Starting phenix.real_space_refine on Sat Jun 14 18:45:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vd9_31911/06_2025/7vd9_31911.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vd9_31911/06_2025/7vd9_31911.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vd9_31911/06_2025/7vd9_31911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vd9_31911/06_2025/7vd9_31911.map" model { file = "/net/cci-nas-00/data/ceres_data/7vd9_31911/06_2025/7vd9_31911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vd9_31911/06_2025/7vd9_31911.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10421 2.51 5 N 2895 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "B" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "C" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "D" Number of atoms: 4011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Conformer: "B" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} bond proxies already assigned to first conformer: 4109 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ASER A 120 " occ=0.63 ... (10 atoms not shown) pdb=" OG BSER A 120 " occ=0.37 residue: pdb=" N AGLY A 121 " occ=0.63 ... (6 atoms not shown) pdb=" O BGLY A 121 " occ=0.37 residue: pdb=" N ASER B 120 " occ=0.82 ... (10 atoms not shown) pdb=" OG BSER B 120 " occ=0.18 residue: pdb=" N AGLY B 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY B 121 " occ=0.18 residue: pdb=" N ASER C 120 " occ=0.64 ... (10 atoms not shown) pdb=" OG BSER C 120 " occ=0.36 residue: pdb=" N AGLY C 121 " occ=0.64 ... (6 atoms not shown) pdb=" O BGLY C 121 " occ=0.36 residue: pdb=" N ASER D 120 " occ=0.89 ... (10 atoms not shown) pdb=" OG BSER D 120 " occ=0.11 residue: pdb=" N AGLY D 121 " occ=0.89 ... (6 atoms not shown) pdb=" O BGLY D 121 " occ=0.11 Time building chain proxies: 17.94, per 1000 atoms: 1.09 Number of scatterers: 16426 At special positions: 0 Unit cell: (113.1, 109.2, 83.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3042 8.00 N 2895 7.00 C 10421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.37 Conformation dependent library (CDL) restraints added in 4.0 seconds 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 40.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 6.744A pdb=" N MET A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 202 through 205 removed outlier: 3.740A pdb=" N ILE A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.500A pdb=" N HIS A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET A 212 " --> pdb=" O HIS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 367 removed outlier: 3.728A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.519A pdb=" N GLU B 101 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 202 through 205 removed outlier: 3.896A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.526A pdb=" N HIS B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET B 212 " --> pdb=" O HIS B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 246 through 257 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 367 removed outlier: 3.755A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 486 through 501 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 205 removed outlier: 3.721A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 208 through 212 removed outlier: 4.054A pdb=" N MET C 212 " --> pdb=" O HIS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.709A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 486 through 501 Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.620A pdb=" N ARG D 19 " --> pdb=" O TRP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.548A pdb=" N GLU D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.712A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 removed outlier: 4.082A pdb=" N MET D 212 " --> pdb=" O HIS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 257 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.717A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 486 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.170A pdb=" N GLY C 427 " --> pdb=" O TYR D 425 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 425 " --> pdb=" O GLY C 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 429 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE