Starting phenix.real_space_refine on Thu Mar 13 14:14:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvw_52444/03_2025/9hvw_52444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvw_52444/03_2025/9hvw_52444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hvw_52444/03_2025/9hvw_52444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvw_52444/03_2025/9hvw_52444.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvw_52444/03_2025/9hvw_52444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvw_52444/03_2025/9hvw_52444.cif" } resolution = 3.1 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= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5639 2.51 5 N 1473 2.21 5 O 1774 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 465 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain breaks: 1 Chain: "B" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 465 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain breaks: 1 Chain: "C" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 465 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain breaks: 1 Chain: "D" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1916 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 237} Chain breaks: 1 Chain: "E" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1959 Classifications: {'peptide': 252} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 243} Chain: "F" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1916 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 237} Chain breaks: 1 Chain: "H" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 927 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 837 Classifications: {'peptide': 111} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Time building chain proxies: 5.85, per 1000 atoms: 0.65 Number of scatterers: 8950 At special positions: 0 Unit cell: (87.5, 87.5, 126.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1774 8.00 N 1473 7.00 C 5639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS D 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS E 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS F 439 " distance=2.03 Simple disulfide: pdb=" SG CYS D 313 " - pdb=" SG CYS D 343 " distance=2.03 Simple disulfide: pdb=" SG CYS D 322 " - pdb=" SG CYS D 333 " distance=2.03 Simple disulfide: pdb=" SG CYS D 358 " - pdb=" SG CYS D 367 " distance=2.03 Simple disulfide: pdb=" SG CYS D 382 " - pdb=" SG CYS D 393 " distance=2.03 Simple disulfide: pdb=" SG CYS D 416 " - pdb=" SG CYS D 422 " distance=2.03 Simple disulfide: pdb=" SG CYS E 313 " - pdb=" SG CYS E 343 " distance=2.03 Simple disulfide: pdb=" SG CYS E 322 " - pdb=" SG CYS E 333 " distance=2.04 Simple disulfide: pdb=" SG CYS E 358 " - pdb=" SG CYS E 367 " distance=2.03 Simple disulfide: pdb=" SG CYS E 382 " - pdb=" SG CYS E 393 " distance=2.03 Simple disulfide: pdb=" SG CYS E 416 " - pdb=" SG CYS E 422 " distance=2.03 Simple disulfide: pdb=" SG CYS F 313 " - pdb=" SG CYS F 343 " distance=2.03 Simple disulfide: pdb=" SG CYS F 322 " - pdb=" SG CYS F 333 " distance=2.03 Simple disulfide: pdb=" SG CYS F 358 " - pdb=" SG CYS F 367 " distance=2.03 Simple disulfide: pdb=" SG CYS F 382 " - pdb=" SG CYS F 393 " distance=2.03 Simple disulfide: pdb=" SG CYS F 416 " - pdb=" SG CYS F 422 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 941.8 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2170 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 16 sheets defined 20.2% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 80 through 95 Processing helix chain 'B' and resid 80 through 95 Processing helix chain 'C' and resid 80 through 97 removed outlier: 3.698A pdb=" N MET C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 Processing helix chain 'D' and resid 227 through 240 removed outlier: 3.854A pdb=" N ILE D 233 " --> pdb=" O ARG D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 267 through 277 removed outlier: 3.631A pdb=" N ASN D 276 " --> pdb=" O LYS D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 284 Processing helix chain 'D' and resid 376 through 383 removed outlier: 3.640A pdb=" N VAL D 379 " --> pdb=" O PRO D 376 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ASN D 380 " --> pdb=" O SER D 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 227 Processing helix chain 'E' and resid 227 through 241 removed outlier: 3.705A pdb=" N ILE E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN E 240 " --> pdb=" O GLU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 262 Processing helix chain 'E' and resid 267 through 277 Processing helix chain 'E' and resid 281 through 285 removed outlier: 3.689A pdb=" N SER E 285 " --> pdb=" O ARG E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 384 removed outlier: 3.690A pdb=" N VAL E 379 " --> pdb=" O PRO E 376 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASN E 380 " --> pdb=" O SER E 377 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU E 381 " --> pdb=" O GLU E 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 227 removed outlier: 3.504A pdb=" N ASN F 227 " --> pdb=" O PHE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 