Starting phenix.real_space_refine on Thu Sep 18 11:39:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vd9_31911/09_2025/7vd9_31911.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vd9_31911/09_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_31911/09_2025/7vd9_31911.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vd9_31911/09_2025/7vd9_31911.map" model { file = "/net/cci-nas-00/data/ceres_data/7vd9_31911/09_2025/7vd9_31911.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vd9_31911/09_2025/7vd9_31911.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.72, per 1000 atoms: 0.35 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: 1.29 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.58 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: 3.52 Time building geometry restraints manager: 1.70 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 602)) selection = (chain 'B' and (resid 5 through 119 or resid 122 through 1202)) selection = (chain 'C' and (resid 5 through 119 or resid 122 through 602)) selection = (chain 'D' and (resid 5 through 119 or resid 122 through 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.580 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:9.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.640 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.19), 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 ARG 0.002 0.000 ARG B 19 TYR 0.012 0.001 TYR D 236 PHE 0.015 0.001 PHE D 409 TRP 0.009 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00239 (16950) covalent geometry : angle 0.54313 (23128) hydrogen bonds : bond 0.15135 ( 668) hydrogen bonds : angle 7.83343 ( 1884) 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 : 0.650 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: 0.5228 time to fit residues: 135.5171 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 : 0.571 ------------------------------------------------------------------------------- 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 98 optimal weight: 5.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 466 HIS B 494 GLN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN D 415 GLN ** 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 = 0.3929 r_free = 0.3929 target = 0.165234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.138653 restraints weight = 27757.018| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.50 r_work: 0.3460 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1115 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= 0.194 Angle : 0.706 7.351 23128 Z= 0.368 Chirality : 0.049 0.148 2335 Planarity : 0.006 0.070 3067 Dihedral : 9.793 92.825 2322 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.19 % Allowed : 17.45 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.19), residues: 1999 helix: 0.64 (0.20), residues: 696 sheet: 0.32 (0.31), residues: 296 loop : -0.57 (0.20), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 382 TYR 0.019 0.002 TYR D 280 PHE 0.021 0.003 PHE D 200 TRP 0.016 0.002 TRP B 183 HIS 0.010 0.002 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00458 (16950) covalent geometry : angle 0.70598 (23128) hydrogen bonds : bond 0.05762 ( 668) hydrogen bonds : angle 6.60333 ( 1884) Misc. bond : bond 0.07938 ( 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 249 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 179 time to evaluate : 0.614 Fit side-chains REVERT: A 12 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6849 (mtm) REVERT: A 56 VAL cc_start: 0.6338 (OUTLIER) cc_final: 0.6060 (p) REVERT: A 88 THR cc_start: 0.6753 (p) cc_final: 0.6259 (t) REVERT: B 88 THR cc_start: 0.6540 (p) cc_final: 0.6011 (t) REVERT: B 349 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7106 (mttp) REVERT: B 396 ASP cc_start: 0.5409 (p0) cc_final: 0.5005 (p0) REVERT: C 56 VAL cc_start: 0.6154 (OUTLIER) cc_final: 0.5904 (p) REVERT: D 56 VAL cc_start: 0.6321 (OUTLIER) cc_final: 0.6039 (p) REVERT: D 88 THR cc_start: 0.6731 (p) cc_final: 0.6246 (t) outliers start: 70 outliers final: 39 residues processed: 235 average time/residue: 0.5760 time to fit residues: 151.8631 Evaluate side-chains 215 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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 