D 423 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 removed outlier: 6.009A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 425 removed outlier: 4.327A pdb=" N ILE A 423 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 429 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 427 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 423 through 424 removed outlier: 4.312A pdb=" N ILE B 423 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 44 removed outlier: 4.357A pdb=" N ILE C 423 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 344 removed outlier: 6.059A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 344 removed outlier: 6.402A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 345 removed outlier: 5.999A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.91 Time building geometry restraints manager: 5.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 7276 1.39 - 1.56: 9542 1.56 - 1.73: 20 1.73 - 1.89: 96 1.89 - 2.06: 16 Bond restraints: 16950 Sorted by residual: bond pdb=" CG PRO D 406 " pdb=" CD PRO D 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.91e-01 bond pdb=" CG PRO C 406 " pdb=" CD PRO C 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.84e-01 bond pdb=" CG PRO B 406 " pdb=" CD PRO B 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.69e-01 bond pdb=" CB GLU D 290 " pdb=" CG GLU D 290 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.57e-01 bond pdb=" CB GLN B 195 " pdb=" CG GLN B 195 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.06e-01 ... (remaining 16945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 22828 2.08 - 4.16: 262 4.16 - 6.24: 37 6.24 - 8.32: 0 8.32 - 10.40: 1 Bond angle restraints: 23128 Sorted by residual: angle pdb=" C ARG D 388 " pdb=" N ASP D 389 " pdb=" CA ASP D 389 " ideal model delta sigma weight residual 121.31 126.88 -5.57 1.49e+00 4.50e-01 1.40e+01 angle pdb=" C ARG B 388 " pdb=" N ASP B 389 " pdb=" CA ASP B 389 " ideal model delta sigma weight residual 121.31 126.77 -5.46 1.49e+00 4.50e-01 1.34e+01 angle pdb=" CB MET D 394 " pdb=" CG MET D 394 " pdb=" SD MET D 394 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C ARG A 388 " pdb=" N ASP A 389 " pdb=" CA ASP A 389 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.74e+00 angle pdb=" N ASP D 389 " pdb=" CA ASP D 389 " pdb=" C ASP D 389 " ideal model delta sigma weight residual 110.35 114.40 -4.05 1.40e+00 5.10e-01 8.39e+00 ... (remaining 23123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8631 17.69 - 35.38: 876 35.38 - 53.07: 273 53.07 - 70.76: 80 70.76 - 88.45: 36 Dihedral angle restraints: 9896 sinusoidal: 4087 harmonic: 5809 Sorted by residual: dihedral pdb=" CA CYS D 393 " pdb=" C CYS D 393 " pdb=" N MET D 394 " pdb=" CA MET D 394 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP D 180 " pdb=" CB ASP D 180 " pdb=" CG ASP D 180 " pdb=" OD1 ASP D 180 " ideal model delta sinusoidal sigma weight residual -30.00 -88.06 58.06 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 180 " pdb=" CB ASP A 180 " pdb=" CG ASP A 180 " pdb=" OD1 ASP A 180 " ideal model delta sinusoidal sigma weight residual -30.00 -87.20 57.20 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 9893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1331 0.029 - 0.059: 650 0.059 - 0.088: 208 0.088 - 0.118: 127 0.118 - 0.147: 19 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE C 373 " pdb=" N ILE C 373 " pdb=" C ILE C 373 " pdb=" CB ILE C 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA TYR C 358 " pdb=" N TYR C 358 " pdb=" C TYR C 358 " pdb=" CB TYR C 358 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2332 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 6 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO C 7 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 346 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO C 347 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 346 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 347 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 347 " -0.026 5.00e-02 4.00e+02 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1006 2.74 - 3.28: 16113 3.28 - 3.82: 29648 3.82 - 4.36: 36594 4.36 - 4.90: 60754 Nonbonded interactions: 144115 Sorted by model distance: nonbonded