Starting phenix.real_space_refine on Fri Sep 11 09:53:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pup_71873/09_2026/9pup_71873.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pup_71873/09_2026/9pup_71873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pup_71873/09_2026/9pup_71873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pup_71873/09_2026/9pup_71873.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pup_71873/09_2026/9pup_71873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pup_71873/09_2026/9pup_71873.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 5378 2.51 5 N 1464 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8564 Number of models: 1 Model: "" Number of chains: 4 Chain: "I" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 880 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "B" Number of atoms: 3346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3346 Classifications: {'peptide': 427} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 400} Chain breaks: 1 Chain: "C" 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: 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 Restraints were copied for chains: H, A, D Time building chain proxies: 3.20, per 1000 atoms: 0.37 Number of scatterers: 8564 At special positions: 0 Unit cell: (99.831, 113.826, 87.702, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1674 8.00 N 1464 7.00 C 5378 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 159 " - pdb=" SG CYS B 571 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 214 " distance=2.03 Simple disulfide: pdb=" SG CYS B 256 " - pdb=" SG CYS B 269 " distance=2.03 Simple disulfide: pdb=" SG CYS B 350 " - pdb=" SG CYS B 363 " distance=2.03 Simple disulfide: pdb=" SG CYS B 355 " - pdb=" SG CYS B 469 " distance=2.03 Simple disulfide: pdb=" SG CYS B 463 " - pdb=" SG CYS B 473 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 544 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 571 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 214 " distance=2.03 Simple disulfide: pdb=" SG CYS A 256 " - pdb=" SG CYS A 269 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 363 " distance=2.03 Simple disulfide: pdb=" SG CYS A 355 " - pdb=" SG CYS A 469 " distance=2.03 Simple disulfide: pdb=" SG CYS A 463 " - pdb=" SG CYS A 473 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 544 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 601 " - " ASN A 308 " " NAG A 602 " - " ASN A 523 " " NAG B 601 " - " ASN B 308 " " NAG B 602 " - " ASN B 523 " " NAG C 1 " - " ASN B 351 " " NAG D 1 " - " ASN A 351 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 327.1 milliseconds 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2000 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 20 sheets defined 8.3% alpha, 42.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.691A pdb=" N ASN B 252 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 281 Processing helix chain 'B' and resid 295 through 297 No H-bonds generated for 'chain 'B' and resid 295 through 297' Processing helix chain 'B' and resid 305 through 309 removed outlier: 3.607A pdb=" N ILE B 309 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 367 through 368 No H-bonds generated for 'chain 'B' and resid 367 through 368' Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 400 through 404 Processing helix chain 'B' and resid 441 through 445 removed outlier: 4.143A pdb=" N ILE B 445 " --> pdb=" O TYR B 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.691A pdb=" N ASN A 252 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 281 Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.608A pdb=" N ILE A 309 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 367 through 368 No H-bonds generated for 'chain 'A' and resid 367 through 368' Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 441 through 445 removed outlier: 4.143A pdb=" N ILE A 445 " --> pdb=" O TYR A 442 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 4 through 7 removed outlier: 4.082A pdb=" N VAL I 78 " --> pdb=" O CYS I 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.695A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL I 89 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN I 32 " --> pdb=" O THR I 52 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N THR I 52 " --> pdb=" O ASN I 32 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET I 34 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N ALA I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.695A pdb=" N GLY I 10 " --> pdb=" O THR I 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 150 removed outlier: 6.429A pdb=" N ALA B 528 " --> pdb=" O ASN B 551 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ASN B 551 " --> pdb=" O ALA B 528 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N TYR B 530 " --> pdb=" O GLU B 549 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 557 " --> pdb=" O HIS B 552 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 190 through 198 removed outlier: 6.552A pdb=" N THR B 206 " --> pdb=" O PRO B 194 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU B 196 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA B 204 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER B 207 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE B 228 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR B 230 " --> pdb=" O LEU B 239 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N LEU B 239 " --> pdb=" O THR B 230 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 254 through 261 removed outlier: 5.484A pdb=" N SER B 255 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER B 270 " --> pdb=" O SER B 255 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 315 through 320 removed outlier: 4.945A pdb=" N LEU B 318 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 337 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU B 335 " --> pdb=" O PRO B 320 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 315 through 320 removed outlier: 4.945A pdb=" N LEU B 318 " --> pdb=" O TYR