Starting phenix.real_space_refine on Fri Sep 27 16:01:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/09_2024/7vd9_31911.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/09_2024/7vd9_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/09_2024/7vd9_31911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/09_2024/7vd9_31911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/09_2024/7vd9_31911.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vd9_31911/09_2024/7vd9_31911.cif" } resolution = 2.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 12 5.49 5 S 52 5.16 5 C 10421 2.51 5 N 2895 2.21 5 O 3042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16426 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "B" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "C" Number of atoms: 4017 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} Conformer: "B" Number of residues, atoms: 498, 4007 Classifications: {'peptide': 498} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 461} bond proxies already assigned to first conformer: 4115 Chain: "D" Number of atoms: 4011 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} Conformer: "B" Number of residues, atoms: 497, 4001 Classifications: {'peptide': 497} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 460} bond proxies already assigned to first conformer: 4109 Chain: "A" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'HEM': 1, 'NDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N ASER A 120 " occ=0.63 ... (10 atoms not shown) pdb=" OG BSER A 120 " occ=0.37 residue: pdb=" N AGLY A 121 " occ=0.63 ... (6 atoms not shown) pdb=" O BGLY A 121 " occ=0.37 residue: pdb=" N ASER B 120 " occ=0.82 ... (10 atoms not shown) pdb=" OG BSER B 120 " occ=0.18 residue: pdb=" N AGLY B 121 " occ=0.82 ... (6 atoms not shown) pdb=" O BGLY B 121 " occ=0.18 residue: pdb=" N ASER C 120 " occ=0.64 ... (10 atoms not shown) pdb=" OG BSER C 120 " occ=0.36 residue: pdb=" N AGLY C 121 " occ=0.64 ... (6 atoms not shown) pdb=" O BGLY C 121 " occ=0.36 residue: pdb=" N ASER D 120 " occ=0.89 ... (10 atoms not shown) pdb=" OG BSER D 120 " occ=0.11 residue: pdb=" N AGLY D 121 " occ=0.89 ... (6 atoms not shown) pdb=" O BGLY D 121 " occ=0.11 Time building chain proxies: 17.13, per 1000 atoms: 1.04 Number of scatterers: 16426 At special positions: 0 Unit cell: (113.1, 109.2, 83.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 52 16.00 P 12 15.00 O 3042 8.00 N 2895 7.00 C 10421 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 4.0 seconds 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3726 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 40.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 6.744A pdb=" N MET A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N GLN A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 65 Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 157 through 159 No H-bonds generated for 'chain 'A' and resid 157 through 159' Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 192 through 201 Processing helix chain 'A' and resid 202 through 205 removed outlier: 3.740A pdb=" N ILE A 205 " --> pdb=" O ASP A 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 208 through 212 removed outlier: 3.500A pdb=" N HIS A 211 " --> pdb=" O GLY A 208 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N MET A 212 " --> pdb=" O HIS A 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 212' Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 259 through 271 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 348 through 367 removed outlier: 3.728A pdb=" N PHE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Proline residue: A 359 - end of helix Processing helix chain 'A' and resid 369 through 373 Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 440 through 450 Processing helix chain 'A' and resid 452 through 468 Processing helix chain 'A' and resid 471 through 486 Processing helix chain 'A' and resid 486 through 501 Processing helix chain 'B' and resid 10 through 19 Processing helix chain 'B' and resid 54 through 65 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.519A pdb=" N GLU B 101 " --> pdb=" O LYS B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 159 No H-bonds generated for 'chain 'B' and resid 157 through 159' Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 192 through 201 Processing helix chain 'B' and resid 202 through 205 removed outlier: 3.896A pdb=" N ILE B 205 " --> pdb=" O ASP B 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.526A pdb=" N HIS B 211 " --> pdb=" O GLY B 208 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N MET B 212 " --> pdb=" O HIS B 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 212' Processing helix chain 'B' and resid 246 through 257 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 285 through 291 Processing helix chain 'B' and resid 324 through 329 Processing helix chain 'B' and resid 348 through 367 removed outlier: 3.755A pdb=" N PHE B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR B 358 " --> pdb=" O ARG B 354 " (cutoff:3.500A) Proline residue: B 359 - end of helix Processing helix chain 'B' and resid 369 through 373 Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 452 through 468 Processing helix chain 'B' and resid 471 through 486 Processing helix chain 'B' and resid 486 through 501 Processing helix chain 'C' and resid 10 through 19 Processing helix chain 'C' and resid 54 through 65 Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'C' and resid 160 through 169 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 192 through 201 Processing helix chain 'C' and resid 202 through 205 removed outlier: 3.721A pdb=" N ILE C 205 " --> pdb=" O ASP C 202 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 208 through 212 removed outlier: 4.054A pdb=" N MET C 212 " --> pdb=" O HIS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 259 through 271 Processing helix chain 'C' and resid 285 through 291 Processing helix chain 'C' and resid 324 through 329 Processing helix chain 'C' and resid 348 through 366 removed outlier: 3.709A pdb=" N PHE C 356 " --> pdb=" O GLN C 352 " (cutoff:3.500A) Proline residue: C 359 - end of helix Processing helix chain 'C' and resid 369 through 373 Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 440 through 450 Processing helix chain 'C' and resid 452 through 468 Processing helix chain 'C' and resid 471 through 486 Processing helix chain 'C' and resid 486 through 501 Processing helix chain 'D' and resid 10 through 20 removed outlier: 3.620A pdb=" N ARG D 19 " --> pdb=" O TRP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 65 Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.548A pdb=" N GLU D 101 " --> pdb=" O LYS D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 160 through 169 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 192 through 200 Processing helix chain 'D' and resid 201 through 205 removed outlier: 3.712A pdb=" N ILE D 205 " --> pdb=" O ASP D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 removed outlier: 4.082A pdb=" N MET D 212 " --> pdb=" O HIS D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 257 Processing helix chain 'D' and resid 259 through 271 Processing helix chain 'D' and resid 285 through 292 Processing helix chain 'D' and resid 324 through 329 Processing helix chain 'D' and resid 348 through 366 removed outlier: 3.717A pdb=" N PHE D 356 " --> pdb=" O GLN D 352 " (cutoff:3.500A) Proline residue: D 359 - end of helix Processing helix chain 'D' and resid 369 through 373 Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 452 through 468 Processing helix chain 'D' and resid 471 through 486 Processing helix chain 'D' and resid 486 through 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 removed outlier: 4.170A pdb=" N GLY C 427 " --> pdb=" O TYR D 425 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 425 " --> pdb=" O GLY C 427 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 429 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE D 423 " --> pdb=" O VAL C 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 343 through 344 removed outlier: 6.009A pdb=" N ILE A 281 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LEU A 316 " --> pdb=" O GLU A 86 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N GLU A 86 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N LEU A 318 " --> pdb=" O TYR A 84 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N TYR A 84 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 423 through 425 removed outlier: 4.327A pdb=" N ILE A 423 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 429 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N GLY B 427 " --> pdb=" O TYR A 425 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 423 through 424 removed outlier: 4.312A pdb=" N ILE B 423 " --> pdb=" O VAL A 429 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 42 through 44 removed outlier: 4.357A pdb=" N ILE C 423 " --> pdb=" O VAL D 429 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 343 through 344 removed outlier: 6.059A pdb=" N ILE B 281 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU B 316 " --> pdb=" O GLU B 86 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLU B 86 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 318 " --> pdb=" O TYR B 84 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N TYR B 84 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 343 through 344 removed outlier: 6.402A pdb=" N TRP C 277 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS C 315 " --> pdb=" O TRP C 277 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N PHE C 279 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU C 316 " --> pdb=" O GLU C 86 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLU C 86 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 318 " --> pdb=" O TYR C 84 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR C 84 " --> pdb=" O LEU C 318 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 343 through 345 removed outlier: 5.999A pdb=" N ILE D 281 " --> pdb=" O PRO D 312 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU D 316 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N GLU D 86 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N LEU D 318 " --> pdb=" O TYR D 84 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TYR D 84 " --> pdb=" O LEU D 318 " (cutoff:3.500A) 668 hydrogen bonds defined for protein. 