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 349 LYS 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 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 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 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 126 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 95 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 93 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 439 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.138820 restraints weight = 35951.448| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.18 r_work: 0.3407 rms_B_bonded: 3.19 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 = 0.19 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 = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1143 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= 0.173 Angle : 0.672 6.642 23128 Z= 0.349 Chirality : 0.047 0.149 2335 Planarity : 0.006 0.062 3067 Dihedral : 9.243 89.230 2308 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.78 % Allowed : 18.03 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.19), residues: 1999 helix: 0.57 (0.20), residues: 692 sheet: 0.28 (0.31), residues: 296 loop : -0.57 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 382 TYR 0.019 0.002 TYR C 280 PHE 0.019 0.002 PHE D 200 TRP 0.014 0.002 TRP B 183 HIS 0.009 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00409 (16950) covalent geometry : angle 0.67160 (23128) hydrogen bonds : bond 0.05338 ( 668) hydrogen bonds : angle 6.43881 ( 1884) Misc. bond : bond 0.07282 ( 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 240 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 177 time to evaluate : 0.626 Fit side-chains REVERT: A 12 MET cc_start: 0.7439 (OUTLIER) cc_final: 0.6787 (mtm) REVERT: A 56 VAL cc_start: 0.6323 (OUTLIER) cc_final: 0.6042 (p) REVERT: A 88 THR cc_start: 0.6679 (p) cc_final: 0.6234 (t) REVERT: A 178 ASP cc_start: 0.6008 (OUTLIER) cc_final: 0.5536 (m-30) REVERT: B 88 THR cc_start: 0.6471 (p) cc_final: 0.5949 (t) REVERT: B 396 ASP cc_start: 0.5197 (p0) cc_final: 0.4885 (p0) REVERT: C 56 VAL cc_start: 0.6190 (OUTLIER) cc_final: 0.5928 (p) REVERT: D 56 VAL cc_start: 0.6327 (OUTLIER) cc_final: 0.6058 (p) REVERT: D 88 THR cc_start: 0.6644 (p) cc_final: 0.6146 (t) REVERT: D 178 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5532 (m-30) REVERT: D 389 ASP cc_start: 0.5112 (OUTLIER) cc_final: 0.4838 (m-30) outliers start: 63 outliers final: 37 residues processed: 229 average time/residue: 0.5360 time to fit residues: 137.6541 Evaluate side-chains 214 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 170 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 56 VAL Chi-restraints excluded: chain A residue 93 LYS 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 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 39 LEU Chi-restraints excluded: chain B residue 56 VAL 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 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 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 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL 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 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 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 389 ASP Chi-restraints excluded: chain D residue 413 GLU 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 19 optimal weight: 0.9990 chunk 124 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN D 415 GLN 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 = 0.3931 r_free = 0.3931 target = 0.165422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.139221 restraints weight = 26291.310| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.47 r_work: 0.3474 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16954 Z= 0.152 Angle : 0.635 6.047 23128 Z= 0.329 Chirality : 0.046 0.148 2335 Planarity : 0.006 0.061 3067 Dihedral : 8.755 83.731 2295 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.66 % Allowed : 18.27 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.19), residues: 1999 helix: 0.70 (0.20), residues: 692 sheet: 0.34 (0.31), residues: 294 loop : -0.55 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 