pdb=" NE2 GLN A 415 " pdb=" OG SER A 417 " model vdw 2.194 3.120 nonbonded pdb=" OE1 GLN D 415 " pdb=" OG SER D 417 " model vdw 2.224 3.040 nonbonded pdb=" NZ LYS B 301 " pdb=" O ASP B 438 " model vdw 2.226 3.120 nonbonded pdb=" OD2 ASP A 360 " pdb=" NH1 ARG C 66 " model vdw 2.231 3.120 nonbonded pdb=" NZ LYS D 301 " pdb=" O ASP D 438 " model vdw 2.232 3.120 ... (remaining 144110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 5 through 119 or resid 122 through 501 or resid 1201 throu \ gh 1202)) selection = (chain 'C' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) selection = (chain 'D' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) } 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=0.11 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: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 49.940 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.100 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 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 0.044 16954 Z= 0.102 Angle : 0.543 10.399 23128 Z= 0.272 Chirality : 0.042 0.147 2335 Planarity : 0.005 0.063 3067 Dihedral : 17.252 88.450 6170 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.33 % Allowed : 18.62 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1999 helix: 1.21 (0.20), residues: 698 sheet: 0.61 (0.33), residues: 283 loop : -0.45 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.015 0.001 PHE D 409 TYR 0.012 0.001 TYR D 236 ARG 0.002 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.15135 ( 668) hydrogen bonds : angle 7.83343 ( 1884) covalent geometry : bond 0.00239 (16950) covalent geometry : angle 0.54313 (23128) Misc. bond : bond 0.03062 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 1.821 Fit side-chains REVERT: A 56 VAL cc_start: 0.5998 (m) cc_final: 0.5692 (p) REVERT: A 88 THR cc_start: 0.6685 (p) cc_final: 0.6219 (t) REVERT: A 93 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.6060 (mtmm) REVERT: B 88 THR cc_start: 0.6459 (p) cc_final: 0.5977 (t) REVERT: B 396 ASP cc_start: 0.4877 (p0) cc_final: 0.4614 (p0) REVERT: B 455 GLN cc_start: 0.6161 (mt0) cc_final: 0.5922 (mt0) REVERT: C 43 THR cc_start: 0.6639 (p) cc_final: 0.6249 (t) REVERT: C 178 ASP cc_start: 0.5934 (t0) cc_final: 0.5711 (m-30) REVERT: C 306 LYS cc_start: 0.5656 (mppt) cc_final: 0.5157 (mmtt) REVERT: C 488 ASP cc_start: 0.5925 (m-30) cc_final: 0.5691 (t0) REVERT: D 88 THR cc_start: 0.6537 (p) cc_final: 0.6064 (t) outliers start: 38 outliers final: 35 residues processed: 231 average time/residue: 1.2250 time to fit residues: 317.3352 Evaluate side-chains 216 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 180 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 413 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.164576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.140822 restraints weight = 20922.530| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.21 r_work: 0.3476 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 16954 Z= 0.246 Angle : 0.795 8.944 23128 Z= 0.417 Chirality : 0.052 0.152 2335 Planarity : 0.007 0.082 3067 Dihedral : 10.238 94.069 2322 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 4.65 % Allowed : 17.10 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1999 helix: 0.25 (0.19), residues: 696 sheet: 0.30 (0.31), residues: 294 loop : -0.68 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 183 HIS 0.012 0.002 HIS A 102 PHE 0.026 0.003 PHE D 200 TYR 0.021 0.003 TYR C 280 ARG 0.012 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.06504 ( 668) hydrogen bonds : angle 6.88099 ( 1884) covalent geometry : bond 0.00583 (16950) covalent geometry : angle 0.79531 (23128) Misc. bond : bond 0.09334 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 173 time to evaluate : 1.783 Fit side-chains REVERT: A 12 MET cc_start: 0.7391 (OUTLIER) cc_final: 0.6765 (mtm) REVERT: B 88 THR cc_start: 0.6496 (p) cc_final: 0.5955 (t) REVERT: B 396 ASP cc_start: 0.5398 (p0) cc_final: 0.5010 (p0) REVERT: C 56 VAL cc_start: 0.6327 (OUTLIER) cc_final: 0.6059 (p) REVERT: C 306 LYS cc_start: 0.5578 (OUTLIER) cc_final: 0.5334 (mppt) REVERT: D 88 THR cc_start: 0.6675 (p) cc_final: 0.6192 (t) outliers start: 78 outliers final: 46 residues processed: 238 average time/residue: 1.1734 time to fit residues: 315.8556 Evaluate side-chains 216 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 306 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 25 optimal weight: 0.0570 chunk 123 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 156 optimal weight: 7.