240 Processing helix chain 'F' and resid 253 through 262 removed outlier: 3.652A pdb=" N ASN F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 275 Processing helix chain 'F' and resid 277 through 283 Processing helix chain 'F' and resid 376 through 383 removed outlier: 3.656A pdb=" N VAL F 379 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN F 380 " --> pdb=" O SER F 377 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU F 381 " --> pdb=" O GLU F 378 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 99 removed outlier: 3.602A pdb=" N SER H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 33 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 54 current: chain 'D' and resid 286 through 292 removed outlier: 5.642A pdb=" N SER D 287 " --> pdb=" O GLN D 302 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLN D 302 " --> pdb=" O SER D 287 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N MET D 289 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N VAL D 300 " --> pdb=" O MET D 289 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 349 through 352 current: chain 'D' and resid 364 through 368 Processing sheet with id=AA2, first strand: chain 'B' and resid 29 through 33 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 54 current: chain 'E' and resid 286 through 292 removed outlier: 3.706A pdb=" N TYR E 286 " --> pdb=" O GLN E 302 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA E 298 " --> pdb=" O SER E 290 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ILE E 292 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL E 296 " --> pdb=" O ILE E 292 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 349 through 352 current: chain 'E' and resid 364 through 368 Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 33 removed outlier: 9.226A pdb=" N GLN D 462 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP C 52 " --> pdb=" O GLN D 462 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N GLY D 464 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N THR C 54 " --> pdb=" O GLY D 464 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N SER D 466 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL C 56 " --> pdb=" O SER D 466 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 462 through 467 current: chain 'F' and resid 286 through 292 removed outlier: 5.636A pdb=" N SER F 287 " --> pdb=" O GLN F 302 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLN F 302 " --> pdb=" O SER F 287 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N MET F 289 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL F 300 " --> pdb=" O MET F 289 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 349 through 352 current: chain 'F' and resid 364 through 368 Processing sheet with id=AA4, first strand: chain 'D' and resid 321 through 323 removed outlier: 3.548A pdb=" N THR D 323 " --> pdb=" O ILE D 332 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 332 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'D' and resid 430 through 435 removed outlier: 5.111A pdb=" N ILE D 431 " --> pdb=" O ASN D 426 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ASN D 426 " --> pdb=" O ILE D 431 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N CYS D 422 " --> pdb=" O PHE D 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 335 through 336 Processing sheet with id=AA8, first strand: chain 'E' and resid 405 through 407 Processing sheet with id=AA9, first strand: chain 'E' and resid 430 through 434 removed outlier: 3.536A pdb=" N GLY E 430 " --> pdb=" O ASN E 426 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA E 424 " --> pdb=" O ILE E 432 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N THR E 434 " --> pdb=" O CYS E 422 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N CYS E 422 " --> pdb=" O THR E 434 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 321 through 323 Processing sheet with id=AB2, first strand: chain 'F' and resid 404 through 407 Processing sheet with id=AB3, first strand: chain 'F' and resid 430 through 434 removed outlier: 6.652A pdb=" N ALA F 424 " --> pdb=" O ILE F 432 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N THR F 434 " --> pdb=" O CYS F 422 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N CYS F 422 " --> pdb=" O THR F 434 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.403A pdb=" N GLU H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS H 43 " --> pdb=" O TRP H 52 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TRP H 52 " --> pdb=" O LYS H 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.937A pdb=" N VAL L 13 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA L 100 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE L 39 " --> pdb=" O TYR L 55 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N TYR L 55 " --> pdb=" O ILE L 39 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR L 55 " --> pdb=" O ASN L 66 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 831 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: 2.52 Time building geometry restraints manager: 4.