1185 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.74 % Favored : 94.97 % Rotamer: Outliers : 3.05 % Allowed : 15.23 % 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 aren not related in a simple way. whole: 0.05 (0.26), residues: 1033 helix: -1.08 (0.49), residues: 104 sheet: 1.10 (0.26), residues: 398 loop : -0.55 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 106 TYR 0.009 0.001 TYR C 425 PHE 0.011 0.001 PHE C 369 TRP 0.010 0.001 TRP D 276 HIS 0.007 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8173) covalent geometry : angle 0.60101 (11155) SS BOND : bond 0.00269 ( 19) SS BOND : angle 1.49780 ( 38) hydrogen bonds : bond 0.03545 ( 289) hydrogen bonds : angle 4.72106 ( 939) Misc. bond : bond 0.00139 ( 1) link_BETA1-4 : bond 0.00288 ( 1) link_BETA1-4 : angle 1.08140 ( 3) link_NAG-ASN : bond 0.00296 ( 3) link_NAG-ASN : angle 1.31364 ( 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 154 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.406 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: A 317 LYS cc_start: 0.6850 (ttmt) cc_final: 0.6586 (ttmm) REVERT: A 405 THR cc_start: 0.7783 (p) cc_final: 0.7546 (p) REVERT: B 291 GLN cc_start: 0.6686 (pp30) cc_final: 0.6271 (pp30) REVERT: B 401 GLU cc_start: 0.5989 (tp30) cc_final: 0.5763 (tp30) REVERT: C 244 GLN cc_start: 0.6848 (tp40) cc_final: 0.6311 (mp10) REVERT: C 253 LEU cc_start: 0.8319 (tt) cc_final: 0.8066 (tp) REVERT: C 274 PHE cc_start: 0.5082 (m-80) cc_final: 0.4754 (m-80) REVERT: C 317 LYS cc_start: 0.6871 (mptt) cc_final: 0.6167 (tppt) REVERT: C 420 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8486 (ttmm) REVERT: D 296 CYS cc_start: 0.6515 (m) cc_final: 0.6046 (m) REVERT: J 3 GLU cc_start: 0.5319 (pt0) cc_final: 0.4887 (mm-30) REVERT: J 113 MET cc_start: 0.7573 (mmt) cc_final: 0.7317 (mmp) outliers start: 28 outliers final: 24 residues processed: 145 average time/residue: 0.1999 time to fit residues: 39.4216 Evaluate side-chains 139 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 443 ILE Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 449 LYS 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 446 LEU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 50 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 29 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.193278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.148361 restraints weight = 27495.715| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.46 r_work: 0.3764 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8197 Z= 0.134 Angle : 0.578 4.543 11205 Z= 0.296 Chirality : 0.045 0.190 1320 Planarity : 0.005 0.054 1441 Dihedral : 5.102 37.366 1185 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.74 % Favored : 94.87 % 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 aren not related in a simple way. whole: 0.05 (0.26), residues: 1033 helix: -0.97 (0.50), residues: 103 sheet: 1.07 (0.26), residues: 404 loop : -0.57 (0.27), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 245 TYR 0.008 0.001 TYR C 425 PHE 0.009 0.002 PHE D 316 TRP 0.011 0.001 TRP D 276 HIS 0.012 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8173) covalent geometry : angle 0.57533 (11155) SS BOND : bond 0.00239 ( 19) SS BOND : angle 0.84905 ( 38) hydrogen bonds : bond 0.03444 ( 289) hydrogen bonds : angle 4.63300 ( 939) Misc. bond : bond 0.00129 ( 1) link_BETA1-4 : bond 0.00251 ( 1) link_BETA1-4 : angle 1.14582 ( 3) link_NAG-ASN : bond 0.00335 ( 3) link_NAG-ASN : angle 1.25631 ( 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 140 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.497 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: 0.6910 (ttmt) cc_final: 0.6647 (ttmm) REVERT: A 405 THR cc_start: 0.7840 (p) cc_final: 0.7582 (p) REVERT: B 291 GLN cc_start: 0.6709 (pp30) cc_final: 0.6326 (pp30) REVERT: B 401 GLU cc_start: 0.6010 (tp30) cc_final: 0.5757 (tp30) REVERT: C 244 GLN cc_start: 0.6843 (tp40) cc_final: 0.6212 (mp10) REVERT: C 253 LEU cc_start: 0.8307 (tt) cc_final: 0.8077 (tp) REVERT: C 274 PHE cc_start: 0.5060 (m-80) cc_final: 0.4734 (m-80) REVERT: C 317 LYS cc_start: 0.6844 (mptt) cc_final: 0.6106 (tppt) REVERT: C 420 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8518 (ttmm) REVERT: D 296 CYS cc_start: 0.6756 (m) cc_final: 0.6272 (m) REVERT: D 309 ARG cc_start: 0.7498 (mtp-110) cc_final: 0.7291 (mtp85) REVERT: J 3 GLU cc_start: 0.5302 (pt0) cc_final: 0.4835 (mm-30) outliers start: 23 outliers final: 22 residues processed: 132 average time/residue: 0.1947 time to fit residues: 36.1091 Evaluate side-chains 137 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain B residue 369 PHE Chi-restraints excluded: chain B residue 383 GLU Chi-restraints excluded: chain B residue 439 THR Chi-restraints excluded: chain B residue 449 LYS 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 446 LEU Chi-restraints excluded: chain J residue 14 CYS Chi-restraints excluded: chain J residue 50 SER 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: 2.9990 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 10.