B 337 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TYR B 337 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU B 335 " --> pdb=" O PRO B 320 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ILE B 332 " --> pdb=" O VAL B 384 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 410 through 415 removed outlier: 4.976A pdb=" N ILE B 419 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLN B 433 " --> pdb=" O THR B 423 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 481 through 483 Processing sheet with id=AB2, first strand: chain 'H' and resid 4 through 7 removed outlier: 4.082A pdb=" N VAL H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.695A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL H 89 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N ASN H 32 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR H 52 " --> pdb=" O ASN H 32 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.695A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 148 through 150 removed outlier: 6.430A pdb=" N ALA A 528 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ASN A 551 " --> pdb=" O ALA A 528 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N TYR A 530 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 557 " --> pdb=" O HIS A 552 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 190 through 198 removed outlier: 6.552A pdb=" N THR A 206 " --> pdb=" O PRO A 194 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 196 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA A 204 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER A 207 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE A 228 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N THR A 230 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU A 239 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 254 through 261 removed outlier: 5.484A pdb=" N SER A 255 " --> pdb=" O SER A 270 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 270 " --> pdb=" O SER A 255 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 315 through 320 removed outlier: 4.945A pdb=" N LEU A 318 " --> pdb=" O TYR A 337 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR A 337 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU A 335 " --> pdb=" O PRO A 320 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 315 through 320 removed outlier: 4.945A pdb=" N LEU A 318 " --> pdb=" O TYR A 337 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TYR A 337 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N LEU A 335 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE A 332 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 410 through 415 removed outlier: 4.977A pdb=" N ILE A 419 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N GLN A 433 " --> pdb=" O THR A 423 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 481 through 483 298 hydrogen bonds defined for protein. 750 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.57 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2756 1.34 - 1.46: 1750 1.46 - 1.58: 4188 1.58 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 8758 Sorted by residual: bond pdb=" CA VAL A 503 " pdb=" CB VAL A 503 " ideal model delta sigma weight residual 1.544 1.557 -0.014 1.50e-02 4.44e+03 8.32e-01 bond pdb=" CA VAL B 503 " pdb=" CB VAL B 503 " ideal model delta sigma weight residual 1.544 1.557 -0.013 1.50e-02 4.44e+03 7.45e-01 bond pdb=" CG1 ILE A 447 " pdb=" CD1 ILE A 447 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.42e-01 bond pdb=" CG1 ILE B 447 " pdb=" CD1 ILE B 447 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 7.22e-01 bond pdb=" CA ILE B 202 " pdb=" CB ILE B 202 " ideal model delta sigma weight residual 1.548 1.560 -0.012 1.49e-02 4.50e+03 6.22e-01 ... (remaining 8753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 11300 1.21 - 2.42: 501 2.42 - 3.63: 95 3.63 - 4.84: 25 4.84 - 6.05: 5 Bond angle restraints: 11926 Sorted by residual: angle pdb=" CA VAL B 503 " pdb=" CB VAL B 503 " pdb=" CG1 VAL B 503 " ideal model delta sigma weight residual 110.40 115.02 -4.62 1.70e+00 3.46e-01 7.37e+00 angle pdb=" CA VAL A 503 " pdb=" CB VAL A 503 " pdb=" CG1 VAL A 503 " ideal model delta sigma weight residual 110.40 114.93 -4.53 1.70e+00 3.46e-01 7.10e+00 angle pdb=" C VAL B 503 " pdb=" N ASN B 504 " pdb=" CA ASN B 504 " ideal model delta sigma weight residual 121.80 127.85 -6.05 2.44e+00 1.68e-01 6.14e+00 angle pdb=" C VAL A 503 " pdb=" N ASN A 504 " pdb=" CA ASN A 504 " ideal model delta sigma weight residual 121.80 127.77 -5.97 2.44e+00 1.68e-01 5.98e+00 angle pdb=" N TYR B 509 " pdb=" CA TYR B 509 " pdb=" C TYR B 509 " ideal model delta sigma weight residual 108.02 103.92 4.10 1.75e+00 3.27e-01 5.48e+00 ... (remaining 11921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.08: 4968 17.08 - 34.16: 318 34.16 - 51.25: 54 51.25 - 68.33: 14 68.33 - 85.41: 10 Dihedral angle restraints: 5364 sinusoidal: 2224 harmonic: 3140 Sorted by residual: dihedral pdb=" CB MET I 82 " pdb=" CG MET I 82 " pdb=" SD MET I 82 " pdb=" CE MET I 82 " ideal model delta sinusoidal sigma weight residual -180.00 -122.33 -57.67 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" CB MET H 82 " pdb=" CG MET H 82 " pdb=" SD MET H 82 " pdb=" CE MET H 82 " ideal model delta sinusoidal sigma weight residual 180.00 -122.37 -57.63 3 1.50e+01 4.44e-03 9.44e+00 dihedral pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " pdb=" CD1 LEU A 455 " ideal model delta sinusoidal sigma weight residual 60.00 115.57 -55.57 3 1.50e+01 4.44e-03 9.35e+00 ... (remaining 5361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 798 0.032 - 0.064: 341 0.064 - 0.095: 122 0.095 - 0.127: 91 0.127 - 0.159: 12 Chirality restraints: 1364 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 308 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.32e-01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 308 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.15e-01 chirality pdb=" CA PRO B 486 " pdb=" N PRO B 486 " pdb=" C PRO B 486 " pdb=" CB PRO B 486 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 