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN C 40 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN D 305 HIS D 415 GLN D 433 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.165418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.137603 restraints weight = 25168.629| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 1.47 r_work: 0.3474 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16954 Z= 0.174 Angle : 0.679 6.735 23128 Z= 0.353 Chirality : 0.048 0.149 2335 Planarity : 0.006 0.064 3067 Dihedral : 9.436 88.556 2315 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.84 % Allowed : 18.03 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.19), residues: 1999 helix: 0.43 (0.19), residues: 692 sheet: 0.26 (0.31), residues: 296 loop : -0.63 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 183 HIS 0.009 0.001 HIS A 102 PHE 0.019 0.002 PHE D 200 TYR 0.018 0.002 TYR B 236 ARG 0.007 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.05390 ( 668) hydrogen bonds : angle 6.48108 ( 1884) covalent geometry : bond 0.00412 (16950) covalent geometry : angle 0.67886 (23128) Misc. bond : bond 0.07235 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 185 time to evaluate : 2.174 Fit side-chains REVERT: A 12 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6802 (mtm) REVERT: A 56 VAL cc_start: 0.6285 (OUTLIER) cc_final: 0.5999 (p) REVERT: A 88 THR cc_start: 0.6626 (p) cc_final: 0.6238 (t) REVERT: A 221 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7831 (tttm) REVERT: B 88 THR cc_start: 0.6486 (p) cc_final: 0.5937 (t) REVERT: B 396 ASP cc_start: 0.5197 (p0) cc_final: 0.4911 (p0) REVERT: C 56 VAL cc_start: 0.6214 (OUTLIER) cc_final: 0.5936 (p) REVERT: C 178 ASP cc_start: 0.6033 (OUTLIER) cc_final: 0.5541 (m-30) REVERT: D 56 VAL cc_start: 0.6309 (OUTLIER) cc_final: 0.6027 (p) REVERT: D 88 THR cc_start: 0.6662 (p) cc_final: 0.6142 (t) outliers start: 64 outliers final: 36 residues processed: 238 average time/residue: 1.5679 time to fit residues: 419.4671 Evaluate side-chains 219 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 468 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 57 optimal weight: 8.9990 chunk 183 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 170 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 chunk 185 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.140133 restraints weight = 21850.052| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.28 r_work: 0.3461 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 16954 Z= 0.264 Angle : 0.825 9.157 23128 Z= 0.433 Chirality : 0.053 0.158 2335 Planarity : 0.008 0.077 3067 Dihedral : 10.119 94.243 2300 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.04 % Favored : 94.91 % Rotamer: Outliers : 5.06 % Allowed : 16.75 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.18), residues: 1999 helix: -0.09 (0.19), residues: 694 sheet: 0.15 (0.30), residues: 298 loop : -0.90 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 183 HIS 0.010 0.002 HIS A 102 PHE 0.027 0.003 PHE D 200 TYR 0.024 0.003 TYR C 280 ARG 0.012 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.06577 ( 668) hydrogen bonds : angle 6.88213 ( 1884) covalent geometry : bond 0.00625 (16950) covalent geometry : angle 0.82545 (23128) Misc. bond : bond 0.10573 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 175 time to evaluate : 1.989 Fit side-chains REVERT: A 12 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6875 (mtm) REVERT: A 88 THR cc_start: 0.6540 (p) cc_final: 0.6182 (t) REVERT: A 178 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.5490 (m-30) REVERT: A 221 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7858 (tttm) REVERT: B 88 THR cc_start: 0.6420 (p) cc_final: 0.5902 (t) REVERT: C 178 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5533 (m-30) REVERT: C 294 PHE cc_start: 0.5930 (OUTLIER) cc_final: 0.5521 (m-80) REVERT: D 88 THR cc_start: 0.6591 (p) cc_final: 0.6151 (t) REVERT: D 