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN ** D 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.185642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.140777 restraints weight = 27591.653| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 3.33 r_work: 0.3678 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 8197 Z= 0.220 Angle : 0.659 5.105 11205 Z= 0.339 Chirality : 0.047 0.178 1320 Planarity : 0.006 0.058 1441 Dihedral : 5.473 41.859 1185 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.42 % Favored : 94.09 % Rotamer: Outliers : 2.61 % Allowed : 16.76 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.25), residues: 1033 helix: -1.37 (0.46), residues: 105 sheet: 0.78 (0.26), residues: 395 loop : -0.85 (0.26), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 57 TYR 0.012 0.002 TYR A 467 PHE 0.017 0.002 PHE C 369 TRP 0.014 0.002 TRP A 310 HIS 0.025 0.002 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 8173) covalent geometry : angle 0.65531 (11155) SS BOND : bond 0.00329 ( 19) SS BOND : angle 1.26095 ( 38) hydrogen bonds : bond 0.03842 ( 289) hydrogen bonds : angle 4.93663 ( 939) Misc. bond : bond 0.00157 ( 1) link_BETA1-4 : bond 0.00207 ( 1) link_BETA1-4 : angle 1.09277 ( 3) link_NAG-ASN : bond 0.00348 ( 3) link_NAG-ASN : angle 1.42436 ( 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 143 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.447 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: A 317 LYS cc_start: 0.7054 (ttmt) cc_final: 0.6780 (ttmm) REVERT: A 405 THR cc_start: 0.7967 (p) cc_final: 0.7749 (p) REVERT: B 291 GLN cc_start: 0.6784 (pp30) cc_final: 0.6414 (pp30) REVERT: B 401 GLU cc_start: 0.6226 (tp30) cc_final: 0.5943 (tp30) REVERT: C 244 GLN cc_start: 0.7048 (tp40) cc_final: 0.6475 (mp10) REVERT: C 253 LEU cc_start: 0.8393 (tt) cc_final: 0.8125 (tp) REVERT: C 317 LYS cc_start: 0.6940 (mptt) cc_final: 0.6316 (tppt) REVERT: C 420 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8596 (ttmm) REVERT: D 296 CYS cc_start: 0.6711 (m) cc_final: 0.6211 (m) REVERT: D 309 ARG cc_start: 0.7462 (mtp-110) cc_final: 0.7135 (mtp85) REVERT: J 3 GLU cc_start: 0.5538 (pt0) cc_final: 0.4996 (mm-30) REVERT: J 113 MET cc_start: 0.8133 (mmp) cc_final: 0.7804 (mmp) outliers start: 24 outliers final: 20 residues processed: 136 average time/residue: 0.2032 time to fit residues: 38.1717 Evaluate side-chains 133 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.458 ------------------------------------------------------------------------------- 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 263 LEU Chi-restraints excluded: chain B residue 338 ASN Chi-restraints excluded: chain B residue 369 PHE 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 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 446 LEU Chi-restraints excluded: chain J residue 45 ASN Chi-restraints excluded: chain J residue 50 SER 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 36 optimal weight: 0.4980 chunk 102 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 89 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.186799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.144126 restraints weight = 26622.166| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 3.05 r_work: 0.3709 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.7735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8197 Z= 0.130 Angle : 0.609 10.457 11205 Z= 0.311 Chirality : 0.045 0.177 1320 Planarity : 0.005 0.056 1441 Dihedral : 5.304 41.825 1185 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.84 % Favored : 94.77 % Rotamer: Outliers : 2.07 % Allowed : 18.61 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.26), residues: 1033 helix: -1.12 (0.49), residues: 105 sheet: 0.91 (0.26), residues: 409 loop : -0.68 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 413 TYR 0.010 0.001 TYR C 425 PHE 0.017 0.002 PHE B 438 TRP 0.012 0.001 TRP D 276 HIS 0.014 0.001 HIS D 431 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8173) covalent geometry : angle 0.59745 (11155) SS BOND : bond 0.00429 ( 19) SS BOND : angle 2.00818 ( 38) hydrogen bonds : bond 0.03453 ( 289) hydrogen bonds : angle 4.70559 ( 939) Misc. bond : bond 0.00126 ( 1) link_BETA1-4 : bond 0.00044 ( 1) link_BETA1-4 : angle 1.10107 ( 3) link_NAG-ASN : bond 0.00393 ( 3) link_NAG-ASN : angle 1.36896 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5434.77 seconds wall clock time: 92 minutes 43.11 seconds (5563.11 seconds total)