1361 not shown) Planarity restraints: 1524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 502 " -0.127 9.50e-02 1.11e+02 5.75e-02 2.61e+00 pdb=" NE ARG A 502 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 502 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 502 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 502 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 502 " -0.127 9.50e-02 1.11e+02 5.74e-02 2.59e+00 pdb=" NE ARG B 502 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 502 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 502 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG B 502 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 152 " -0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO B 153 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 153 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 153 " -0.020 5.00e-02 4.00e+02 ... (remaining 1521 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1857 2.79 - 3.32: 7949 3.32 - 3.85: 14050 3.85 - 4.37: 16136 4.37 - 4.90: 28696 Nonbonded interactions: 68688 Sorted by model distance: nonbonded pdb=" NH2 ARG A 515 " pdb=" OE1 GLU A 518 " model vdw 2.266 3.120 nonbonded pdb=" NH2 ARG B 515 " pdb=" OE1 GLU B 518 " model vdw 2.267 3.120 nonbonded pdb=" OD1 ASP B 216 " pdb=" NZ LYS B 254 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASP A 216 " pdb=" NZ LYS A 254 " model vdw 2.340 3.120 nonbonded pdb=" O SER I 29 " pdb=" OG SER I 96 " model vdw 2.400 3.040 ... (remaining 68683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'A' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.140 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7159 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 : 0.002 0.034 8782 Z= 0.096 Angle : 0.602 6.048 11982 Z= 0.331 Chirality : 0.047 0.159 1364 Planarity : 0.006 0.058 1518 Dihedral : 12.246 85.412 3316 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.62 % Allowed : 3.54 % Favored : 95.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.24), residues: 1078 helix: -3.74 (0.53), residues: 34 sheet: -0.30 (0.27), residues: 392 loop : -1.73 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.003 ARG A 502 TYR 0.016 0.003 TYR A 509 PHE 0.021 0.002 PHE B 156 TRP 0.016 0.002 TRP H 36 HIS 0.002 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.10 ( 8758) covalent geometry : angle 0.59979 / 0.33 (11926) SS BOND : bond 0.00152 / 0.09 ( 16) SS BOND : angle 0.83191 / 0.51 ( 32) hydrogen bonds : bond 0.24224 / 16.35 ( 290) hydrogen bonds : angle 9.80848 / 6.71 ( 750) link_BETA1-4 : bond 0.00313 / 0.16 ( 2) link_BETA1-4 : angle 0.99901 / 0.51 ( 6) link_NAG-ASN : bond 0.00286 / 0.14 ( 6) link_NAG-ASN : angle 1.02432 / 0.56 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 228 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7729 (tttp) cc_final: 0.7501 (tttp) REVERT: B 158 ARG cc_start: 0.6533 (ttp80) cc_final: 0.6206 (ttp-170) REVERT: B 183 MET cc_start: 0.6550 (mmm) cc_final: 0.5986 (mmm) REVERT: B 190 CYS cc_start: 0.6946 (t) cc_final: 0.6534 (t) REVERT: B 273 LYS cc_start: 0.7816 (mmtp) cc_final: 0.7589 (mmmm) REVERT: B 332 ILE cc_start: 0.7989 (mm) cc_final: 0.7665 (tt) REVERT: B 358 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7714 (mmtt) REVERT: B 411 ARG cc_start: 0.7984 (ttp-170) cc_final: 0.7320 (ptm160) REVERT: B 461 ASN cc_start: 0.8116 (m-40) cc_final: 0.7893 (m110) REVERT: B 558 PHE cc_start: 0.8531 (m-80) cc_final: 0.8321 (m-80) REVERT: B 567 ILE cc_start: 0.7466 (mt) cc_final: 0.7138 (mt) REVERT: A 157 TRP cc_start: 0.7776 (t-100) cc_final: 0.7107 (t-100) REVERT: A 165 SER cc_start: 0.7474 (t) cc_final: 0.7262 (t) REVERT: A 183 MET cc_start: 0.6480 (mmm) cc_final: 0.5949 (mmm) REVERT: A 190 CYS cc_start: 0.7002 (t) cc_final: 0.6561 (t) REVERT: A 315 TYR cc_start: 0.7139 (m-80) cc_final: 0.6796 (m-80) REVERT: A 406 TRP cc_start: 0.7668 (t-100) cc_final: 0.7320 (t-100) REVERT: A 411 ARG cc_start: 0.8014 (ttp-170) cc_final: 0.7518 (ttp-170) REVERT: A 489 SER cc_start: 0.7999 (m) cc_final: 0.7656 (p) REVERT: A 558 PHE cc_start: 0.8518 (m-80) cc_final: 0.8285 (m-80) outliers start: 6 outliers final: 6 residues processed: 230 average time/residue: 0.1103 time to fit residues: 33.5911 Evaluate side-chains 205 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 199 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 235 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 429 HIS ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 538 HIS A 429 HIS A 461 ASN ** A 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.155610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134363 restraints weight = 11476.043| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.65 r_work: 0.3667 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8782 Z= 0.199 Angle : 0.614 6.553 11982 Z= 0.327 Chirality : 0.048 0.162 1364 Planarity : 0.005 0.041 1518 Dihedral : 5.273 50.095 1370 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.08 % Allowed : 11.35 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.25), residues: 1078 helix: -2.79 (0.54), residues: 34 sheet: -0.05 (0.26), residues: 416 loop : -1.08 (0.24), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 45 TYR 0.021 0.002 TYR B 478 PHE 0.022 0.002 PHE B 156 TRP 0.014 0.002 TRP A 406 HIS 0.003 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.20 ( 8758) covalent geometry : angle 0.61142 / 0.33 (11926) SS BOND : bond 0.00314 / 0.19 ( 16) SS BOND : angle 0.82396 / 0.49 ( 32) hydrogen bonds : bond 0.04841 / 3.21 ( 290) hydrogen bonds : angle 6.97406 / 4.80 ( 750) link_BETA1-4 : bond 0.00137 / 0.07 ( 2) link_BETA1-4 : angle 1.09947 / 0.57 ( 6) link_NAG-ASN : bond 0.00341 / 0.18 ( 6) link_NAG-ASN : angle 1.31137 / 0.76 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 219 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7474 (tttp) cc_final: 0.7228 (tttp) REVERT: B 158 ARG cc_start: 0.6780 (ttp80) cc_final: 0.6496 (ttp-170) REVERT: B 183 MET cc_start: 0.7062 (mmm) cc_final: 0.6427 (mmm) REVERT: B 190 CYS cc_start: 0.7200 (t) cc_final: 0.6855 (t) REVERT: B 277 ARG cc_start: 0.8219 (mpt-90) cc_final: 0.7997 (mmt180) REVERT: B 303 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7346 (ttm-80) REVERT: B 310 SER cc_start: 0.8329 (m) cc_final: 0.8090 (p) REVERT: B 331 LYS cc_start: 0.7471 (mttt) cc_final: 0.7074 (mttt) REVERT: B 358 LYS cc_start: 0.8094 (mmtt) cc_final: 0.7822 (mmtt) REVERT: B 377 MET cc_start: 0.7716 (mmm) cc_final: 0.7438 (mmm) REVERT: B 395 LYS cc_start: 0.7449 (mtmt) cc_final: 0.7048 (mtmt) REVERT: B 411 ARG cc_start: 0.8190 (ttp-170) cc_final: 0.7881 (ptm160) REVERT: B 487 THR cc_start: 0.8316 (t) cc_final: 0.7900 (p) REVERT: B 567 ILE cc_start: 0.7656 (mt) cc_final: 0.7409 (mt) REVERT: A 158 ARG cc_start: 0.6840 (ttp80) cc_final: 0.6635 (ttp80) REVERT: A 165 SER cc_start: 0.7976 (t) cc_final: 0.7772 (t) REVERT: A 183 MET cc_start: 0.7182 (mmm) cc_final: 0.6597 (mmm) REVERT: A 190 CYS cc_start: 0.7176 (t) cc_final: 0.6776 (t) REVERT: A 192 ARG cc_start: 0.6685 (mmm160) cc_final: 0.6191 (mmm160) REVERT: A 303 ARG cc_start: 0.7875 (ttm-80) cc_final: 0.7462 (ttm-80) REVERT: A 310 SER cc_start: 0.8358 (m) cc_final: 0.8085 (p) REVERT: A 315 TYR cc_start: 0.7332 (m-80) cc_final: 0.6800 (m-80) REVERT: A 411 ARG cc_start: 0.8201 (ttp-170) cc_final: 0.7929 (ptm160) REVERT: A 473 CYS cc_start: 0.6109 (p) cc_final: 0.5692 (p) REVERT: A 487 THR cc_start: 0.8452 (t) cc_final: 0.8243 (t) REVERT: A 489 SER cc_start: 0.8080 (m) cc_final: 0.7661 (p) outliers start: 20 outliers final: 15 residues processed: 227 average time/residue: 0.1272 time to fit residues: 37.3140 Evaluate side-chains 225 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 210 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 399 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 0.0980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 54 optimal weight: 0.0020 chunk 96 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.155731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134294 restraints weight = 11342.335| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.63 r_work: 0.3671 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3501 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8782 Z= 0.149 Angle : 0.559 8.037 11982 Z= 0.294 Chirality : 0.046 0.161 1364 Planarity : 0.005 0.039 1518 Dihedral : 5.031 49.962 1366 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.92 % Allowed : 13.02 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.26), residues: 1078 helix: -2.15 (0.70), residues: 34 sheet: 0.02 (0.27), residues: 412 loop : -0.98 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 45 TYR 0.013 0.002 TYR B 420 PHE 0.015 0.002 PHE B 156 TRP 0.015 0.002 TRP I 103 HIS 0.003 0.001 HIS B 546 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 ( 8758) covalent geometry : angle 0.55600 / 0.29 (11926) SS BOND : bond 0.00265 / 0.15 ( 16) SS BOND : angle 0.79706 / 0.51 ( 32) hydrogen bonds : bond 0.04192 / 2.77 ( 290) hydrogen bonds : angle 6.40752 / 4.43 ( 750) link_BETA1-4 : bond 0.00361 / 0.18 ( 2) link_BETA1-4 : angle 1.19675 / 0.62 ( 6) link_NAG-ASN : bond 0.00270 / 0.14 ( 6) link_NAG-ASN : angle 1.38355 / 0.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7431 (tttp) cc_final: 0.7143 (tttp) REVERT: B 157 TRP cc_start: 0.7828 (t-100) cc_final: 0.7565 (t-100) REVERT: B 158 ARG cc_start: 0.6782 (ttp80) cc_final: 0.6494 (ttp80) REVERT: B 183 MET cc_start: 0.7012 (mmm) cc_final: 0.6373 (mmm) REVERT: B 190 CYS cc_start: 0.7266 (t) cc_final: 0.6967 (t) REVERT: B 277 ARG cc_start: 0.8180 (mpt-90) cc_final: 0.7965 (mmt180) REVERT: B 303 ARG cc_start: 0.7831 (ttm-80) cc_final: 0.7327 (ttm-80) REVERT: B 310 SER cc_start: 0.8356 (m) cc_final: 0.8051 (p) REVERT: B 331 LYS cc_start: 0.7402 (mttt) cc_final: 0.7028 (mttt) REVERT: B 358 LYS cc_start: 0.8129 (mmtt) cc_final: 0.7796 (mmtt) REVERT: B 377 MET cc_start: 0.7743 (mmm) cc_final: 0.7436 (mmm) REVERT: B 395 LYS cc_start: 0.7409 (mtmt) cc_final: 0.7064 (mtmt) REVERT: B 411 ARG cc_start: 0.8234 (ttp-170) cc_final: 0.7914 (ptm160) REVERT: B 489 SER cc_start: 0.7924 (m) cc_final: 0.7643 (p) REVERT: B 567 ILE cc_start: 0.7648 (mt) cc_final: 0.7407 (mt) REVERT: H 100 TYR cc_start: 0.8872 (m-80) cc_final: 0.8506 (m-80) REVERT: A 165 SER cc_start: 0.8011 (t) cc_final: 0.7806 (t) REVERT: A 183 MET cc_start: 0.7188 (mmm) cc_final: 0.6474 (mmm) REVERT: A 190 CYS cc_start: 0.7228 (t) cc_final: 0.6855 (t) REVERT: A 266 TYR cc_start: 0.7576 (m-10) cc_final: 0.7309 (m-10) REVERT: A 310 SER cc_start: 0.8423 (m) cc_final: 0.8080 (p) REVERT: A 315 TYR cc_start: 0.7246 (m-80) cc_final: 0.6593 (m-80) REVERT: A 358 LYS cc_start: 0.8501 (mmtt) cc_final: 0.8268 (mmpt) REVERT: A 374 ASP cc_start: 0.7749 (m-30) cc_final: 0.7531 (m-30) REVERT: A 411 ARG cc_start: 0.8212 (ttp-170) cc_final: 0.7914 (ptm160) REVERT: A 424 ARG cc_start: 0.8463 (ttp-170) cc_final: 0.8230 (ttp-170) REVERT: A 487 THR cc_start: 0.8486 (t) cc_final: 0.8219 (t) REVERT: A 489 SER cc_start: 0.8071 (m) cc_final: 0.7659 (p) REVERT: A 522 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7542 (ttm110) outliers start: 28 outliers final: 21 residues processed: 220 average time/residue: 0.1230 time to fit residues: 35.3215 Evaluate side-chains 228 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 421 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 492 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 32 ASN B 144 HIS ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 144 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.151278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.130153 restraints weight = 11625.657| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.63 r_work: 0.3622 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 8782 Z= 0.259 Angle : 0.632 7.658 11982 Z= 0.331 Chirality : 0.048 0.191 1364 Planarity : 0.005 0.039 1518 Dihedral : 5.308 48.296 1366 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 3.54 % Allowed : 12.92 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.05 (0.26), residues: 1078 helix: -2.08 (0.71), residues: 34 sheet: -0.11 (0.26), residues: 410 loop : -1.01 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 402 TYR 0.023 0.002 TYR B 478 PHE 0.023 0.003 PHE B 156 TRP 0.021 0.002 TRP I 103 HIS 0.005 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.26 ( 8758) covalent geometry : angle 0.62820 / 0.33 (11926) SS BOND : bond 0.00376 / 0.22 ( 16) SS BOND : angle 1.05634 / 0.64 ( 32) hydrogen bonds : bond 0.04271 / 2.82 ( 290) hydrogen bonds : angle 6.35032 / 4.42 ( 750) link_BETA1-4 : bond 0.00208 / 0.10 ( 2) link_BETA1-4 : angle 1.24169 / 0.63 ( 6) link_NAG-ASN : bond 0.00396 / 0.21 ( 6) link_NAG-ASN : angle 1.42094 / 0.