382 TYR 0.018 0.002 TYR B 236 PHE 0.016 0.002 PHE A 279 TRP 0.013 0.002 TRP B 183 HIS 0.008 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00360 (16950) covalent geometry : angle 0.63454 (23128) hydrogen bonds : bond 0.04963 ( 668) hydrogen bonds : angle 6.24501 ( 1884) Misc. bond : bond 0.06299 ( 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 246 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 0.585 Fit side-chains REVERT: A 12 MET cc_start: 0.7509 (OUTLIER) cc_final: 0.6938 (mtm) REVERT: A 56 VAL cc_start: 0.6355 (OUTLIER) cc_final: 0.6067 (p) REVERT: A 178 ASP cc_start: 0.6031 (OUTLIER) cc_final: 0.5552 (m-30) REVERT: A 221 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7850 (tttm) REVERT: B 88 THR cc_start: 0.6549 (p) cc_final: 0.6003 (t) REVERT: B 396 ASP cc_start: 0.5239 (p0) cc_final: 0.4936 (p0) REVERT: B 454 GLU cc_start: 0.5480 (pp20) cc_final: 0.5171 (pp20) REVERT: C 5 ARG cc_start: 0.2926 (OUTLIER) cc_final: 0.2618 (mtm180) REVERT: C 56 VAL cc_start: 0.6185 (OUTLIER) cc_final: 0.5915 (p) REVERT: C 88 THR cc_start: 0.6506 (p) cc_final: 0.6136 (t) REVERT: C 294 PHE cc_start: 0.5915 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: D 56 VAL cc_start: 0.6345 (OUTLIER) cc_final: 0.6075 (p) REVERT: D 88 THR cc_start: 0.6697 (p) cc_final: 0.6198 (t) REVERT: D 178 ASP cc_start: 0.6024 (OUTLIER) cc_final: 0.5549 (m-30) REVERT: D 389 ASP cc_start: 0.5217 (OUTLIER) cc_final: 0.4906 (m-30) outliers start: 61 outliers final: 35 residues processed: 236 average time/residue: 0.5437 time to fit residues: 143.5704 Evaluate side-chains 225 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 56 VAL Chi-restraints excluded: chain A residue 93 LYS 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 26 VAL Chi-restraints excluded: chain B residue 56 VAL 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 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 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 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 294 PHE 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 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 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 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 51 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 184 optimal weight: 0.0670 chunk 97 optimal weight: 9.9990 chunk 105 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.165790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.142201 restraints weight = 18741.972| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.21 r_work: 0.3521 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16954 Z= 0.139 Angle : 0.609 5.502 23128 Z= 0.315 Chirality : 0.046 0.145 2335 Planarity : 0.005 0.060 3067 Dihedral : 8.431 80.510 2295 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.61 % Allowed : 18.15 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 1999 helix: 0.82 (0.20), residues: 692 sheet: 0.31 (0.31), residues: 298 loop : -0.53 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 382 TYR 0.018 0.002 TYR B 236 PHE 0.015 0.002 PHE D 200 TRP 0.013 0.001 TRP B 183 HIS 0.007 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00329 (16950) covalent geometry : angle 0.60934 (23128) hydrogen bonds : bond 0.04664 ( 668) hydrogen bonds : angle 6.09492 ( 1884) Misc. bond : bond 0.05632 ( 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 245 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 0.657 Fit side-chains REVERT: A 12 MET cc_start: 0.7438 (OUTLIER) cc_final: 0.6809 (mtm) REVERT: A 56 VAL cc_start: 0.6300 (m) cc_final: 0.6028 (p) REVERT: A 88 THR cc_start: 0.6641 (p) cc_final: 0.6256 (t) REVERT: A 178 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5474 (m-30) REVERT: A 221 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7800 (tttm) REVERT: B 88 THR cc_start: 0.6494 (p) cc_final: 0.5945 (t) REVERT: B 396 ASP cc_start: 0.5175 (p0) cc_final: 0.4889 (p0) REVERT: B 454 GLU cc_start: 0.5482 (pp20) cc_final: 0.5133 (pp20) REVERT: C 56 VAL cc_start: 0.6062 (m) cc_final: 0.5792 (p) REVERT: C 88 THR cc_start: 0.6495 (p) cc_final: 0.6128 (t) REVERT: C 178 ASP cc_start: 0.5959 (t0) cc_final: 0.5558 (m-30) REVERT: D 56 VAL cc_start: 0.6284 (OUTLIER) cc_final: 