1884 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.54 Time building geometry restraints manager: 4.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.39: 7276 1.39 - 1.56: 9542 1.56 - 1.73: 20 1.73 - 1.89: 96 1.89 - 2.06: 16 Bond restraints: 16950 Sorted by residual: bond pdb=" CG PRO D 406 " pdb=" CD PRO D 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.91e-01 bond pdb=" CG PRO C 406 " pdb=" CD PRO C 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.84e-01 bond pdb=" CG PRO B 406 " pdb=" CD PRO B 406 " ideal model delta sigma weight residual 1.512 1.487 0.025 2.70e-02 1.37e+03 8.69e-01 bond pdb=" CB GLU D 290 " pdb=" CG GLU D 290 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.57e-01 bond pdb=" CB GLN B 195 " pdb=" CG GLN B 195 " ideal model delta sigma weight residual 1.520 1.543 -0.023 3.00e-02 1.11e+03 6.06e-01 ... (remaining 16945 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 22828 2.08 - 4.16: 262 4.16 - 6.24: 37 6.24 - 8.32: 0 8.32 - 10.40: 1 Bond angle restraints: 23128 Sorted by residual: angle pdb=" C ARG D 388 " pdb=" N ASP D 389 " pdb=" CA ASP D 389 " ideal model delta sigma weight residual 121.31 126.88 -5.57 1.49e+00 4.50e-01 1.40e+01 angle pdb=" C ARG B 388 " pdb=" N ASP B 389 " pdb=" CA ASP B 389 " ideal model delta sigma weight residual 121.31 126.77 -5.46 1.49e+00 4.50e-01 1.34e+01 angle pdb=" CB MET D 394 " pdb=" CG MET D 394 " pdb=" SD MET D 394 " ideal model delta sigma weight residual 112.70 123.10 -10.40 3.00e+00 1.11e-01 1.20e+01 angle pdb=" C ARG A 388 " pdb=" N ASP A 389 " pdb=" CA ASP A 389 " ideal model delta sigma weight residual 121.54 127.19 -5.65 1.91e+00 2.74e-01 8.74e+00 angle pdb=" N ASP D 389 " pdb=" CA ASP D 389 " pdb=" C ASP D 389 " ideal model delta sigma weight residual 110.35 114.40 -4.05 1.40e+00 5.10e-01 8.39e+00 ... (remaining 23123 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8631 17.69 - 35.38: 876 35.38 - 53.07: 273 53.07 - 70.76: 80 70.76 - 88.45: 36 Dihedral angle restraints: 9896 sinusoidal: 4087 harmonic: 5809 Sorted by residual: dihedral pdb=" CA CYS D 393 " pdb=" C CYS D 393 " pdb=" N MET D 394 " pdb=" CA MET D 394 " ideal model delta harmonic sigma weight residual -180.00 -154.75 -25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA ASP D 180 " pdb=" CB ASP D 180 " pdb=" CG ASP D 180 " pdb=" OD1 ASP D 180 " ideal model delta sinusoidal sigma weight residual -30.00 -88.06 58.06 1 2.00e+01 2.50e-03 1.13e+01 dihedral pdb=" CA ASP A 180 " pdb=" CB ASP A 180 " pdb=" CG ASP A 180 " pdb=" OD1 ASP A 180 " ideal model delta sinusoidal sigma weight residual -30.00 -87.20 57.20 1 2.00e+01 2.50e-03 1.10e+01 ... (remaining 9893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1331 0.029 - 0.059: 650 0.059 - 0.088: 208 0.088 - 0.118: 127 0.118 - 0.147: 19 Chirality restraints: 2335 Sorted by residual: chirality pdb=" CA ILE B 373 " pdb=" N ILE B 373 " pdb=" C ILE B 373 " pdb=" CB ILE B 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA ILE C 373 " pdb=" N ILE C 373 " pdb=" C ILE C 373 " pdb=" CB ILE C 373 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA TYR C 358 " pdb=" N TYR C 358 " pdb=" C TYR C 358 " pdb=" CB TYR C 358 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2332 not shown) Planarity restraints: 3067 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 6 " -0.041 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO C 7 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 7 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 7 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 346 " 0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO C 347 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 347 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO C 347 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 346 " -0.031 5.00e-02 4.00e+02 4.70e-02 3.53e+00 pdb=" N PRO D 347 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 347 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 347 " -0.026 5.00e-02 4.00e+02 ... (remaining 3064 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1006 2.74 - 3.28: 16113 3.28 - 3.82: 29648 3.82 - 4.36: 36594 4.36 - 4.90: 60754 Nonbonded interactions: 144115 Sorted by model distance: nonbonded pdb=" NE2 GLN A 415 " pdb=" OG SER A 417 " model vdw 2.194 3.120 nonbonded pdb=" OE1 GLN D 415 " pdb=" OG SER D 417 " model vdw 2.224 3.040 nonbonded pdb=" NZ LYS B 301 " pdb=" O ASP B 438 " model vdw 2.226 3.120 nonbonded pdb=" OD2 ASP A 360 " pdb=" NH1 ARG C 66 " model vdw 2.231 3.120 nonbonded pdb=" NZ LYS D 301 " pdb=" O ASP D 438 " model vdw 2.232 3.120 ... (remaining 144110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) selection = (chain 'B' and (resid 5 through 119 or resid 122 through 501 or resid 1201 throu \ gh 1202)) selection = (chain 'C' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) selection = (chain 'D' and (resid 5 through 119 or resid 122 through 501 or resid 601 throug \ h 602)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.11 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 46.880 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.050 ------------------------------------------------------------------------------- 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 16950 Z= 0.158 Angle : 0.543 10.399 23128 Z= 0.272 Chirality : 0.042 0.147 2335 Planarity : 0.005 0.063 3067 Dihedral : 17.252 88.450 6170 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.33 % Allowed : 18.62 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.19), residues: 1999 helix: 1.21 (0.20), residues: 698 sheet: 0.61 (0.33), residues: 283 loop : -0.45 (0.20), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.015 0.001 PHE D 409 TYR 0.012 0.001 TYR D 236 ARG 0.002 0.000 ARG B 19 *********************** 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 fitting. rotamer outliers: 38 poor density : 195 time to evaluate : 1.791 Fit side-chains REVERT: A 56 VAL cc_start: 0.5998 (m) cc_final: 0.5692 (p) REVERT: A 88 THR cc_start: 0.6685 (p) cc_final: 0.6219 (t) REVERT: A 93 LYS cc_start: 0.6270 (OUTLIER) cc_final: 0.6060 (mtmm) REVERT: B 88 THR cc_start: 0.6459 (p) cc_final: 0.5977 (t) REVERT: B 396 ASP cc_start: 0.4877 (p0) cc_final: 0.4614 (p0) REVERT: B 455 GLN cc_start: 0.6161 (mt0) cc_final: 0.5922 (mt0) REVERT: C 43 THR cc_start: 0.6639 (p) cc_final: 0.6249 (t) REVERT: C 178 ASP cc_start: 0.5934 (t0) cc_final: 0.5711 (m-30) REVERT: C 306 LYS cc_start: 0.5656 (mppt) cc_final: 0.5157 (mmtt) REVERT: C 488 ASP cc_start: 0.5925 (m-30) cc_final: 0.5691 (t0) REVERT: D 88 THR cc_start: 0.6537 (p) cc_final: 0.6064 (t) outliers start: 38 outliers final: 35 residues processed: 231 average time/residue: 1.1893 time to fit residues: 308.4847 Evaluate side-chains 216 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 180 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 361 THR Chi-restraints excluded: chain D residue 413 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN ** D 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 492 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 16950 Z= 0.383 Angle : 0.795 8.944 23128 Z= 0.417 Chirality : 0.052 0.152 2335 Planarity : 0.007 0.082 3067 Dihedral : 10.238 94.069 2322 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 4.65 % Allowed : 17.10 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 1999 helix: 0.25 (0.19), residues: 696 sheet: 0.30 (0.31), residues: 294 loop : -0.68 (0.20), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 183 HIS 0.012 0.002 HIS A 102 PHE 0.026 0.003 PHE D 200 TYR 0.021 0.003 TYR C 280 ARG 0.012 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3998 Ramachandran restraints generated. 1999 Oldfield, 0 Emsley, 1999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 173 time to evaluate : 1.983 Fit side-chains REVERT: A 12 MET cc_start: 0.7313 (OUTLIER) cc_final: 0.6681 (mtm) REVERT: B 88 THR cc_start: 0.6421 (p) cc_final: 0.5917 (t) REVERT: B 396 ASP cc_start: 0.5232 (p0) cc_final: 0.4877 (p0) REVERT: C 56 VAL cc_start: 0.6331 (OUTLIER) cc_final: 0.6070 (p) REVERT: C 306 LYS cc_start: 0.5601 (OUTLIER) cc_final: 0.5355 (mppt) REVERT: D 88 THR cc_start: 0.6572 (p) cc_final: 0.6105 (t) outliers start: 78 outliers final: 46 residues processed: 238 average time/residue: 1.1442 time to fit residues: 307.7873 Evaluate side-chains 216 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 167 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 115 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 306 LYS Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 148 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 413 GLU Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 0.0970 chunk 121 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 178 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 176 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 143 optimal weight: 5.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN C 40 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN D 305 HIS D 415 GLN D 433 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 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 : 0.004 0.046 16950 Z= 0.233 Angle : 0.635 5.768 23128 Z= 0.330 Chirality : 0.046 0.148 2335 Planarity : 0.006 0.063 3067 Dihedral : 9.037 84.984 2315 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.32 % Allowed : 18.56 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 1999 helix: 0.62 (0.20), residues: 692 sheet: 0.33 (0.31), residues: 294 loop : -0.57 (0.20), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 183 HIS 0.008 0.001 HIS A 102 PHE 0.015 0.002 PHE D 200 TYR 0.018 0.002 TYR B 236 ARG 0.005 0.001 ARG A 382 *********************** 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 241 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 186 time to evaluate : 2.028 Fit side-chains REVERT: A 12 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6668 (mtm) REVERT: A 56 VAL cc_start: 0.6294 (OUTLIER) cc_final: 0.6017 (p) REVERT: A 88 THR cc_start: 0.6574 (p) cc_final: 0.6202 (t) REVERT: B 88 THR cc_start: 0.6433 (p) cc_final: 0.5922 (t) REVERT: B 396 ASP cc_start: 0.5016 (p0) cc_final: 0.4795 (p0) REVERT: C 5 ARG cc_start: 0.3044 (OUTLIER) cc_final: 0.2741 (mtm180) REVERT: C 56 VAL cc_start: 0.6151 (OUTLIER) cc_final: 0.5896 (p) REVERT: C 178 ASP cc_start: 0.5943 (OUTLIER) cc_final: 0.5448 (m-30) REVERT: D 56 VAL cc_start: 0.6349 (OUTLIER) cc_final: 0.6098 (p) REVERT: D 88 THR cc_start: 0.6603 (p) cc_final: 0.6112 (t) outliers start: 55 outliers final: 27 residues processed: 229 average time/residue: 1.2538 time to fit residues: 321.9474 Evaluate side-chains 206 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.804 ------------------------------------------------------------------------------- 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 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 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 178 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain 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 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 323 VAL Chi-restraints excluded: chain D residue 468 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 119 optimal weight: 20.0000 chunk 178 optimal weight: 0.0030 chunk 189 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 169 optimal weight: 2.9990 chunk 51 optimal weight: 0.0770 overall best weight: 1.8152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS B 433 ASN ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 ASN C 466 HIS D 415 GLN D 433 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16950 Z= 0.203 Angle : 0.595 5.461 23128 Z= 0.307 Chirality : 0.045 0.145 2335 Planarity : 0.005 0.060 3067 Dihedral : 8.273 77.460 2296 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.85 % Allowed : 18.85 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.19), residues: 1999 helix: 0.87 (0.20), residues: 692 sheet: 0.35 (0.31), residues: 292 loop : -0.49 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 183 HIS 0.007 0.001 HIS A 102 PHE 0.014 0.002 PHE D 279 TYR 0.018 0.002 TYR B 236 ARG 0.004 0.000 ARG A 382 *********************** 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 238 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 191 time to evaluate : 2.149 Fit side-chains REVERT: A 12 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6744 (mtm) REVERT: A 56 VAL cc_start: 0.6182 (m) cc_final: 0.5916 (p) REVERT: A 88 THR cc_start: 0.6568 (p) cc_final: 0.6188 (t) REVERT: A 178 ASP cc_start: 0.6004 (OUTLIER) cc_final: 0.5521 (m-30) REVERT: A 221 LYS cc_start: 0.8089 (OUTLIER) cc_final: 0.7692 (tttm) REVERT: B 88 THR cc_start: 0.6463 (p) cc_final: 0.5941 (t) REVERT: B 396 ASP cc_start: 0.5016 (p0) cc_final: 0.4808 (p0) REVERT: B 454 GLU cc_start: 0.5378 (pp20) cc_final: 0.5051 (pp20) REVERT: C 56 VAL cc_start: 0.5977 (m) cc_final: 0.5728 (p) REVERT: C 88 THR cc_start: 0.6408 (p) cc_final: 0.6056 (t) REVERT: D 56 VAL cc_start: 0.6256 (m) cc_final: 0.6014 (p) REVERT: D 88 THR cc_start: 0.6579 (p) cc_final: 0.6093 (t) REVERT: D 178 ASP cc_start: 0.6011 (OUTLIER) cc_final: 0.5534 (m-30) REVERT: D 396 ASP cc_start: 0.5646 (OUTLIER) cc_final: 0.5381 (t70) outliers start: 47 outliers final: 28 residues processed: 231 average time/residue: 1.2133 time to fit residues: 314.6266 Evaluate side-chains 213 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 180 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 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 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 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 422 SER Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 178 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 396 ASP Chi-restraints excluded: chain D residue 468 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 20.0000 chunk 78 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16950 Z= 0.237 Angle : 0.631 6.042 23128 Z= 0.327 Chirality : 0.046 0.145 2335 Planarity : 0.006 0.060 3067 Dihedral : 8.572 79.927 2291 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.61 % Allowed : 18.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.19), residues: 1999 helix: 0.75 (0.20), residues: 692 sheet: 0.26 (0.31), residues: 296 loop : -0.54 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 183 HIS 0.008 0.001 HIS A 102 PHE 0.016 0.002 PHE D 200 TYR 0.018 0.002 TYR B 236 ARG 0.005 0.001 ARG A 382 *********************** 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 243 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 183 time to evaluate : 2.034 Fit side-chains REVERT: A 12 MET cc_start: 0.7368 (OUTLIER) cc_final: 0.6768 (mtm) REVERT: A 56 VAL cc_start: 0.6305 (OUTLIER) cc_final: 0.6029 (p) REVERT: A 88 THR cc_start: 0.6492 (p) cc_final: 0.6121 (t) REVERT: A 178 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5502 (m-30) REVERT: A 221 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7766 (tttm) REVERT: B 38 LYS cc_start: 0.6040 (OUTLIER) cc_final: 0.5798 (tttp) REVERT: B 88 THR cc_start: 0.6426 (p) cc_final: 0.5903 (t) REVERT: B 396 ASP cc_start: 0.5049 (p0) cc_final: 0.4806 (p0) REVERT: C 56 VAL cc_start: 0.6121 (m) cc_final: 0.5877 (p) REVERT: C 88 THR cc_start: 0.6417 (p) cc_final: 0.6087 (t) REVERT: D 56 VAL cc_start: 0.6315 (OUTLIER) cc_final: 0.6071 (p) REVERT: D 88 THR cc_start: 0.6574 (p) cc_final: 0.6084 (t) REVERT: D 178 ASP cc_start: 0.5952 (OUTLIER) cc_final: 0.5477 (m-30) REVERT: D 389 ASP cc_start: 0.4839 (OUTLIER) cc_final: 0.4551 (m-30) REVERT: D 396 ASP cc_start: 0.5665 (OUTLIER) cc_final: 0.5453 (t0) outliers start: 60 outliers final: 34 residues processed: 232 average time/residue: 1.2048 time to fit residues: 315.4446 Evaluate side-chains 223 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 180 time to evaluate : 1.869 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 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 38 LYS Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 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 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 178 ASP Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 255 GLN Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 389 ASP Chi-restraints excluded: chain D residue 396 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 37 optimal weight: 0.0010 chunk 111 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** C 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS D 63 HIS D 102 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16950 Z= 0.219 Angle : 0.609 5.476 23128 Z= 0.314 Chirality : 0.045 0.145 2335 Planarity : 0.005 0.059 3067 Dihedral : 8.269 76.814 2290 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.43 % Allowed : 18.27 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.19), residues: 1999 helix: 0.84 (0.20), residues: 692 sheet: 0.30 (0.31), residues: 295 loop : -0.52 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 183 HIS 0.007 0.001 HIS A 102 PHE 0.015 0.002 PHE A 279 TYR 0.018 0.002 TYR B 236 ARG 0.005 0.001 ARG A 382 *********************** 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 244 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 187 time to evaluate : 1.796 Fit side-chains REVERT: A 12 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.6754 (mtm) REVERT: A 56 VAL cc_start: 0.6236 (m) cc_final: 0.5968 (p) REVERT: A 88 THR cc_start: 0.6491 (p) cc_final: 0.6118 (t) REVERT: A 178 ASP cc_start: 0.6008 (OUTLIER) cc_final: 0.5518 (m-30) REVERT: A 221 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7759 (tttm) REVERT: B 38 LYS cc_start: 0.6062 (OUTLIER) cc_final: 0.5826 (tttp) REVERT: B 88 THR cc_start: 0.6396 (p) cc_final: 0.5882 (t) REVERT: B 396 ASP cc_start: 0.5047 (p0) cc_final: 0.4812 (p0) REVERT: B 454 GLU cc_start: 0.5393 (pp20) cc_final: 0.5051 (pp20) REVERT: C 56 VAL cc_start: 0.6079 (OUTLIER) cc_final: 0.5831 (p) REVERT: C 88 THR cc_start: 0.6422 (p) cc_final: 0.6094 (t) REVERT: D 38 LYS cc_start: 0.6063 (OUTLIER) cc_final: 0.5801 (tttp) REVERT: D 56 VAL cc_start: 0.6270 (OUTLIER) cc_final: 0.6028 (p) REVERT: D 88 THR cc_start: 0.6559 (p) cc_final: 0.6069 (t) REVERT: D 389 ASP cc_start: 0.4801 (OUTLIER) cc_final: 0.4512 (m-30) outliers start: 57 outliers final: 35 residues processed: 232 average time/residue: 1.1983 time to fit residues: 311.4358 Evaluate side-chains 225 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 1.670 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain A residue 44 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 38 LYS 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 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 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 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 38 LYS 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 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 255 GLN 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 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 182 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 159 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 188 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS ** C 338 ASN ** 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** D 466 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16950 Z= 0.250 Angle : 0.645 6.378 23128 Z= 0.334 Chirality : 0.047 0.145 2335 Planarity : 0.006 0.059 3067 Dihedral : 8.628 81.080 2290 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.61 % Allowed : 18.03 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.19), residues: 1999 helix: 0.69 (0.20), residues: 692 sheet: 0.26 (0.31), residues: 295 loop : -0.57 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 183 HIS 0.008 0.001 HIS A 102 PHE 0.017 0.002 PHE D 200 TYR 0.019 0.002 TYR B 236 ARG 0.006 0.001 ARG A 382 *********************** 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 242 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 182 time to evaluate : 2.342 Fit side-chains REVERT: A 12 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6715 (mtm) REVERT: A 56 VAL cc_start: 0.6289 (OUTLIER) cc_final: 0.6014 (p) REVERT: A 88 THR cc_start: 0.6465 (p) cc_final: 0.6100 (t) REVERT: A 178 ASP cc_start: 0.5977 (OUTLIER) cc_final: 0.5490 (m-30) REVERT: A 221 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7761 (tttm) REVERT: B 88 THR cc_start: 0.6396 (p) cc_final: 0.5889 (t) REVERT: B 396 ASP cc_start: 0.5061 (p0) cc_final: 0.4777 (p0) REVERT: B 454 GLU cc_start: 0.5383 (pp20) cc_final: 0.5055 (pp20) REVERT: C 56 VAL cc_start: 0.6158 (OUTLIER) cc_final: 0.5912 (p) REVERT: C 88 THR cc_start: 