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 227 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7517 (tttp) cc_final: 0.7273 (tttp) REVERT: B 157 TRP cc_start: 0.7939 (t-100) cc_final: 0.7578 (t-100) REVERT: B 158 ARG cc_start: 0.7009 (ttp80) cc_final: 0.6698 (ttp80) REVERT: B 183 MET cc_start: 0.7249 (mmm) cc_final: 0.6569 (mmm) REVERT: B 202 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8021 (mm) REVERT: B 258 LEU cc_start: 0.8518 (mt) cc_final: 0.8302 (mp) REVERT: B 331 LYS cc_start: 0.7395 (mttt) cc_final: 0.7022 (mttt) REVERT: B 358 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7845 (mmtt) REVERT: B 377 MET cc_start: 0.7850 (mmm) cc_final: 0.7550 (mmm) REVERT: B 395 LYS cc_start: 0.7495 (mtmt) cc_final: 0.7166 (mtmt) REVERT: B 567 ILE cc_start: 0.7716 (mt) cc_final: 0.7514 (mt) REVERT: A 183 MET cc_start: 0.7408 (mmm) cc_final: 0.6633 (mmm) REVERT: A 202 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7860 (mm) REVERT: A 266 TYR cc_start: 0.7748 (m-10) cc_final: 0.7513 (m-10) REVERT: A 358 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8261 (mmpt) REVERT: A 374 ASP cc_start: 0.7928 (m-30) cc_final: 0.7705 (m-30) REVERT: A 411 ARG cc_start: 0.8224 (ttp-170) cc_final: 0.7756 (ptm160) REVERT: A 487 THR cc_start: 0.8461 (t) cc_final: 0.8184 (t) REVERT: A 489 SER cc_start: 0.8067 (m) cc_final: 0.7592 (p) REVERT: A 551 ASN cc_start: 0.7884 (t0) cc_final: 0.7573 (t0) REVERT: A 559 GLN cc_start: 0.8350 (tp40) cc_final: 0.7607 (tp-100) outliers start: 34 outliers final: 25 residues processed: 235 average time/residue: 0.1121 time to fit residues: 35.1480 Evaluate side-chains 243 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 331 LYS Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 103 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.152154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131065 restraints weight = 11410.418| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.61 r_work: 0.3632 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3458 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8782 Z= 0.201 Angle : 0.601 9.430 11982 Z= 0.313 Chirality : 0.047 0.184 1364 Planarity : 0.005 0.050 1518 Dihedral : 5.222 47.338 1366 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.06 % Allowed : 13.96 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.25), residues: 1078 helix: -1.92 (0.75), residues: 34 sheet: -0.31 (0.27), residues: 386 loop : -0.99 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 402 TYR 0.016 0.002 TYR B 478 PHE 0.021 0.002 PHE A 156 TRP 0.019 0.002 TRP I 103 HIS 0.003 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 ( 8758) covalent geometry : angle 0.59654 / 0.31 (11926) SS BOND : bond 0.00332 / 0.20 ( 16) SS BOND : angle 0.91115 / 0.55 ( 32) hydrogen bonds : bond 0.03910 / 2.59 ( 290) hydrogen bonds : angle 6.21064 / 4.33 ( 750) link_BETA1-4 : bond 0.00292 / 0.15 ( 2) link_BETA1-4 : angle 1.23120 / 0.64 ( 6) link_NAG-ASN : bond 0.00337 / 0.17 ( 6) link_NAG-ASN : angle 1.54793 / 0.88 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 223 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7500 (tttp) cc_final: 0.7268 (tttp) REVERT: B 157 TRP cc_start: 0.7877 (t-100) cc_final: 0.7543 (t-100) REVERT: B 158 ARG cc_start: 0.6943 (ttp80) cc_final: 0.6623 (ttp80) REVERT: B 183 MET cc_start: 0.7237 (mmm) cc_final: 0.6397 (mmm) REVERT: B 202 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8004 (mm) REVERT: B 258 LEU cc_start: 0.8534 (mt) cc_final: 0.8225 (mm) REVERT: B 303 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7515 (ttm-80) REVERT: B 331 LYS cc_start: 0.7403 (mttt) cc_final: 0.7051 (mttt) REVERT: B 358 LYS cc_start: 0.8175 (mmtt) cc_final: 0.7853 (mmtt) REVERT: B 377 MET cc_start: 0.7818 (mmm) cc_final: 0.7522 (mmm) REVERT: B 394 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7020 (tt) REVERT: B 395 LYS cc_start: 0.7488 (mtmt) cc_final: 0.7112 (mtmt) REVERT: B 489 SER cc_start: 0.7986 (m) cc_final: 0.7704 (p) REVERT: H 100 TYR cc_start: 0.8845 (m-80) cc_final: 0.8625 (m-80) REVERT: A 183 MET cc_start: 0.7437 (mmm) cc_final: 0.6763 (mmm) REVERT: A 202 ILE cc_start: 0.8156 (OUTLIER) cc_final: 0.7838 (mm) REVERT: A 254 LYS cc_start: 0.6743 (mmmt) cc_final: 0.6530 (mttt) REVERT: A 358 LYS cc_start: 0.8537 (mmtt) cc_final: 0.8236 (mmpt) REVERT: A 374 ASP cc_start: 0.7879 (m-30) cc_final: 0.7653 (m-30) REVERT: A 411 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7767 (ptm160) REVERT: A 485 ASN cc_start: 0.7123 (t0) cc_final: 0.6834 (t0) REVERT: A 487 THR cc_start: 0.8432 (t) cc_final: 0.8073 (t) REVERT: A 489 SER cc_start: 0.8073 (m) cc_final: 0.7781 (p) REVERT: A 551 ASN cc_start: 0.7900 (t0) cc_final: 0.7603 (t0) outliers start: 39 outliers final: 26 residues processed: 235 average time/residue: 0.1172 time to fit residues: 36.2441 Evaluate side-chains 248 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 219 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain H residue 96 SER Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 399 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.151188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.130214 restraints weight = 11341.731| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.53 r_work: 0.3644 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 8782 Z= 0.269 Angle : 0.646 9.382 11982 Z= 0.338 Chirality : 0.049 0.221 1364 Planarity : 0.005 0.050 1518 Dihedral : 5.394 46.117 1366 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.00 % Allowed : 15.21 