0.6029 (p) REVERT: D 88 THR cc_start: 0.6653 (p) cc_final: 0.6151 (t) REVERT: D 178 ASP cc_start: 0.6033 (OUTLIER) cc_final: 0.5546 (m-30) REVERT: D 389 ASP cc_start: 0.5049 (OUTLIER) cc_final: 0.4726 (m-30) outliers start: 60 outliers final: 39 residues processed: 236 average time/residue: 0.5235 time to fit residues: 139.2808 Evaluate side-chains 222 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 177 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 18 GLN 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 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 B residue 18 GLN 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 26 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 192 optimal weight: 4.9990 chunk 178 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 170 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 338 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.166141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.141893 restraints weight = 30072.728| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 1.39 r_work: 0.3485 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16954 Z= 0.141 Angle : 0.612 5.700 23128 Z= 0.316 Chirality : 0.046 0.145 2335 Planarity : 0.005 0.059 3067 Dihedral : 8.376 78.371 2291 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 4.19 % Allowed : 17.39 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.19), residues: 1999 helix: 0.81 (0.20), residues: 692 sheet: 0.36 (0.31), residues: 292 loop : -0.53 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 382 TYR 0.019 0.002 TYR B 236 PHE 0.015 0.002 PHE D 200 TRP 0.013 0.002 TRP B 183 HIS 0.007 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00335 (16950) covalent geometry : angle 0.61213 (23128) hydrogen bonds : bond 0.04702 ( 668) hydrogen bonds : angle 6.08460 ( 1884) Misc. bond : bond 0.05855 ( 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 253 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 183 time to evaluate : 0.587 Fit side-chains REVERT: A 12 MET cc_start: 0.7504 (OUTLIER) cc_final: 0.6892 (mtm) REVERT: A 56 VAL cc_start: 0.6328 (OUTLIER) cc_final: 0.6055 (p) REVERT: A 88 THR cc_start: 0.6674 (p) cc_final: 0.6286 (t) REVERT: A 178 ASP cc_start: 0.5994 (OUTLIER) cc_final: 0.5514 (m-30) REVERT: A 221 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7834 (tttm) REVERT: B 38 LYS cc_start: 0.6228 (OUTLIER) cc_final: 0.5938 (tttp) REVERT: B 88 THR cc_start: 0.6527 (p) cc_final: 0.5993 (t) REVERT: B 396 ASP cc_start: 0.5216 (p0) cc_final: 0.4921 (p0) REVERT: B 454 GLU cc_start: 0.5554 (pp20) cc_final: 0.5222 (pp20) REVERT: C 56 VAL cc_start: 0.6058 (m) cc_final: 0.5781 (p) REVERT: C 88 THR cc_start: 0.6529 (p) cc_final: 0.6168 (t) REVERT: C 178 ASP cc_start: 0.5982 (t0) cc_final: 0.5576 (m-30) REVERT: D 56 VAL cc_start: 0.6295 (OUTLIER) cc_final: 0.6037 (p) REVERT: D 88 THR cc_start: 0.6720 (p) cc_final: 0.6220 (t) REVERT: D 178 ASP cc_start: 0.5990 (OUTLIER) cc_final: 0.5520 (m-30) REVERT: D 389 ASP cc_start: 0.5186 (OUTLIER) cc_final: 0.4865 (m-30) outliers start: 70 outliers final: 47 residues processed: 242 average time/residue: 0.4868 time to fit residues: 132.6834 Evaluate side-chains 235 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 18 GLN 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 26 VAL Chi-restraints excluded: chain B residue 38 LYS 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 26 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 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 283 VAL 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 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 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 165 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 121 optimal weight: 0.1980 chunk 161 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS D 63 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.166817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.139131 restraints weight = 27936.760| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.51 r_work: 0.3490 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1120 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= 0.129 Angle : 0.590 5.320 23128 Z= 0.304 Chirality : 0.045 0.144 2335 Planarity : 0.005 0.058 3067 Dihedral : 8.001 71.560 2291 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 3.61 % Allowed : 18.