0.6431 (p) cc_final: 0.6108 (t) REVERT: D 38 LYS cc_start: 0.6049 (OUTLIER) cc_final: 0.5789 (tttp) REVERT: D 56 VAL cc_start: 0.6324 (OUTLIER) cc_final: 0.6082 (p) REVERT: D 88 THR cc_start: 0.6538 (p) cc_final: 0.6047 (t) REVERT: D 389 ASP cc_start: 0.4822 (OUTLIER) cc_final: 0.4533 (m-30) outliers start: 60 outliers final: 36 residues processed: 228 average time/residue: 1.2079 time to fit residues: 308.7482 Evaluate side-chains 224 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 180 time to evaluate : 1.942 ------------------------------------------------------------------------------- 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 41 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 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 99 VAL Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 323 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 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 38 LYS 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 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 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 116 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 37 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 120 optimal weight: 0.1980 chunk 128 optimal weight: 0.0670 chunk 93 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 148 optimal weight: 10.0000 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 492 HIS C 338 ASN D 397 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16950 Z= 0.163 Angle : 0.546 5.897 23128 Z= 0.277 Chirality : 0.044 0.147 2335 Planarity : 0.005 0.058 3067 Dihedral : 7.188 60.877 2290 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.75 % Allowed : 20.19 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.19), residues: 1999 helix: 1.17 (0.20), residues: 692 sheet: 0.50 (0.32), residues: 293 loop : -0.42 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.013 0.001 PHE C 409 TYR 0.018 0.001 TYR B 236 ARG 0.003 0.000 ARG B 19 *********************** 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 246 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 218 time to evaluate : 2.037 Fit side-chains REVERT: A 12 MET cc_start: 0.7333 (OUTLIER) cc_final: 0.6746 (mtm) REVERT: A 56 VAL cc_start: 0.5980 (m) cc_final: 0.5683 (p) REVERT: A 88 THR cc_start: 0.6497 (p) cc_final: 0.6074 (t) REVERT: A 178 ASP cc_start: 0.6046 (OUTLIER) cc_final: 0.5629 (m-30) REVERT: A 221 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7696 (tttm) REVERT: A 456 ARG cc_start: 0.6231 (mtt180) cc_final: 0.5981 (mtt180) REVERT: B 88 THR cc_start: 0.6467 (p) cc_final: 0.5949 (t) REVERT: B 455 GLN cc_start: 0.6281 (mt0) cc_final: 0.5983 (mt0) REVERT: C 56 VAL cc_start: 0.5852 (m) cc_final: 0.5587 (p) REVERT: C 61 MET cc_start: 0.6811 (tpp) cc_final: 0.6486 (tpp) REVERT: C 88 THR cc_start: 0.6457 (p) cc_final: 0.6080 (t) REVERT: C 178 ASP cc_start: 0.6080 (t0) cc_final: 0.5722 (m-30) REVERT: C 306 LYS cc_start: 0.5618 (mppt) cc_final: 0.5077 (mmtt) REVERT: C 339 MET cc_start: 0.7154 (mtm) cc_final: 0.6832 (mtm) REVERT: D 56 VAL cc_start: 0.6175 (m) cc_final: 0.5930 (p) REVERT: D 88 THR cc_start: 0.6520 (p) cc_final: 0.6013 (t) outliers start: 28 outliers final: 18 residues processed: 241 average time/residue: 1.2550 time to fit residues: 338.1690 Evaluate side-chains 210 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 189 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 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 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 17 GLU 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 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 468 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 10.0000 chunk 180 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 176 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 76 optimal weight: 0.8980 chunk 138 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 166 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 421 HIS ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS A 492 HIS B 492 HIS ** C 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 HIS D 397 ASN D 421 HIS ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 466 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16950 Z= 0.307 Angle : 0.708 7.670 23128 Z= 0.368 Chirality : 0.049 0.141 2335 Planarity : 0.006 0.060 3067 Dihedral : 9.153 86.770 2290 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.21 % Allowed : 19.66 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.19), residues: 1999 helix: 0.58 (0.20), residues: 692 sheet: 0.24 (0.31), residues: 297 loop : -0.57 (0.20), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 183 HIS 0.008 0.002 HIS A 102 PHE 0.022 0.003 PHE B 279 TYR 0.019 0.002 TYR C 280 ARG 0.008 0.001 ARG A 382 *********************** 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 202 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 2.057 Fit side-chains REVERT: A 12 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6717 (mtm) REVERT: A 88 THR cc_start: 0.6420 (p) cc_final: 0.6069 (t) REVERT: A 178 ASP cc_start: 0.5998 (OUTLIER) cc_final: 0.5483 (m-30) REVERT: A 221 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7788 (tttm) REVERT: B 88 THR cc_start: 0.6400 (p) cc_final: 0.5896 (t) REVERT: C 339 MET cc_start: 0.7141 (mtm) cc_final: 0.6850 (mtm) REVERT: D 88 THR cc_start: 0.6458 (p) cc_final: 0.5983 (t) outliers start: 36 outliers final: 25 residues processed: 195 average time/residue: 1.2362 time to fit residues: 270.1210 Evaluate side-chains 193 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 165 time to evaluate : 1.