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.25), residues: 1078 helix: -2.14 (0.71), residues: 34 sheet: -0.36 (0.26), residues: 400 loop : -1.10 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 402 TYR 0.023 0.002 TYR B 478 PHE 0.022 0.003 PHE B 156 TRP 0.025 0.002 TRP I 103 HIS 0.004 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.27 ( 8758) covalent geometry : angle 0.64186 / 0.34 (11926) SS BOND : bond 0.00413 / 0.24 ( 16) SS BOND : angle 0.99243 / 0.58 ( 32) hydrogen bonds : bond 0.04185 / 2.78 ( 290) hydrogen bonds : angle 6.30854 / 4.40 ( 750) link_BETA1-4 : bond 0.00210 / 0.10 ( 2) link_BETA1-4 : angle 1.31967 / 0.68 ( 6) link_NAG-ASN : bond 0.00420 / 0.23 ( 6) link_NAG-ASN : angle 1.50556 / 0.86 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 222 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7560 (tttp) cc_final: 0.7344 (tttp) REVERT: B 157 TRP cc_start: 0.7950 (t-100) cc_final: 0.7482 (t-100) REVERT: B 158 ARG cc_start: 0.6954 (ttp80) cc_final: 0.6699 (ttp80) REVERT: B 183 MET cc_start: 0.7294 (mmm) cc_final: 0.6478 (mmm) REVERT: B 202 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7967 (mm) REVERT: B 277 ARG cc_start: 0.8096 (mpt-90) cc_final: 0.7825 (mpt180) REVERT: B 303 ARG cc_start: 0.8006 (ttm-80) cc_final: 0.7640 (ttm-80) REVERT: B 331 LYS cc_start: 0.7423 (mttt) cc_final: 0.7087 (mttt) REVERT: B 358 LYS cc_start: 0.8207 (mmtt) cc_final: 0.7915 (mmtt) REVERT: B 377 MET cc_start: 0.7871 (mmm) cc_final: 0.7592 (mmm) REVERT: B 394 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7024 (tt) REVERT: B 395 LYS cc_start: 0.7584 (mtmt) cc_final: 0.7227 (mtmt) REVERT: B 453 ASN cc_start: 0.8221 (m-40) cc_final: 0.7793 (m-40) REVERT: B 489 SER cc_start: 0.7973 (m) cc_final: 0.7696 (p) REVERT: H 34 MET cc_start: 0.7968 (ppp) cc_final: 0.7714 (ptm) REVERT: A 183 MET cc_start: 0.7512 (mmm) cc_final: 0.6837 (mmm) REVERT: A 202 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 254 LYS cc_start: 0.6819 (mmmt) cc_final: 0.6566 (mttt) REVERT: A 264 ASP cc_start: 0.6643 (m-30) cc_final: 0.6416 (m-30) REVERT: A 358 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8219 (mmpt) REVERT: A 374 ASP cc_start: 0.7905 (m-30) cc_final: 0.7686 (m-30) REVERT: A 394 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7275 (tt) REVERT: A 487 THR cc_start: 0.8497 (t) cc_final: 0.8192 (t) REVERT: A 551 ASN cc_start: 0.7888 (t0) cc_final: 0.7578 (t0) outliers start: 48 outliers final: 33 residues processed: 239 average time/residue: 0.1179 time to fit residues: 37.0116 Evaluate side-chains 255 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 218 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 532 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.152511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131396 restraints weight = 11478.632| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.56 r_work: 0.3658 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8782 Z= 0.201 Angle : 0.607 10.389 11982 Z= 0.316 Chirality : 0.047 0.171 1364 Planarity : 0.005 0.055 1518 Dihedral : 5.298 46.369 1366 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.58 % Allowed : 15.73 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.25), residues: 1078 helix: -2.11 (0.71), residues: 34 sheet: -0.37 (0.26), residues: 396 loop : -1.06 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 402 TYR 0.019 0.002 TYR B 478 PHE 0.018 0.002 PHE B 156 TRP 0.022 0.002 TRP I 103 HIS 0.003 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 ( 8758) covalent geometry : angle 0.60272 / 0.32 (11926) SS BOND : bond 0.00307 / 0.18 ( 16) SS BOND : angle 0.88974 / 0.52 ( 32) hydrogen bonds : bond 0.03856 / 2.55 ( 290) hydrogen bonds : angle 6.19729 / 4.32 ( 750) link_BETA1-4 : bond 0.00295 / 0.15 ( 2) link_BETA1-4 : angle 1.24298 / 0.65 ( 6) link_NAG-ASN : bond 0.00317 / 0.17 ( 6) link_NAG-ASN : angle 1.50693 / 0.86 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 223 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7554 (tttp) cc_final: 0.7322 (tttp) REVERT: B 157 TRP cc_start: 0.7902 (t-100) cc_final: 0.7525 (t-100) REVERT: B 183 MET cc_start: 0.7325 (mmm) cc_final: 0.6787 (mmm) REVERT: B 202 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7931 (mm) REVERT: B 303 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7607 (ttm-80) REVERT: B 331 LYS cc_start: 0.7416 (mttt) cc_final: 0.7086 (mttt) REVERT: B 358 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7941 (mmtt) REVERT: B 377 MET cc_start: 0.7857 (mmm) cc_final: 0.7565 (mmm) REVERT: B 395 LYS cc_start: 0.7549 (mtmt) cc_final: 0.7186 (mtmt) REVERT: B 453 ASN cc_start: 0.8195 (m-40) cc_final: 0.7790 (m-40) REVERT: B 489 SER cc_start: 0.7920 (m) cc_final: 0.7657 (p) REVERT: H 34 MET cc_start: 0.7988 (ppp) cc_final: 0.7705 (ptm) REVERT: A 201 LEU cc_start: 0.8348 (mp) cc_final: 0.8087 (mp) REVERT: A 202 ILE cc_start: 0.8093 (OUTLIER) cc_final: 0.7780 (mm) REVERT: A 254 LYS cc_start: 0.6856 (mmmt) cc_final: 0.6631 (mttt) REVERT: A 331 LYS cc_start: 0.7590 (mtmt) cc_final: 0.7164 (ttmt) REVERT: A 358 LYS cc_start: 0.8507 (mmtt) cc_final: 0.8214 (mmpt) REVERT: A 374 ASP cc_start: 0.7902 (m-30) cc_final: 0.7686 (m-30) REVERT: A 394 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7253 (tt) REVERT: A 411 ARG cc_start: 0.8252 (ttp-170) cc_final: 0.7998 (ptm160) REVERT: A 424 ARG cc_start: 0.8515 (ttp-170) cc_final: 0.8232 (ttt180) REVERT: A 487 THR cc_start: 0.8479 (t) cc_final: 0.7943 (p) REVERT: A 551 ASN cc_start: 0.7907 (t0) cc_final: 0.7614 (t0) outliers start: 44 outliers final: 36 residues processed: 238 average time/residue: 0.1158 time to fit residues: 36.3851 Evaluate side-chains 256 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 195 SER Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 495 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 96 optimal weight: 0.0270 chunk 55 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 7 optimal weight: 0.0770 chunk 6 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.153322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.132143 restraints weight = 