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2853 1.34 - 1.47: 2128 1.47 - 1.59: 4026 1.59 - 1.71: 0 1.71 - 1.84: 88 Bond restraints: 9095 Sorted by residual: bond pdb=" C VAL H 13 " pdb=" N LYS H 14 " ideal model delta sigma weight residual 1.330 1.364 -0.034 1.47e-02 4.63e+03 5.41e+00 bond pdb=" CB GLU F 378 " pdb=" CG GLU F 378 " ideal model delta sigma weight residual 1.520 1.573 -0.053 3.00e-02 1.11e+03 3.10e+00 bond pdb=" CA ASN E 363 " pdb=" CB ASN E 363 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.69e-02 3.50e+03 3.08e+00 bond pdb=" CB ASP D 263 " pdb=" CG ASP D 263 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.05e+00 bond pdb=" CB ASN D 426 " pdb=" CG ASN D 426 " ideal model delta sigma weight residual 1.516 1.558 -0.042 2.50e-02 1.60e+03 2.85e+00 ... (remaining 9090 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 11861 1.81 - 3.62: 372 3.62 - 5.44: 61 5.44 - 7.25: 27 7.25 - 9.06: 4 Bond angle restraints: 12325 Sorted by residual: angle pdb=" C GLN E 361 " pdb=" N SER E 362 " pdb=" CA SER E 362 " ideal model delta sigma weight residual 121.54 130.31 -8.77 1.91e+00 2.74e-01 2.11e+01 angle pdb=" CA ASP D 263 " pdb=" CB ASP D 263 " pdb=" CG ASP D 263 " ideal model delta sigma weight residual 112.60 116.90 -4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" CB GLU F 378 " pdb=" CG GLU F 378 " pdb=" CD GLU F 378 " ideal model delta sigma weight residual 112.60 119.79 -7.19 1.70e+00 3.46e-01 1.79e+01 angle pdb=" N ILE E 386 " pdb=" CA ILE E 386 " pdb=" C ILE E 386 " ideal model delta sigma weight residual 111.81 108.23 3.58 8.60e-01 1.35e+00 1.73e+01 angle pdb=" C GLN D 361 " pdb=" N SER D 362 " pdb=" CA SER D 362 " ideal model delta sigma weight residual 120.82 126.59 -5.77 1.50e+00 4.44e-01 1.48e+01 ... (remaining 12320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4811 17.94 - 35.88: 600 35.88 - 53.83: 112 53.83 - 71.77: 26 71.77 - 89.71: 8 Dihedral angle restraints: 5557 sinusoidal: 2195 harmonic: 3362 Sorted by residual: dihedral pdb=" CA PHE H 111 " pdb=" C PHE H 111 " pdb=" N VAL H 112 " pdb=" CA VAL H 112 " ideal model delta harmonic sigma weight residual 180.00 -147.82 -32.18 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA GLY H 113 " pdb=" C GLY H 113 " pdb=" N ALA H 114 " pdb=" CA ALA H 114 " ideal model delta harmonic sigma weight residual -180.00 -151.48 -28.52 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA GLN E 361 " pdb=" C GLN E 361 " pdb=" N SER E 362 " pdb=" CA SER E 362 " ideal model delta harmonic sigma weight residual 180.00 153.29 26.71 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 5554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1209 0.067 - 0.134: 223 0.134 - 0.201: 21 0.201 - 0.268: 1 0.268 - 0.335: 2 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CB ILE H 56 " pdb=" CA ILE H 56 " pdb=" CG1 ILE H 56 " pdb=" CG2 ILE H 56 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB THR L 99 " pdb=" CA THR L 99 " pdb=" OG1 THR L 99 " pdb=" CG2 THR L 99 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CG LEU E 334 " pdb=" CB LEU E 334 " pdb=" CD1 LEU E 334 " pdb=" CD2 LEU E 334 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 1453 not shown) Planarity restraints: 1547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN E 363 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C ASN E 363 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN E 363 " -0.015 2.00e-02 2.50e+03 pdb=" N ARG E 364 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 263 " -0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C ASP D 263 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP D 263 " -0.014 2.00e-02 2.50e+03 pdb=" N MET D 264 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 319 " 0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO D 320 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 320 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 320 " 0.030 5.00e-02 4.00e+02 ... (remaining 1544 not shown) Histogram of nonbonded interaction distances: 2.57 - 3.04: 4998 3.04 - 3.50: 8748 3.50 - 3.97: 14446 3.97 - 4.43: 17101 4.43 - 4.90: 28171 Nonbonded interactions: 73464 Sorted by model distance: nonbonded pdb=" N GLN D 361 " pdb=" O GLN D 361 " model vdw 2.573 2.496 nonbonded pdb=" N SER E 398 " pdb=" O SER E 398 " model vdw 2.595 2.496 nonbonded pdb=" N THR D 267 " pdb=" OG1 THR D 267 " model vdw 2.606 2.496 nonbonded pdb=" C THR D 311 " pdb=" OG1 THR D 311 " model vdw 2.611 2.616 nonbonded pdb=" N GLY H 113 " pdb=" N ALA H 114 " model vdw 2.618 2.560 ... (remaining 73459 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and (resid 217 through 325 or resid 332 through 468)) selection = chain 'F' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.610 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 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 : 0.004 0.053 9095 Z= 0.276 Angle : 0.818 9.062 12325 Z= 0.459 Chirality : 0.052 0.335 1456 Planarity : 0.006 0.066 1547 Dihedral : 16.156 89.711 3327 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.53 % Allowed : 19.73 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.70 (0.22), residues: 1123 helix: -1.76 (0.28), residues: 