178 ASP cc_start: 0.5937 (OUTLIER) cc_final: 0.5507 (m-30) REVERT: D 389 ASP cc_start: 0.5410 (OUTLIER) cc_final: 0.5119 (m-30) outliers start: 85 outliers final: 53 residues processed: 250 average time/residue: 1.2040 time to fit residues: 339.4729 Evaluate side-chains 233 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 173 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 306 LYS Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 143 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 117 optimal weight: 0.9990 chunk 58 optimal weight: 0.0670 chunk 187 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 chunk 195 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS B 466 HIS C 40 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 369 ASN C 433 ASN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 HIS ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 481 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.138490 restraints weight = 23735.576| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.46 r_work: 0.3466 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3335 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3335 r_free = 0.3335 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3335 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 16954 Z= 0.200 Angle : 0.725 7.634 23128 Z= 0.379 Chirality : 0.049 0.152 2335 Planarity : 0.007 0.068 3067 Dihedral : 9.568 89.905 2300 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.64 % Favored : 95.31 % Rotamer: Outliers : 4.54 % Allowed : 17.10 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 1999 helix: 0.12 (0.19), residues: 692 sheet: 0.19 (0.30), residues: 298 loop : -0.83 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 183 HIS 0.009 0.001 HIS A 102 PHE 0.021 0.003 PHE D 200 TYR 0.020 0.002 TYR C 280 ARG 0.009 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.05714 ( 668) hydrogen bonds : angle 6.59376 ( 1884) covalent geometry : bond 0.00475 (16950) covalent geometry : angle 0.72539 (23128) Misc. bond : bond 0.08010 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 1.929 Fit side-chains REVERT: A 12 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.6839 (mtm) REVERT: A 88 THR cc_start: 0.6626 (p) cc_final: 0.6264 (t) REVERT: A 178 ASP cc_start: 0.5963 (OUTLIER) cc_final: 0.5517 (m-30) REVERT: A 221 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7868 (tttm) REVERT: B 88 THR cc_start: 0.6498 (p) cc_final: 0.5990 (t) REVERT: B 454 GLU cc_start: 0.5480 (pp20) cc_final: 0.5159 (pp20) REVERT: C 56 VAL cc_start: 0.6266 (OUTLIER) cc_final: 0.5982 (p) REVERT: C 178 ASP cc_start: 0.6060 (OUTLIER) cc_final: 0.5588 (m-30) REVERT: C 294 PHE cc_start: 0.5939 (OUTLIER) cc_final: 0.5546 (m-80) REVERT: D 88 THR cc_start: 0.6640 (p) cc_final: 0.6188 (t) REVERT: D 178 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5523 (m-30) REVERT: D 389 ASP cc_start: 0.5374 (OUTLIER) cc_final: 0.5090 (m-30) outliers start: 76 outliers final: 52 residues processed: 238 average time/residue: 1.4108 time to fit residues: 378.4360 Evaluate side-chains 227 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 167 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 306 LYS Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 79 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 180 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS B 466 HIS ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN D 415 GLN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139935 restraints weight = 23386.525| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.46 r_work: 0.3481 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16954 Z= 0.181 Angle : 0.693 7.081 23128 Z= 0.361 Chirality : 0.048 0.152 2335 Planarity : 0.006 0.064 3067 Dihedral : 9.282 86.398 2300 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.54 % Favored : 95.41 % Rotamer: Outliers : 4.13 % Allowed : 17.74 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1999 helix: 0.29 (0.19), residues: 692 sheet: 0.18 (0.31), residues: 296 loop : -0.77 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 183 HIS 0.008 0.001 HIS A 102 PHE 0.020 0.002 PHE D 200 TYR 0.020 0.002 TYR C 280 ARG 0.007 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.05413 ( 668) hydrogen bonds : angle 6.46380 ( 1884) covalent geometry : bond 0.00428 (16950) covalent geometry : angle 0.69306 (23128) Misc. bond : bond 0.07205 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 173 time to evaluate : 1.995 Fit side-chains REVERT: A 12 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.6882 (mtm) REVERT: A 88 THR cc_start: 0.6585 (p) cc_final: 0.6214 (t) REVERT: A 178 ASP cc_start: 0.5976 (OUTLIER) cc_final: 0.5529 (m-30) REVERT: A 221 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.7835 (tttm) REVERT: B 88 THR cc_start: 0.6489 (p) cc_final: 0.5981 (t) REVERT: B 454 GLU cc_start: 0.5461 (pp20) cc_final: 0.5142 (pp20) REVERT: C 56 VAL cc_start: 0.6248 (OUTLIER) cc_final: 0.5977 (p) REVERT: C 88 THR cc_start: 0.6510 (p) cc_final: 0.6174 (t) REVERT: C 178 ASP cc_start: 0.6044 (OUTLIER) cc_final: 0.5562 (m-30) REVERT: C 294 PHE cc_start: 0.5963 (OUTLIER) cc_final: 0.5572 (m-80) REVERT: C 306 LYS cc_start: 0.5576 (OUTLIER) cc_final: 0.5245 (mppt) REVERT: D 56 VAL cc_start: 0.6307 (OUTLIER) cc_final: 0.6028 (p) REVERT: D 88 THR cc_start: 0.6647 (p) cc_final: 0.6199 (t) REVERT: D 178 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5517 (m-30) REVERT: D 389 ASP cc_start: 0.5295 (OUTLIER) cc_final: 0.5002 (m-30) outliers start: 69 outliers final: 50 residues processed: 230 average time/residue: 1.2370 time to fit residues: 318.8812 Evaluate side-chains 225 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 165 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 315 LYS Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 23 LYS Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 306 LYS Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 306 LYS Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 184 optimal weight: 0.8980 chunk 185 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 189 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS B 466 HIS C 433 ASN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 GLN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.165683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.139575 restraints weight = 27724.263| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.44 r_work: 0.3481 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16954 Z= 0.143 Angle : 0.625 6.078 23128 Z= 0.324 Chirality : 0.046 0.151 2335 Planarity : 0.006 0.064 3067 Dihedral : 8.596 79.021 2298 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.26 % Allowed : 18.38 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.19), residues: 1999 helix: 0.60 (0.20), residues: 692 sheet: 0.27 (0.31), residues: 295 loop : -0.65 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 183 HIS 0.007 0.001 HIS A 102 PHE 0.016 0.002 PHE D 279 TYR 0.019 0.002 TYR D 236 ARG 0.005 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 668) hydrogen bonds : angle 6.17174 ( 1884) covalent geometry : bond 0.00339 (16950) covalent geometry : angle 0.62488 (23128) Misc. bond : bond 0.05523 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 1.901 Fit side-chains REVERT: A 12 MET cc_start: 0.7499 (OUTLIER) cc_final: 0.6905 (mtm) REVERT: A 56 VAL cc_start: 0.6279 (m) cc_final: 0.6003 (p) REVERT: A 88 THR cc_start: 0.6603 (p) cc_final: 0.6227 (t) REVERT: A 178 ASP cc_start: 0.6039 (OUTLIER) cc_final: 0.5566 (m-30) REVERT: B 88 THR cc_start: 0.6515 (p) cc_final: 0.5987 (t) REVERT: B 396 ASP cc_start: 0.5248 (p0) cc_final: 0.4986 (p0) REVERT: B 454 GLU cc_start: 0.5532 (pp20) cc_final: 0.5179 (pp20) REVERT: B 456 ARG cc_start: 0.6314 (mtt90) cc_final: 0.6090 (mtt180) REVERT: C 56 VAL cc_start: 0.6130 (m) cc_final: 0.5853 (p) REVERT: C 88 THR cc_start: 0.6528 (p) cc_final: 0.6194 (t) REVERT: C 178 ASP cc_start: 0.6028 (OUTLIER) cc_final: 0.5531 (m-30) REVERT: C 294 PHE cc_start: 0.5914 (OUTLIER) cc_final: 0.5617 (m-80) REVERT: D 56 VAL cc_start: 0.6291 (OUTLIER) cc_final: 0.6027 (p) REVERT: D 88 THR cc_start: 0.6652 (p) cc_final: 0.6208 (t) REVERT: D 178 ASP cc_start: 0.6018 (OUTLIER) cc_final: 0.5529 (m-30) REVERT: D 493 ILE cc_start: 0.7304 (mm) cc_final: 0.7041 (mt) outliers start: 54 outliers final: 36 residues processed: 232 average time/residue: 1.2953 time to fit residues: 336.8943 Evaluate side-chains 220 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 1.