11389.956| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.57 r_work: 0.3662 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8782 Z= 0.165 Angle : 0.586 11.410 11982 Z= 0.305 Chirality : 0.046 0.186 1364 Planarity : 0.005 0.054 1518 Dihedral : 5.223 46.745 1366 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.58 % Allowed : 16.25 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.25), residues: 1078 helix: -2.00 (0.73), residues: 34 sheet: -0.39 (0.26), residues: 396 loop : -1.02 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 402 TYR 0.018 0.002 TYR B 482 PHE 0.016 0.002 PHE B 156 TRP 0.023 0.002 TRP I 103 HIS 0.002 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 8758) covalent geometry : angle 0.58222 / 0.30 (11926) SS BOND : bond 0.00241 / 0.14 ( 16) SS BOND : angle 0.82581 / 0.48 ( 32) hydrogen bonds : bond 0.03662 / 2.44 ( 290) hydrogen bonds : angle 6.12593 / 4.27 ( 750) link_BETA1-4 : bond 0.00289 / 0.15 ( 2) link_BETA1-4 : angle 1.23232 / 0.64 ( 6) link_NAG-ASN : bond 0.00267 / 0.14 ( 6) link_NAG-ASN : angle 1.42077 / 0.81 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7581 (tttp) cc_final: 0.7360 (tttp) REVERT: B 157 TRP cc_start: 0.7867 (t-100) cc_final: 0.7486 (t-100) REVERT: B 183 MET cc_start: 0.7310 (mmm) cc_final: 0.6776 (mmm) REVERT: B 202 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7934 (mm) REVERT: B 277 ARG cc_start: 0.8033 (mpt-90) cc_final: 0.7804 (mmt180) REVERT: B 303 ARG cc_start: 0.7949 (ttm-80) cc_final: 0.7428 (ttm-80) REVERT: B 331 LYS cc_start: 0.7432 (mttt) cc_final: 0.7083 (mttt) REVERT: B 358 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7956 (mmtt) REVERT: B 377 MET cc_start: 0.7813 (mmm) cc_final: 0.7518 (mmm) REVERT: B 394 LEU cc_start: 0.7379 (OUTLIER) cc_final: 0.7008 (tt) REVERT: B 395 LYS cc_start: 0.7529 (mtmt) cc_final: 0.7127 (mtmt) REVERT: B 453 ASN cc_start: 0.8182 (m-40) cc_final: 0.7780 (m-40) REVERT: B 489 SER cc_start: 0.7951 (m) cc_final: 0.7701 (p) REVERT: H 34 MET cc_start: 0.7926 (ppp) cc_final: 0.7583 (ptm) REVERT: H 100 TYR cc_start: 0.8872 (m-80) cc_final: 0.8609 (m-80) REVERT: A 201 LEU cc_start: 0.8358 (mp) cc_final: 0.8078 (mp) REVERT: A 202 ILE cc_start: 0.8069 (OUTLIER) cc_final: 0.7743 (mm) REVERT: A 254 LYS cc_start: 0.6859 (mmmt) cc_final: 0.6621 (mttt) REVERT: A 358 LYS cc_start: 0.8509 (mmtt) cc_final: 0.8221 (mmpt) REVERT: A 374 ASP cc_start: 0.7910 (m-30) cc_final: 0.7696 (m-30) REVERT: A 411 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7952 (ptm160) REVERT: A 424 ARG cc_start: 0.8438 (ttp-170) cc_final: 0.8134 (ttt180) REVERT: A 487 THR cc_start: 0.8416 (t) cc_final: 0.8028 (p) REVERT: A 551 ASN cc_start: 0.7907 (t0) cc_final: 0.7609 (t0) outliers start: 44 outliers final: 36 residues processed: 238 average time/residue: 0.1125 time to fit residues: 35.5109 Evaluate side-chains 256 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 217 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 495 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.151536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.130447 restraints weight = 11378.520| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.55 r_work: 0.3644 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.095 8782 Z= 0.267 Angle : 0.652 12.581 11982 Z= 0.341 Chirality : 0.048 0.218 1364 Planarity : 0.005 0.057 1518 Dihedral : 5.426 46.017 1366 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.27 % Allowed : 17.60 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.25), residues: 1078 helix: -2.19 (0.69), residues: 34 sheet: -0.41 (0.26), residues: 396 loop : -1.08 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 402 TYR 0.024 0.002 TYR B 482 PHE 0.023 0.003 PHE B 156 TRP 0.030 0.003 TRP H 103 HIS 0.003 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.27 ( 8758) covalent geometry : angle 0.64904 / 0.34 (11926) SS BOND : bond 0.00324 / 0.19 ( 16) SS BOND : angle 0.89315 / 0.51 ( 32) hydrogen bonds : bond 0.04048 / 2.69 ( 290) hydrogen bonds : angle 6.28687 / 4.40 ( 750) link_BETA1-4 : bond 0.00213 / 0.10 ( 2) link_BETA1-4 : angle 1.22617 / 0.62 ( 6) link_NAG-ASN : bond 0.00351 / 0.19 ( 6) link_NAG-ASN : angle 1.44497 / 0.82 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 222 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 34 MET cc_start: 0.7788 (ptm) cc_final: 0.7571 (ptt) REVERT: B 149 LYS cc_start: 0.7424 (tttp) cc_final: 0.7188 (tttp) REVERT: B 157 TRP cc_start: 0.7931 (t-100) cc_final: 0.7462 (t-100) REVERT: B 183 MET cc_start: 0.7405 (mmm) cc_final: 0.6821 (mmm) REVERT: B 202 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7910 (mm) REVERT: B 277 ARG cc_start: 0.7962 (mpt-90) cc_final: 0.7699 (mmt180) REVERT: B 303 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7576 (ttm-80) REVERT: B 331 LYS cc_start: 0.7472 (mttt) cc_final: 0.7117 (mttt) REVERT: B 358 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7958 (mmtt) REVERT: B 361 ARG cc_start: 0.7667 (ttm-80) cc_final: 0.7424 (ttm-80) REVERT: B 377 MET cc_start: 0.7867 (mmm) cc_final: 0.7588 (mmm) REVERT: B 394 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7002 (tt) REVERT: B 395 LYS cc_start: 0.7539 (mtmt) cc_final: 0.7195 (mtmt) REVERT: B 489 SER cc_start: 0.7951 (m) cc_final: 0.7679 (p) REVERT: H 34 MET cc_start: 0.8089 (ppp) cc_final: 0.7697 (ptm) REVERT: A 202 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7784 (mm) REVERT: A 254 LYS cc_start: 0.6952 (mmmt) cc_final: 0.6737 (mttt) REVERT: A 358 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8256 (mmpt) REVERT: A 361 ARG cc_start: 0.7717 (ttm-80) cc_final: 0.7486 (ttm-80) REVERT: A 374 ASP cc_start: 0.7935 (m-30) cc_final: 0.7702 (m-30) REVERT: A 411 ARG cc_start: 0.8266 (ttp-170) cc_final: 0.7934 (ptm160) REVERT: A 487 THR cc_start: 0.8441 (t) cc_final: 0.8037 (p) REVERT: A 551 ASN cc_start: 0.7899 (t0) cc_final: 0.7597 (t0) REVERT: A 559 GLN cc_start: 0.8426 (tp40) cc_final: 0.8145 (tp40) outliers start: 41 outliers final: 36 residues processed: 234 average time/residue: 0.1179 time to fit residues: 36.1787 Evaluate side-chains 257 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 