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.19), residues: 1999 helix: 0.93 (0.20), residues: 692 sheet: 0.37 (0.31), residues: 293 loop : -0.48 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 382 TYR 0.018 0.002 TYR B 236 PHE 0.014 0.002 PHE A 279 TRP 0.012 0.001 TRP B 183 HIS 0.007 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00306 (16950) covalent geometry : angle 0.59016 (23128) hydrogen bonds : bond 0.04419 ( 668) hydrogen bonds : angle 5.95721 ( 1884) Misc. bond : bond 0.05164 ( 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 254 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 194 time to evaluate : 0.648 Fit side-chains REVERT: A 12 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6835 (mtm) REVERT: A 56 VAL cc_start: 0.6229 (m) cc_final: 0.5940 (p) REVERT: A 88 THR cc_start: 0.6621 (p) cc_final: 0.6217 (t) REVERT: A 221 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7801 (tttm) REVERT: B 38 LYS cc_start: 0.6198 (OUTLIER) cc_final: 0.5908 (tttp) REVERT: B 88 THR cc_start: 0.6541 (p) cc_final: 0.5995 (t) REVERT: B 396 ASP cc_start: 0.5227 (p0) cc_final: 0.4937 (p0) REVERT: B 454 GLU cc_start: 0.5491 (pp20) cc_final: 0.5134 (pp20) REVERT: C 56 VAL cc_start: 0.5966 (m) cc_final: 0.5672 (p) REVERT: C 88 THR cc_start: 0.6477 (p) cc_final: 0.6109 (t) REVERT: C 178 ASP cc_start: 0.5971 (t0) cc_final: 0.5547 (m-30) REVERT: C 306 LYS cc_start: 0.5609 (mppt) cc_final: 0.5076 (mmtt) REVERT: D 22 GLN cc_start: 0.3244 (OUTLIER) cc_final: 0.2960 (pt0) REVERT: D 56 VAL cc_start: 0.6275 (OUTLIER) cc_final: 0.6000 (p) REVERT: D 88 THR cc_start: 0.6684 (p) cc_final: 0.6159 (t) REVERT: D 389 ASP cc_start: 0.5181 (OUTLIER) cc_final: 0.4852 (m-30) outliers start: 60 outliers final: 44 residues processed: 243 average time/residue: 0.5278 time to fit residues: 144.6424 Evaluate side-chains 233 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 18 GLN 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 115 THR 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 12 MET Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 38 LYS 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 39 LEU Chi-restraints excluded: chain C residue 44 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 315 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 22 GLN 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 2 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 155 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 chunk 146 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.166163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.141131 restraints weight = 28196.303| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.31 r_work: 0.3495 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16954 Z= 0.151 Angle : 0.630 6.046 23128 Z= 0.326 Chirality : 0.046 0.145 2335 Planarity : 0.006 0.059 3067 Dihedral : 8.433 77.371 2290 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 4.07 % Allowed : 17.68 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.19), residues: 1999 helix: 0.78 (0.20), residues: 692 sheet: 0.33 (0.31), residues: 292 loop : -0.54 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 382 TYR 0.019 0.002 TYR B 236 PHE 0.017 0.002 PHE D 200 TRP 0.014 0.002 TRP B 183 HIS 0.008 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00359 (16950) covalent geometry : angle 0.62977 (23128) hydrogen bonds : bond 0.04867 ( 668) hydrogen bonds : angle 6.13469 ( 1884) Misc. bond : bond 0.06498 ( 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 247 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 179 time to evaluate : 0.671 Fit side-chains REVERT: A 12 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.6829 (mtm) REVERT: A 56 VAL cc_start: 0.6315 (OUTLIER) cc_final: 0.6030 (p) REVERT: A 88 THR cc_start: 0.6592 (p) cc_final: 0.6198 (t) REVERT: A 221 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7823 (tttm) REVERT: B 88 THR cc_start: 0.6531 (p) cc_final: 0.5980 (t) REVERT: B 396 ASP cc_start: 0.5210 (p0) cc_final: 0.4903 (p0) REVERT: C 56 VAL cc_start: 0.6137 (OUTLIER) cc_final: 0.5870 (p) REVERT: C 88 THR cc_start: 0.6522 (p) cc_final: 0.6170 (t) REVERT: C 178 ASP cc_start: 0.5964 (t0) cc_final: 0.5519 (m-30) REVERT: D 22 GLN cc_start: 0.3208 (OUTLIER) cc_final: 0.2938 (pt0) REVERT: D 56 VAL cc_start: 0.6302 (OUTLIER) cc_final: 0.6025 (p) REVERT: D 88 THR cc_start: 0.6588 (p) cc_final: 0.6059 (t) REVERT: D 178 ASP cc_start: 0.5940 (OUTLIER) cc_final: 0.5481 (m-30) REVERT: D 389 ASP cc_start: 0.5203 (OUTLIER) cc_final: 0.4915 (m-30) outliers start: 68 outliers final: 48 residues processed: 235 average time/residue: 0.5294 time to fit residues: 139.9647 Evaluate side-chains 233 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 177 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 18 GLN 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 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 18 GLN 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 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 26 VAL Chi-restraints excluded: chain C residue 39 LEU 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 283 VAL 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 17 GLU Chi-restraints excluded: chain D residue 22 GLN 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 60 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 191 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 9.9990 chunk 48 optimal weight: 0.0470 overall best weight: 2.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.166293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.140379 restraints weight = 33497.682| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.06 r_work: 0.3433 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16954 Z= 0.146 Angle : 0.621 6.017 23128 Z= 0.321 Chirality : 0.046 0.145 2335 Planarity : 0.005 0.058 3067 Dihedral : 8.311 76.982 2290 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.66 % Allowed : 18.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.19), residues: 1999 helix: 0.80 (0.20), residues: 692 sheet: 0.33 (0.31), residues: 292 loop : -0.53 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 382 TYR 0.019 0.002 TYR B 236 PHE 0.016 0.002 PHE D 200 TRP 0.014 0.002 TRP B 183 HIS 0.007 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00348 (16950) covalent geometry : angle 0.62139 (23128) hydrogen bonds : bond 0.04757 ( 668) hydrogen bonds : angle 6.09767 ( 1884) Misc. bond : bond 0.06125 ( 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 239 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 178 time to evaluate : 0.383 Fit side-chains REVERT: A 12 MET cc_start: 0.7505 (OUTLIER) cc_final: 0.6906 (mtm) REVERT: A 56 VAL cc_start: 0.6310 (OUTLIER) cc_final: 0.6028 (p) REVERT: A 88 THR cc_start: 0.6628 (p) cc_final: 0.6221 (t) REVERT: A 221 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7865 (tttm) REVERT: B 88 THR cc_start: 0.6577 (p) cc_final: 0.6035 (t) REVERT: B 396 ASP cc_start: 0.5191 (p0) cc_final: 0.4881 (p0) REVERT: C 56 VAL cc_start: 0.6129 (m) cc_final: 0.5854 (p) REVERT: C 88 THR cc_start: 0.6564 (p) cc_final: 0.6199 (t) REVERT: C 178 ASP cc_start: 0.5992 (t0) cc_final: 0.5554 (m-30) REVERT: C 389 ASP cc_start: 0.3740 (OUTLIER) cc_final: 0.3518 (t70) REVERT: D 22 GLN cc_start: 0.3237 (OUTLIER) cc_final: 0.2933 (pt0) REVERT: D 56 VAL cc_start: 0.6297 (OUTLIER) cc_final: 0.6014 (p) REVERT: D 88 THR cc_start: 0.6614 (p) cc_final: 0.6099 (t) REVERT: D 178 ASP cc_start: 0.6002 (OUTLIER) cc_final: 0.5540 (m-30) REVERT: D 389 ASP cc_start: 0.5404 (OUTLIER) cc_final: 0.5116 (m-30) outliers start: 61 outliers final: 50 residues processed: 227 average time/residue: 0.4690 time to fit residues: 120.0199 Evaluate side-chains 235 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 177 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 18 GLN 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 221 LYS Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 12 MET Chi-restraints excluded: chain B residue 18 GLN 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 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 479 VAL Chi-restraints excluded: chain C residue 12 MET 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 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 283 VAL Chi-restraints excluded: chain C residue 315 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 22 GLN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 145 optimal weight: 6.9990 chunk 47 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 108 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 97 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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** ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.165203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.138499 restraints weight = 30410.694| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.50 r_work: 0.3479 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 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 = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 16954 Z= 0.214 Angle : 0.737 8.126 23128 Z= 0.384 Chirality : 0.050 0.141 2335 Planarity : 0.007 0.060 3067 Dihedral : 9.203 86.784 2290 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.84 % Allowed : 17.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.19), residues: 1999 helix: 0.34 (0.19), residues: 692 sheet: 0.13 (0.31), residues: 298 loop : -0.66 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 382 TYR 0.021 0.003 TYR C 280 PHE 0.023 0.003 PHE D 200 TRP 0.016 0.002 TRP B 183 HIS 0.008 0.002 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00505 (16950) covalent geometry : angle 0.73674 (23128) hydrogen bonds : bond 0.05806 ( 668) hydrogen bonds : angle 6.51667 ( 1884) Misc. bond : bond 0.09922 ( 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 232 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 168 time to evaluate : 0.706 Fit side-chains REVERT: A 12 MET cc_start: 0.7431 (OUTLIER) cc_final: 0.6797 (mtm) REVERT: A 56 VAL cc_start: 0.6286 (OUTLIER) cc_final: 0.6000 (p) REVERT: A 88 THR cc_start: 0.6531 (p) cc_final: 0.6158 (t) REVERT: A 221 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7837 (tttm) REVERT: B 88 THR cc_start: 0.6428 (p) cc_final: 0.5909 (t) REVERT: C 56 VAL cc_start: 0.6253 (OUTLIER) cc_final: 0.5980 (p) REVERT: D 22 GLN cc_start: 0.3218 (OUTLIER) cc_final: 0.2953 (pt0) REVERT: D 88 THR cc_start: 0.6532 (p) cc_final: 0.6022 (t) REVERT: D 389 ASP cc_start: 0.5354 (OUTLIER) cc_final: 0.5058 (m-30) outliers start: 64 outliers final: 48 residues processed: 223 average time/residue: 0.5043 time to fit residues: 126.6952 Evaluate side-chains 220 residues out of total 1711 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 26 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 479 VAL Chi-restraints excluded: chain C residue 12 MET 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 283 VAL 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 17 GLU Chi-restraints excluded: chain D residue 22 GLN 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 156 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 148 optimal weight: 0.0050 chunk 155 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 chunk 121 optimal weight: 9.9990 chunk 132 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- 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** C 40 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.166653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.141581 restraints weight = 27189.149| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 1.33 r_work: 0.3502 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16954 Z= 0.135 Angle : 0.608 5.385 23128 Z= 0.314 Chirality : 0.045 0.147 2335 Planarity : 0.005 0.059 3067 Dihedral : 8.295 79.049 2290 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.14 % Allowed : 18.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.00 (0.19), residues: 1999 helix: 0.75 (0.20), residues: 692 sheet: 0.26 (0.31), residues: 295 loop : -0.55 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 382 TYR 0.018 0.002 TYR B 236 PHE 0.016 0.002 PHE A 279 TRP 0.014 0.001 TRP B 183 HIS 0.007 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00322 (16950) covalent geometry : angle 0.60755 (23128) hydrogen bonds : bond 0.04609 ( 668) hydrogen bonds : angle 6.08391 ( 1884) Misc. bond : bond 0.04652 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6040.39 seconds wall clock time: 103 minutes 25.64 seconds (6205.64 seconds total)