237 sheet: -1.44 (0.26), residues: 361 loop : -1.95 (0.24), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 118 HIS 0.003 0.001 HIS E 317 PHE 0.027 0.002 PHE D 223 TYR 0.014 0.002 TYR L 55 ARG 0.017 0.002 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 262 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 84 ASP cc_start: 0.7841 (m-30) cc_final: 0.7594 (m-30) REVERT: C 85 LYS cc_start: 0.6392 (ttpt) cc_final: 0.6179 (ttpp) REVERT: D 251 MET cc_start: 0.7165 (tpp) cc_final: 0.6706 (tpp) REVERT: D 342 TYR cc_start: 0.7668 (m-80) cc_final: 0.7431 (m-80) REVERT: D 440 ASP cc_start: 0.7877 (m-30) cc_final: 0.7670 (t0) REVERT: E 227 ASN cc_start: 0.7487 (m-40) cc_final: 0.6995 (m-40) REVERT: E 394 LYS cc_start: 0.6981 (mtpt) cc_final: 0.6383 (mmtm) REVERT: F 361 GLN cc_start: 0.7144 (tp-100) cc_final: 0.6822 (mm-40) REVERT: F 390 LYS cc_start: 0.7268 (mtpp) cc_final: 0.6753 (mppt) REVERT: F 401 ASP cc_start: 0.5828 (m-30) cc_final: 0.4956 (p0) REVERT: H 90 GLU cc_start: 0.5517 (tp30) cc_final: 0.4463 (tp30) REVERT: L 34 PHE cc_start: 0.6362 (m-80) cc_final: 0.6041 (m-80) REVERT: L 48 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7880 (tp40) REVERT: L 55 TYR cc_start: 0.5681 (p90) cc_final: 0.5256 (p90) outliers start: 16 outliers final: 7 residues processed: 272 average time/residue: 0.2038 time to fit residues: 76.2831 Evaluate side-chains 180 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 173 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain F residue 224 GLN Chi-restraints excluded: chain F residue 228 ASN Chi-restraints excluded: chain H residue 125 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 100 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN D 277 ASN E 277 ASN E 444 ASN E 460 ASN F 228 ASN ** F 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 90 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.167662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141016 restraints weight = 9337.668| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.39 r_work: 0.3656 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9095 Z= 0.275 Angle : 0.636 7.419 12325 Z= 0.347 Chirality : 0.046 0.162 1456 Planarity : 0.005 0.037 1547 Dihedral : 5.860 49.952 1237 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 5.27 % Allowed : 19.92 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.07 (0.23), residues: 1123 helix: -0.87 (0.32), residues: 235 sheet: -0.97 (0.27), residues: 330 loop : -1.80 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 341 HIS 0.005 0.002 HIS L 105 PHE 0.013 0.002 PHE E 351 TYR 0.018 0.002 TYR F 342 ARG 0.012 0.001 ARG H 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 208 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: B 95 LEU cc_start: 0.6240 (mt) cc_final: 0.5929 (mt) REVERT: C 95 LEU cc_start: 0.7355 (mt) cc_final: 0.7066 (mt) REVERT: C 97 MET cc_start: 0.4492 (ptp) cc_final: 0.3676 (ptp) REVERT: D 236 GLU cc_start: 0.5736 (pt0) cc_final: 0.5460 (pt0) REVERT: D 263 ASP cc_start: 0.6973 (t0) cc_final: 0.6660 (t0) REVERT: D 373 LEU cc_start: 0.8739 (mm) cc_final: 0.8464 (mp) REVERT: D 419 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7477 (mptt) REVERT: D 440 ASP cc_start: 0.8236 (m-30) cc_final: 0.7965 (t0) REVERT: E 227 ASN cc_start: 0.7625 (m-40) cc_final: 0.7157 (m-40) REVERT: E 293 LYS cc_start: 0.7175 (mtpt) cc_final: 0.6585 (mmtp) REVERT: E 394 LYS cc_start: 0.7297 (mtpt) cc_final: 0.6776 (mmtm) REVERT: F 217 ILE cc_start: 0.5521 (OUTLIER) cc_final: 0.5267 (pt) REVERT: F 390 LYS cc_start: 0.7963 (mtpp) cc_final: 0.6787 (mppt) REVERT: F 401 ASP cc_start: 0.6194 (m-30) cc_final: 0.5053 (p0) REVERT: F 419 LYS cc_start: 0.6812 (mtmm) cc_final: 0.6032 (tppt) REVERT: H 5 GLN cc_start: 0.7821 (mp-120) cc_final: 0.7452 (mp10) REVERT: H 90 GLU cc_start: 0.5551 (tp30) cc_final: 0.4983 (tt0) REVERT: H 92 ARG cc_start: 0.6856 (ptp90) cc_final: 0.6425 (ptp-170) REVERT: H 98 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.6791 (t0) REVERT: H 115 MET cc_start: 0.8017 (mmm) cc_final: 0.7323 (mtt) REVERT: L 48 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7415 (tp40) outliers start: 55 outliers final: 28 residues processed: 245 average time/residue: 0.1941 time to fit residues: 67.1378 Evaluate side-chains 208 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 178 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 31 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 264 MET Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 395 ILE Chi-restraints excluded: chain F residue 413 ILE Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 117 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 79 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 ASN E 460 ASN F 354 GLN F 462 GLN L 90 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.161340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.134198 restraints weight = 9517.309| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.38 r_work: 0.3569 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.6010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 9095 Z= 0.304 Angle : 0.610 