495 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 63 optimal weight: 0.6980 chunk 20 optimal weight: 0.4980 chunk 95 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.152937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.131672 restraints weight = 11354.955| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.60 r_work: 0.3661 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3488 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8782 Z= 0.184 Angle : 0.618 12.837 11982 Z= 0.321 Chirality : 0.047 0.229 1364 Planarity : 0.005 0.063 1518 Dihedral : 5.388 46.574 1366 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.96 % Allowed : 18.54 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.25), residues: 1078 helix: -1.98 (0.72), residues: 34 sheet: -0.42 (0.26), residues: 396 loop : -1.01 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 402 TYR 0.017 0.002 TYR B 482 PHE 0.017 0.002 PHE B 156 TRP 0.027 0.002 TRP H 103 HIS 0.002 0.001 HIS A 467 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 ( 8758) covalent geometry : angle 0.61393 / 0.32 (11926) SS BOND : bond 0.00256 / 0.15 ( 16) SS BOND : angle 0.82101 / 0.48 ( 32) hydrogen bonds : bond 0.03752 / 2.50 ( 290) hydrogen bonds : angle 6.20733 / 4.34 ( 750) link_BETA1-4 : bond 0.00217 / 0.11 ( 2) link_BETA1-4 : angle 1.18185 / 0.61 ( 6) link_NAG-ASN : bond 0.00256 / 0.13 ( 6) link_NAG-ASN : angle 1.71260 / 1.00 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2156 Ramachandran restraints generated. 1078 Oldfield, 0 Emsley, 1078 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 149 LYS cc_start: 0.7423 (tttp) cc_final: 0.7094 (tttp) REVERT: B 157 TRP cc_start: 0.7866 (t-100) cc_final: 0.7483 (t-100) REVERT: B 183 MET cc_start: 0.7352 (mmm) cc_final: 0.6764 (mmm) REVERT: B 202 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7892 (mm) REVERT: B 277 ARG cc_start: 0.7934 (mpt-90) cc_final: 0.7678 (mmt180) REVERT: B 303 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7416 (ttm-80) REVERT: B 331 LYS cc_start: 0.7491 (mttt) cc_final: 0.7124 (mttt) REVERT: B 358 LYS cc_start: 0.8300 (mmtt) cc_final: 0.7958 (mmtt) REVERT: B 361 ARG cc_start: 0.7627 (ttm-80) cc_final: 0.7378 (ttm-80) REVERT: B 377 MET cc_start: 0.7835 (mmm) cc_final: 0.7536 (mmm) REVERT: B 394 LEU cc_start: 0.7368 (OUTLIER) cc_final: 0.6987 (tt) REVERT: B 395 LYS cc_start: 0.7508 (mtmt) cc_final: 0.7159 (mtmt) REVERT: B 489 SER cc_start: 0.7910 (m) cc_final: 0.7627 (p) REVERT: H 34 MET cc_start: 0.8089 (ppp) cc_final: 0.7662 (ptm) REVERT: A 202 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7773 (mm) REVERT: A 254 LYS cc_start: 0.6912 (mmmt) cc_final: 0.6685 (mttt) REVERT: A 358 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8222 (mmpt) REVERT: A 374 ASP cc_start: 0.7925 (m-30) cc_final: 0.7691 (m-30) REVERT: A 411 ARG cc_start: 0.8234 (ttp-170) cc_final: 0.7908 (ptm160) REVERT: A 424 ARG cc_start: 0.8451 (ttp-170) cc_final: 0.8139 (ttt180) REVERT: A 487 THR cc_start: 0.8420 (t) cc_final: 0.8219 (t) REVERT: A 551 ASN cc_start: 0.7875 (t0) cc_final: 0.7584 (t0) REVERT: A 559 GLN cc_start: 0.8444 (tp40) cc_final: 0.8178 (tp40) outliers start: 38 outliers final: 35 residues processed: 228 average time/residue: 0.1146 time to fit residues: 34.1688 Evaluate side-chains 251 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 213 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 63 VAL Chi-restraints excluded: chain I residue 96 SER Chi-restraints excluded: chain I residue 99 SER Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain B residue 144 HIS Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 165 SER Chi-restraints excluded: chain B residue 167 MET Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 203 TYR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 291 ASP Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 337 TYR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 399 ILE Chi-restraints excluded: chain B residue 492 SER Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 99 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain A residue 144 HIS Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 167 MET Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 203 TYR Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 495 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 75 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 91 optimal weight: 0.5980 chunk 101 optimal weight: 0.0770 chunk 95 optimal weight: 0.0770 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 51 optimal weight: 0.0970 chunk 39 optimal weight: 0.0870 chunk 20 optimal weight: 0.0770 overall best weight: 0.0830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 467 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.157138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.136012 restraints weight = 11244.786| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 2.61 r_work: 0.3687 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8782 Z= 0.106 Angle : 0.564 12.470 11982 Z= 0.294 Chirality : 0.046 0.213 1364 Planarity : 0.005 0.057 1518 Dihedral : 5.116 49.104 1366 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.29 % Allowed : 20.42 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.26), residues: 1078 helix: -1.60 (0.76), residues: 34 sheet: -0.35 (0.26), residues: 394 loop : -0.85 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 402 TYR 0.011 0.001 TYR B 420 PHE 0.013 0.002 PHE B 334 TRP 0.015 0.002 TRP H 100 HIS 0.002 0.000 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 ( 8758) covalent geometry : angle 0.56108 / 0.29 (11926) SS BOND : bond 0.00200 / 0.11 ( 16) SS BOND : angle 0.72727 / 0.45 ( 32) hydrogen bonds : bond 0.03229 / 2.17 ( 290) hydrogen bonds : angle 5.97189 / 4.16 ( 750) link_BETA1-4 : bond 0.00230 / 0.11 ( 2) link_BETA1-4 : angle 1.14753 / 0.58 ( 6) link_NAG-ASN : bond 0.00224 / 0.11 ( 6) link_NAG-ASN : angle 1.43260 / 0.84 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3470.13 seconds wall clock time: 60 minutes 2.94 seconds (3602.94 seconds total)