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 87 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 158 optimal weight: 0.0570 chunk 26 optimal weight: 0.8980 chunk 23 optimal weight: 0.0050 chunk 95 optimal weight: 10.0000 chunk 165 optimal weight: 7.9990 chunk 120 optimal weight: 0.3980 chunk 118 optimal weight: 4.9990 chunk 162 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 overall best weight: 1.2714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS B 466 HIS C 433 ASN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 397 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.167361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141620 restraints weight = 30763.529| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.60 r_work: 0.3486 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3361 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16954 Z= 0.117 Angle : 0.576 5.690 23128 Z= 0.296 Chirality : 0.044 0.149 2335 Planarity : 0.005 0.060 3067 Dihedral : 7.738 64.227 2291 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.56 % Allowed : 19.14 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.19), residues: 1999 helix: 0.93 (0.20), residues: 692 sheet: 0.39 (0.31), residues: 296 loop : -0.54 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 183 HIS 0.007 0.001 HIS A 102 PHE 0.014 0.001 PHE B 409 TYR 0.018 0.002 TYR B 236 ARG 0.003 0.000 ARG C 252 Details of bonding type rmsd hydrogen bonds : bond 0.04103 ( 668) hydrogen bonds : angle 5.84451 ( 1884) covalent geometry : bond 0.00278 (16950) covalent geometry : angle 0.57551 (23128) Misc. bond : bond 0.04054 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 1.812 Fit side-chains REVERT: A 12 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6891 (mtm) REVERT: A 56 VAL cc_start: 0.6116 (m) cc_final: 0.5816 (p) REVERT: A 88 THR cc_start: 0.6591 (p) cc_final: 0.6184 (t) REVERT: A 221 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7829 (tttm) REVERT: B 88 THR cc_start: 0.6534 (p) cc_final: 0.6012 (t) REVERT: B 396 ASP cc_start: 0.5064 (p0) cc_final: 0.4846 (p0) REVERT: B 455 GLN cc_start: 0.6419 (mt0) cc_final: 0.6138 (mt0) REVERT: B 456 ARG cc_start: 0.6305 (mtt90) cc_final: 0.6085 (mtt180) REVERT: C 56 VAL cc_start: 0.5957 (m) cc_final: 0.5664 (p) REVERT: C 88 THR cc_start: 0.6529 (p) cc_final: 0.6163 (t) REVERT: C 294 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5614 (m-80) REVERT: C 306 LYS cc_start: 0.5584 (mppt) cc_final: 0.5081 (mmtt) REVERT: D 56 VAL cc_start: 0.6222 (m) cc_final: 0.5959 (p) REVERT: D 88 THR cc_start: 0.6673 (p) cc_final: 0.6213 (t) outliers start: 42 outliers final: 29 residues processed: 236 average time/residue: 1.1917 time to fit residues: 316.3837 Evaluate side-chains 213 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 39 optimal weight: 0.9990 chunk 158 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 120 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS A 492 HIS B 466 HIS B 494 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS D 63 HIS D 397 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.165592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.139515 restraints weight = 30603.130| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.59 r_work: 0.3471 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 16954 Z= 0.192 Angle : 0.705 7.563 23128 Z= 0.367 Chirality : 0.049 0.147 2335 Planarity : 0.006 0.066 3067 Dihedral : 9.157 86.037 2291 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.79 % Allowed : 19.26 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.19), residues: 1999 helix: 0.43 (0.19), residues: 696 sheet: 0.23 (0.31), residues: 297 loop : -0.69 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 183 HIS 0.008 0.002 HIS A 102 PHE 0.022 0.003 PHE A 154 TYR 0.020 0.002 TYR C 280 ARG 0.008 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.05511 ( 668) hydrogen bonds : angle 6.38720 ( 1884) covalent geometry : bond 0.00456 (16950) covalent geometry : angle 0.70470 (23128) Misc. bond : bond 0.07610 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 167 time to evaluate : 1.913 Fit side-chains REVERT: A 12 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6813 (mtm) REVERT: A 56 VAL cc_start: 0.6332 (OUTLIER) cc_final: 0.6044 (p) REVERT: A 88 THR cc_start: 0.6515 (p) cc_final: 0.6149 (t) REVERT: A 178 ASP cc_start: 0.5995 (OUTLIER) cc_final: 0.5494 (m-30) REVERT: A 221 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7845 (tttm) REVERT: B 88 THR cc_start: 0.6493 (p) cc_final: 0.5983 (t) REVERT: C 56 VAL cc_start: 0.6212 (OUTLIER) cc_final: 0.5946 (p) REVERT: C 178 ASP cc_start: 0.5974 (OUTLIER) cc_final: 0.5444 (m-30) REVERT: C 294 PHE cc_start: 0.5934 (OUTLIER) cc_final: 0.5564 (m-80) REVERT: D 88 THR cc_start: 0.6612 (p) cc_final: 0.6152 (t) outliers start: 46 outliers final: 33 residues processed: 206 average time/residue: 1.2325 time to fit residues: 285.4683 Evaluate side-chains 207 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 143 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 2 optimal weight: 0.0770 chunk 82 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 170 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS A 492 HIS B 494 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** D 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.166382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141607 restraints weight = 33154.590| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.22 r_work: 0.3407 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16954 Z= 0.143 Angle : 0.623 6.057 23128 Z= 0.322 Chirality : 0.046 0.150 2335 Planarity : 0.006 0.061 3067 Dihedral : 8.475 79.972 2291 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.56 % Allowed : 19.43 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.19), residues: 1999 helix: 0.65 (0.20), residues: 692 sheet: 0.27 (0.31), residues: 295 loop : -0.60 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 183 HIS 0.007 0.001 HIS A 102 PHE 0.016 0.002 PHE A 279 TYR 0.019 0.002 TYR B 236 ARG 0.005 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.04716 ( 668) hydrogen bonds : angle 6.11775 ( 1884) covalent geometry : bond 0.00341 (16950) covalent geometry : angle 0.62268 (23128) Misc. bond : bond 0.05104 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 1.812 Fit side-chains REVERT: A 12 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6729 (mtm) REVERT: A 56 VAL cc_start: 0.6246 (m) cc_final: 0.5971 (p) REVERT: A 88 THR cc_start: 0.6554 (p) cc_final: 0.6151 (t) REVERT: A 221 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7779 (tttm) REVERT: B 88 THR cc_start: 0.6504 (p) cc_final: 0.5966 (t) REVERT: B 396 ASP cc_start: 0.5109 (p0) cc_final: 0.4836 (p0) REVERT: C 56 VAL cc_start: 0.6121 (m) cc_final: 0.5853 (p) REVERT: C 88 THR cc_start: 0.6485 (p) cc_final: 0.6140 (t) REVERT: C 294 PHE cc_start: 0.5899 (OUTLIER) cc_final: 0.5628 (m-80) REVERT: D 88 THR cc_start: 0.6604 (p) cc_final: 0.6147 (t) outliers start: 42 outliers final: 33 residues processed: 215 average time/residue: 1.2821 time to fit residues: 308.9957 Evaluate side-chains 213 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 PHE Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 107 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS A 492 HIS B 494 GLN ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.165357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.139411 restraints weight = 33220.069| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.35 r_work: 0.3398 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.099 16954 Z= 0.204 Angle : 0.726 7.825 23128 Z= 0.378 Chirality : 0.049 0.146 2335 Planarity : 0.007 0.065 3067 Dihedral : 9.245 86.035 2291 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.97 % Allowed : 19.14 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1999 helix: 0.26 (0.19), residues: 696 sheet: 0.15 (0.31), residues: 297 loop : -0.75 (0.20), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 183 HIS 0.009 0.002 HIS C 466 PHE 0.022 0.003 PHE D 200 TYR 0.021 0.003 TYR C 280 ARG 0.009 0.001 ARG A 382 Details of bonding type rmsd hydrogen bonds : bond 0.05704 ( 668) hydrogen bonds : angle 6.48878 ( 1884) covalent geometry : bond 0.00483 (16950) covalent geometry : angle 0.72640 (23128) Misc. bond : bond 0.09139 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13985.08 seconds wall clock time: 244 minutes 32.88 seconds (14672.88 seconds total)