7.262 12325 Z= 0.331 Chirality : 0.046 0.181 1456 Planarity : 0.004 0.035 1547 Dihedral : 5.576 59.788 1228 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 5.36 % Allowed : 20.98 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -1.97 (0.23), residues: 1123 helix: -0.59 (0.32), residues: 241 sheet: -0.97 (0.29), residues: 312 loop : -1.80 (0.23), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 314 HIS 0.006 0.002 HIS L 105 PHE 0.015 0.002 PHE H 111 TYR 0.022 0.002 TYR H 57 ARG 0.008 0.001 ARG F 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7683 (tt0) cc_final: 0.7405 (tt0) REVERT: D 236 GLU cc_start: 0.6691 (pt0) cc_final: 0.6189 (tt0) REVERT: D 263 ASP cc_start: 0.7375 (t0) cc_final: 0.6871 (t0) REVERT: D 373 LEU cc_start: 0.8873 (mm) cc_final: 0.8655 (mp) REVERT: D 419 LYS cc_start: 0.8216 (mmmt) cc_final: 0.7686 (mptt) REVERT: D 440 ASP cc_start: 0.8293 (m-30) cc_final: 0.8035 (t0) REVERT: E 227 ASN cc_start: 0.8120 (m-40) cc_final: 0.7730 (m-40) REVERT: E 251 MET cc_start: 0.7936 (mmm) cc_final: 0.7682 (mmm) REVERT: E 339 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7589 (mtt180) REVERT: E 364 ARG cc_start: 0.7737 (OUTLIER) cc_final: 0.7322 (mmm160) REVERT: E 401 ASP cc_start: 0.7827 (p0) cc_final: 0.6918 (m-30) REVERT: E 419 LYS cc_start: 0.9126 (ttpp) cc_final: 0.8502 (mmtt) REVERT: E 448 ASP cc_start: 0.7275 (t0) cc_final: 0.6959 (t0) REVERT: E 462 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8108 (mm-40) REVERT: F 370 MET cc_start: 0.8747 (ttt) cc_final: 0.8393 (ttp) REVERT: F 419 LYS cc_start: 0.7596 (mtmm) cc_final: 0.6613 (tppt) REVERT: H 19 VAL cc_start: 0.7561 (p) cc_final: 0.7260 (m) REVERT: H 98 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7135 (t70) REVERT: H 115 MET cc_start: 0.8079 (mmm) cc_final: 0.7837 (mtt) outliers start: 56 outliers final: 33 residues processed: 225 average time/residue: 0.2214 time to fit residues: 68.5782 Evaluate side-chains 200 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 393 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 395 ILE Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 39 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 3 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.0670 chunk 14 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 388 ASN E 462 GLN F 284 GLN F 361 GLN F 462 GLN H 5 GLN L 90 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.161006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134393 restraints weight = 9505.288| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.35 r_work: 0.3560 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.6721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9095 Z= 0.233 Angle : 0.541 7.303 12325 Z= 0.293 Chirality : 0.044 0.149 1456 Planarity : 0.004 0.041 1547 Dihedral : 5.372 59.400 1228 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.69 % Allowed : 22.03 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -1.82 (0.24), residues: 1123 helix: -0.38 (0.33), residues: 241 sheet: -0.88 (0.27), residues: 348 loop : -1.78 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 314 HIS 0.004 0.001 HIS E 317 PHE 0.013 0.002 PHE E 387 TYR 0.012 0.001 TYR L 55 ARG 0.006 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7763 (tt0) cc_final: 0.7507 (tt0) REVERT: D 236 GLU cc_start: 0.6911 (pt0) cc_final: 0.6506 (tt0) REVERT: D 419 LYS cc_start: 0.8210 (mmmt) cc_final: 0.7754 (mptt) REVERT: D 440 ASP cc_start: 0.8344 (OUTLIER) cc_final: 0.8024 (t0) REVERT: E 361 GLN cc_start: 0.8008 (tm-30) cc_final: 0.7763 (tm-30) REVERT: E 364 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6988 (mmm160) REVERT: E 401 ASP cc_start: 0.7804 (p0) cc_final: 0.6963 (m-30) REVERT: E 419 LYS cc_start: 0.9042 (ttpp) cc_final: 0.8492 (mmtt) REVERT: E 448 ASP cc_start: 0.7195 (t0) cc_final: 0.6782 (t0) REVERT: E 462 GLN cc_start: 0.8506 (mm110) cc_final: 0.8100 (mm110) REVERT: F 274 MET cc_start: 0.7752 (mtp) cc_final: 0.7531 (mtm) REVERT: F 370 MET cc_start: 0.8742 (ttt) cc_final: 0.8442 (ttp) REVERT: F 419 LYS cc_start: 0.7885 (mtmm) cc_final: 0.6875 (tppt) REVERT: H 19 VAL cc_start: 0.7519 (p) cc_final: 0.7206 (m) REVERT: H 98 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7269 (t70) REVERT: L 51 LYS cc_start: 0.7040 (tttp) cc_final: 0.6733 (mttm) outliers start: 49 outliers final: 36 residues processed: 207 average time/residue: 0.2098 time to fit residues: 60.1006 Evaluate side-chains 201 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 393 CYS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 395 ILE Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN E 302 GLN F 354 GLN F 462 GLN H 5 GLN L 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.157123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.130652 restraints weight = 9649.836| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.32 r_work: 0.3491 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 9095 Z= 0.372 Angle : 0.624 7.596 12325 Z= 0.336 Chirality : 0.047 0.163 1456 Planarity : 0.004 0.032 1547 Dihedral : 5.680 58.891 1228 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 5.46 % Allowed : 