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 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 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 103 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain D residue 17 GLU Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 50 LEU Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 236 TYR Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 468 LYS Chi-restraints excluded: chain D residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 10.0000 chunk 186 optimal weight: 0.0980 chunk 113 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 129 optimal weight: 9.9990 chunk 195 optimal weight: 8.9990 chunk 179 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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** A 492 HIS B 492 HIS D 397 ASN ** D 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16950 Z= 0.178 Angle : 0.571 5.791 23128 Z= 0.293 Chirality : 0.044 0.148 2335 Planarity : 0.005 0.058 3067 Dihedral : 7.709 70.632 2290 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.51 % Allowed : 20.30 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 1999 helix: 1.03 (0.20), residues: 692 sheet: 0.35 (0.31), residues: 296 loop : -0.44 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 183 HIS 0.007 0.001 HIS A 102 PHE 0.014 0.001 PHE B 279 TYR 0.018 0.001 TYR B 236 ARG 0.003 0.000 ARG B 252 ********************** 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 210 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 186 time to evaluate : 1.874 Fit side-chains REVERT: A 12 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6686 (mtm) REVERT: A 39 LEU cc_start: 0.6448 (mt) cc_final: 0.6228 (mm) REVERT: A 56 VAL cc_start: 0.6150 (m) cc_final: 0.5864 (p) REVERT: A 88 THR cc_start: 0.6491 (p) cc_final: 0.6081 (t) REVERT: A 221 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7726 (tttm) REVERT: A 252 ARG cc_start: 0.5126 (tmm160) cc_final: 0.4902 (tmm160) REVERT: B 88 THR cc_start: 0.6430 (p) cc_final: 0.5903 (t) REVERT: B 455 GLN cc_start: 0.6352 (mt0) cc_final: 0.6048 (mt0) REVERT: C 56 VAL cc_start: 0.5955 (m) cc_final: 0.5686 (p) REVERT: C 88 THR cc_start: 0.6411 (p) cc_final: 0.6056 (t) REVERT: C 178 ASP cc_start: 0.6015 (t0) cc_final: 0.5662 (m-30) REVERT: C 339 MET cc_start: 0.7131 (mtm) cc_final: 0.6832 (mtm) REVERT: D 56 VAL cc_start: 0.6245 (m) cc_final: 0.6000 (p) REVERT: D 88 THR cc_start: 0.6489 (p) cc_final: 0.5995 (t) outliers start: 24 outliers final: 18 residues processed: 208 average time/residue: 1.2241 time to fit residues: 285.0100 Evaluate side-chains 199 residues out of total 1711 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 MET Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 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 99 VAL Chi-restraints excluded: chain B residue 219 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain D residue 17 GLU 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 219 THR Chi-restraints excluded: chain D residue 236 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 0.0570 chunk 165 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 22 optimal weight: 0.0010 chunk 43 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 159 optimal weight: 9.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 overall best weight: 0.7506 ------------------------------------------------------------------------------- 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** A 492 HIS B 492 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 = 0.3972 r_free = 0.3972 target = 0.169186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.144299 restraints weight = 25882.599| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.47 r_work: 0.3536 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3411 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3411 r_free = 0.3411 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3411 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 moved from start: 0.1179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16950 Z= 0.164 Angle : 0.547 6.210 23128 Z= 0.277 Chirality : 0.043 0.147 2335 Planarity : 0.005 0.048 3067 Dihedral : 7.084 60.843 2290 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.34 % Allowed : 20.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.19), residues: 1999 helix: 1.26 (0.20), residues: 692 sheet: 0.41 (0.31), residues: 295 loop : -0.40 (0.20), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 183 HIS 0.006 0.001 HIS A 102 PHE 0.015 0.001 PHE B 279 TYR 0.017 0.001 TYR D 236 ARG 0.002 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5859.07 seconds wall clock time: 103 minutes 49.06 seconds (6229.06 seconds total)