22.22 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -1.97 (0.24), residues: 1123 helix: -0.55 (0.33), residues: 241 sheet: -1.04 (0.27), residues: 351 loop : -1.80 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 52 HIS 0.007 0.003 HIS D 317 PHE 0.015 0.002 PHE E 351 TYR 0.015 0.002 TYR F 342 ARG 0.011 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 168 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: D 236 GLU cc_start: 0.7190 (pt0) cc_final: 0.6787 (tt0) REVERT: D 263 ASP cc_start: 0.7576 (t0) cc_final: 0.6996 (t0) REVERT: E 228 ASN cc_start: 0.7837 (m-40) cc_final: 0.7500 (m-40) REVERT: E 339 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7897 (mtt180) REVERT: E 361 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7778 (tm-30) REVERT: E 364 ARG cc_start: 0.7226 (OUTLIER) cc_final: 0.6627 (mmm160) REVERT: E 368 ASP cc_start: 0.8009 (p0) cc_final: 0.7725 (p0) REVERT: E 387 PHE cc_start: 0.8460 (OUTLIER) cc_final: 0.7686 (m-80) REVERT: E 419 LYS cc_start: 0.9014 (ttpp) cc_final: 0.8525 (mmtt) REVERT: E 448 ASP cc_start: 0.7303 (t0) cc_final: 0.6550 (t0) REVERT: E 462 GLN cc_start: 0.8555 (mm110) cc_final: 0.7931 (mm110) REVERT: F 370 MET cc_start: 0.8746 (ttt) cc_final: 0.8452 (ttp) REVERT: F 419 LYS cc_start: 0.8078 (mtmm) cc_final: 0.7094 (tppt) REVERT: H 19 VAL cc_start: 0.7529 (p) cc_final: 0.7201 (m) outliers start: 57 outliers final: 43 residues processed: 212 average time/residue: 0.1910 time to fit residues: 57.7418 Evaluate side-chains 194 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 148 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 319 SER Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 106 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 0.0170 chunk 75 optimal weight: 0.9980 chunk 73 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 227 ASN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.158658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.132278 restraints weight = 9539.301| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.35 r_work: 0.3533 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.7582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9095 Z= 0.200 Angle : 0.536 7.834 12325 Z= 0.291 Chirality : 0.044 0.142 1456 Planarity : 0.003 0.034 1547 Dihedral : 5.400 59.848 1228 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.41 % Allowed : 23.75 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -1.84 (0.24), residues: 1123 helix: -0.37 (0.33), residues: 241 sheet: -1.04 (0.28), residues: 341 loop : -1.69 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 314 HIS 0.003 0.001 HIS E 317 PHE 0.010 0.002 PHE H 111 TYR 0.013 0.001 TYR L 55 ARG 0.008 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 91 THR cc_start: 0.7003 (m) cc_final: 0.6732 (p) REVERT: D 236 GLU cc_start: 0.6962 (pt0) cc_final: 0.6645 (tt0) REVERT: D 263 ASP cc_start: 0.7291 (t0) cc_final: 0.6756 (t0) REVERT: E 228 ASN cc_start: 0.7686 (m-40) cc_final: 0.7419 (m-40) REVERT: E 295 GLU cc_start: 0.7464 (pm20) cc_final: 0.7108 (pm20) REVERT: E 339 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7945 (mtt180) REVERT: E 364 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6331 (mmm160) REVERT: E 368 ASP cc_start: 0.8013 (p0) cc_final: 0.7724 (p0) REVERT: E 387 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7724 (m-80) REVERT: E 401 ASP cc_start: 0.7899 (p0) cc_final: 0.6877 (m-30) REVERT: E 419 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8573 (mmtt) REVERT: E 448 ASP cc_start: 0.7367 (t0) cc_final: 0.6877 (t0) REVERT: E 462 GLN cc_start: 0.8513 (mm110) cc_final: 0.8069 (mm110) REVERT: F 332 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.6235 (tp) REVERT: F 370 MET cc_start: 0.8548 (ttt) cc_final: 0.8244 (ttp) REVERT: H 19 VAL cc_start: 0.7632 (p) cc_final: 0.7332 (m) REVERT: H 65 ASN cc_start: 0.8319 (p0) cc_final: 0.8094 (p0) REVERT: L 67 GLN cc_start: 0.7055 (mm-40) cc_final: 0.6671 (mm-40) outliers start: 46 outliers final: 35 residues processed: 204 average time/residue: 0.2015 time to fit residues: 58.3469 Evaluate side-chains 201 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 462 GLN ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.160754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.134947 restraints weight = 9629.098| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.28 r_work: 0.3535 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.7739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9095 Z= 0.213 Angle : 0.536 7.745 12325 Z= 0.291 Chirality : 0.044 0.143 1456 Planarity : 0.003 0.040 1547 Dihedral : 5.280 58.713 1228 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 5.17 % Allowed : 23.18 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -1.78 (0.24), residues: 1123 helix: -0.26 (0.33), residues: 241 sheet: -1.14 (0.28), residues: 323 loop : -1.57 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 52 HIS 0.003 0.001 HIS E 317 PHE 0.010 0.001 PHE E 223 TYR 0.012 0.001 TYR L 55 ARG 0.008 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.7100 (m) cc_final: 0.6833 (p) REVERT: D 263 ASP cc_start: 0.7225 (t0) cc_final: 0.6709 (t0) REVERT: E 228 ASN cc_start: 0.7569 (m-40) cc_final: 0.7320 (m-40) REVERT: E 295 GLU cc_start: 0.7808 (pm20) cc_final: 0.7530 (pm20) REVERT: E 339 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7938 (mtt180) REVERT: E 364 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6432 (mmm160) REVERT: E 368 ASP cc_start: 0.7975 (p0) cc_final: 0.7772 (p0) REVERT: E 387 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.7688 (m-80) REVERT: E 401 ASP cc_start: 0.7890 (p0) cc_final: 0.6964 (m-30) REVERT: E 419 LYS cc_start: 0.8842 (ttpp) cc_final: 0.8542 (mmtt) REVERT: E 428 ASN cc_start: 0.8289 (t0) cc_final: 0.8033 (t0) REVERT: E 448 ASP cc_start: 0.7440 (t0) cc_final: 0.6583 (t0) REVERT: E 462 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7830 (mm110) REVERT: F 370 MET cc_start: 0.8447 (ttt) cc_final: 0.8186 (ttp) REVERT: H 19 VAL cc_start: 0.7776 (p) cc_final: 0.7484 (m) REVERT: L 67 GLN cc_start: 0.7128 (mm-40) cc_final: 0.6715 (mm-40) outliers start: 54 outliers final: 42 residues processed: 205 average time/residue: 0.2289 time to fit residues: 65.4632 Evaluate side-chains 202 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 99 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 69 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 0.3980 chunk 5 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 ASN ** 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 = 0.3899 r_free = 0.3899 target = 0.156035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129399 restraints weight = 9810.010| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.40 r_work: 0.3487 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.7947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9095 Z= 0.289 Angle : 0.582 8.352 12325 Z= 0.312 Chirality : 0.045 0.164 1456 Planarity : 0.004 0.037 1547 Dihedral : 5.378 56.492 1228 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.79 % Allowed : 24.14 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -1.85 (0.24), residues: 1123 helix: -0.33 (0.33), residues: 241 sheet: -1.17 (0.29), residues: 322 loop : -1.61 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 52 HIS 0.005 0.002 HIS E 317 PHE 0.011 0.002 PHE D 366 TYR 0.012 0.002 TYR L 55 ARG 0.011 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 263 ASP cc_start: 0.7359 (t0) cc_final: 0.6799 (t0) REVERT: E 228 ASN cc_start: 0.7567 (m-40) cc_final: 0.7302 (m-40) REVERT: E 295 GLU cc_start: 0.7840 (pm20) cc_final: 0.7547 (pm20) REVERT: E 339 ARG cc_start: 0.8256 (OUTLIER) cc_final: 0.7838 (mtt180) REVERT: E 364 ARG cc_start: 0.7101 (OUTLIER) cc_final: 0.6405 (mmm160) REVERT: E 368 ASP cc_start: 0.7978 (p0) cc_final: 0.7742 (p0) REVERT: E 387 PHE cc_start: 0.8631 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: E 401 ASP cc_start: 0.7884 (p0) cc_final: 0.6880 (m-30) REVERT: E 419 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8538 (mmtt) REVERT: E 428 ASN cc_start: 0.8312 (t0) cc_final: 0.8080 (t0) REVERT: E 448 ASP cc_start: 0.7499 (t0) cc_final: 0.6710 (t0) REVERT: E 462 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7829 (mm110) REVERT: F 232 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6639 (mm-30) REVERT: F 370 MET cc_start: 0.8517 (ttt) cc_final: 0.8255 (ttp) REVERT: H 19 VAL cc_start: 0.7667 (p) cc_final: 0.7379 (m) REVERT: L 18 ARG cc_start: 0.7667 (mtp-110) cc_final: 0.7310 (tpp80) outliers start: 50 outliers final: 42 residues processed: 205 average time/residue: 0.1957 time to fit residues: 56.5026 Evaluate side-chains 204 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 158 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 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 = 0.3942 r_free = 0.3942 target = 0.160459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.135214 restraints weight = 9665.853| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.24 r_work: 0.3529 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.8022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9095 Z= 0.210 Angle : 0.538 7.485 12325 Z= 0.292 Chirality : 0.044 0.157 1456 Planarity : 0.003 0.034 1547 Dihedral : 5.263 57.634 1228 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.69 % Allowed : 24.23 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -1.76 (0.24), residues: 1123 helix: -0.23 (0.34), residues: 241 sheet: -1.11 (0.29), residues: 323 loop : -1.58 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 314 HIS 0.004 0.001 HIS E 317 PHE 0.010 0.001 PHE E 366 TYR 0.020 0.001 TYR E 417 ARG 0.009 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 156 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.7042 (m) cc_final: 0.6832 (p) REVERT: D 263 ASP cc_start: 0.7235 (t0) cc_final: 0.6722 (t0) REVERT: E 228 ASN cc_start: 0.7390 (m-40) cc_final: 0.7057 (m-40) REVERT: E 295 GLU cc_start: 0.7888 (pm20) cc_final: 0.7600 (pm20) REVERT: E 339 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7874 (mtt180) REVERT: E 364 ARG cc_start: 0.7083 (OUTLIER) cc_final: 0.6321 (mmm160) REVERT: E 387 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7563 (m-80) REVERT: E 401 ASP cc_start: 0.7864 (p0) cc_final: 0.6964 (m-30) REVERT: E 419 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8512 (mmtt) REVERT: E 428 ASN cc_start: 0.8338 (t0) cc_final: 0.8118 (t0) REVERT: E 448 ASP cc_start: 0.7533 (t0) cc_final: 0.6699 (t0) REVERT: E 462 GLN cc_start: 0.8494 (mm-40) cc_final: 0.7862 (mm110) REVERT: F 232 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6768 (mm-30) REVERT: F 370 MET cc_start: 0.8470 (ttt) cc_final: 0.8211 (ttp) REVERT: H 19 VAL cc_start: 0.7847 (p) cc_final: 0.7621 (m) REVERT: L 18 ARG cc_start: 0.7737 (mtp-110) cc_final: 0.7326 (tpp80) outliers start: 49 outliers final: 44 residues processed: 197 average time/residue: 0.2033 time to fit residues: 56.4908 Evaluate side-chains 198 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 387 PHE Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 98 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 48 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 = 0.3934 r_free = 0.3934 target = 0.159641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.133222 restraints weight = 9679.714| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.39 r_work: 0.3532 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.8103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9095 Z= 0.198 Angle : 0.546 7.909 12325 Z= 0.296 Chirality : 0.044 0.156 1456 Planarity : 0.003 0.035 1547 Dihedral : 5.200 57.573 1228 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 4.50 % Allowed : 24.81 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -1.69 (0.24), residues: 1123 helix: -0.12 (0.34), residues: 241 sheet: -1.07 (0.29), residues: 325 loop : -1.57 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 314 HIS 0.004 0.001 HIS E 317 PHE 0.011 0.001 PHE E 366 TYR 0.011 0.001 TYR L 55 ARG 0.009 0.001 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 THR cc_start: 0.6917 (m) cc_final: 0.6710 (p) REVERT: D 311 THR cc_start: 0.8245 (OUTLIER) cc_final: 0.7840 (p) REVERT: E 228 ASN cc_start: 0.7286 (m-40) cc_final: 0.6979 (m-40) REVERT: E 295 GLU cc_start: 0.7867 (pm20) cc_final: 0.7580 (pm20) REVERT: E 339 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7886 (mtt180) REVERT: E 364 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6332 (mmm160) REVERT: E 396 MET cc_start: 0.7556 (OUTLIER) cc_final: 0.7184 (ptm) REVERT: E 401 ASP cc_start: 0.7821 (p0) cc_final: 0.6883 (m-30) REVERT: E 419 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8515 (mmtt) REVERT: E 448 ASP cc_start: 0.7533 (t0) cc_final: 0.6687 (t0) REVERT: E 462 GLN cc_start: 0.8518 (mm-40) cc_final: 0.7848 (mm110) REVERT: F 217 ILE cc_start: 0.5512 (OUTLIER) cc_final: 0.5173 (pt) REVERT: F 232 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6701 (mm-30) REVERT: F 370 MET cc_start: 0.8471 (ttt) cc_final: 0.8203 (ttp) REVERT: H 19 VAL cc_start: 0.7751 (p) cc_final: 0.7514 (m) REVERT: L 18 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7269 (tpp80) outliers start: 47 outliers final: 40 residues processed: 193 average time/residue: 0.1892 time to fit residues: 51.7037 Evaluate side-chains 192 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 146 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 219 THR Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 309 ILE Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 467 LEU Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 309 ILE Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 364 ARG Chi-restraints excluded: chain E residue 396 MET Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 323 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 443 SER Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 42 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 39 ILE Chi-restraints excluded: chain L residue 71 VAL Chi-restraints excluded: chain L residue 97 VAL Chi-restraints excluded: chain L residue 101 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 73 optimal weight: 0.0060 chunk 88 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 40 ASN ** 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 = 0.159158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133618 restraints weight = 9660.254| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.25 r_work: 0.3519 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3371 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.8187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9095 Z= 0.262 Angle : 0.574 7.335 12325 Z= 0.311 Chirality : 0.045 0.159 1456 Planarity : 0.003 0.036 1547 Dihedral : 5.288 56.958 1228 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 5.17 % Allowed : 23.95 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % 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: -1.77 (0.24), residues: 1123 helix: -0.16 (0.33), residues: 241 sheet: -1.12 (0.28), residues: 326 loop : -1.61 (0.24), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP F 314 HIS 0.005 0.002 HIS E 317 PHE 0.011 0.002 PHE E 366 TYR 0.013 0.002 TYR L 55 ARG 0.010 0.001 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4703.73 seconds wall clock time: 82 minutes 9.75 seconds (4929.75 seconds total)