Starting phenix.real_space_refine on Wed Sep 17 13:48:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvw_52444/09_2025/9hvw_52444.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvw_52444/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9hvw_52444/09_2025/9hvw_52444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvw_52444/09_2025/9hvw_52444.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hvw_52444/09_2025/9hvw_52444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvw_52444/09_2025/9hvw_52444.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.050 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.12, per 1000 atoms: 0.24 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: 0.63 Conformation dependent library (CDL) restraints added in 336.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.30 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: 1.36 Time building geometry restraints manager: 0.84 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: 1.260 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.840 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.730 ------------------------------------------------------------------------------- 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 9115 Z= 0.202 Angle : 0.819 9.062 12365 Z= 0.460 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.017 0.002 ARG B 49 TYR 0.014 0.002 TYR L 55 PHE 0.027 0.002 PHE D 223 TRP 0.014 0.002 TRP H 118 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 9095) covalent geometry : angle 0.81768 (12325) SS BOND : bond 0.00264 ( 20) SS BOND : angle 1.19798 ( 40) hydrogen bonds : bond 0.15774 ( 324) hydrogen bonds : angle 7.27345 ( 831) *********************** 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 : 0.409 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: 0.6178 (ttpp) REVERT: D 251 MET cc_start: 0.7165 (tpp) cc_final: 0.6705 (tpp) REVERT: D 342 TYR cc_start: 0.7668 (m-80) cc_final: 0.7430 (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: 0.6821 (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: 0.0956 time to fit residues: 36.0895 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 : 0.364 ------------------------------------------------------------------------------- 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 108 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 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 = 0.3974 r_free = 0.3974 target = 0.163259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136544 restraints weight = 9471.484| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.36 r_work: 0.3593 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9115 Z= 0.247 Angle : 0.711 7.721 12365 Z= 0.384 Chirality : 0.049 0.176 1456 Planarity : 0.005 0.043 1547 Dihedral : 6.232 47.297 1237 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 6.42 % Allowed : 18.68 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.23), residues: 1123 helix: -1.19 (0.31), residues: 233 sheet: -1.19 (0.27), residues: 322 loop : -1.87 (0.23), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 364 TYR 0.020 0.002 TYR D 299 PHE 0.020 0.002 PHE E 351 TRP 0.015 0.002 TRP D 314 HIS 0.009 0.003 HIS L 105 Details of bonding type rmsd covalent geometry : bond 0.00565 ( 9095) covalent geometry : angle 0.70777 (12325) SS BOND : bond 0.00378 ( 20) SS BOND : angle 1.34609 ( 40) hydrogen bonds : bond 0.04369 ( 324) hydrogen bonds : angle 5.65784 ( 831) *********************** 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 269 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 202 time to evaluate : 0.353 Fit side-chains REVERT: A 49 ARG cc_start: 0.7351 (ttp80) cc_final: 0.6997 (ttp-170) REVERT: C 95 LEU cc_start: 0.7391 (mt) cc_final: 0.6948 (mt) REVERT: D 236 GLU cc_start: 0.6916 (pt0) cc_final: 0.6602 (pt0) REVERT: D 373 LEU cc_start: 0.8895 (mm) cc_final: 0.8601 (mp) REVERT: D 394 LYS cc_start: 0.7282 (mttm) cc_final: 0.7068 (mtpt) REVERT: D 419 LYS cc_start: 0.8187 (mmmt) cc_final: 0.7696 (mptt) REVERT: D 434 THR cc_start: 0.8208 (p) cc_final: 0.8000 (m) REVERT: E 227 ASN cc_start: 0.7986 (m-40) cc_final: 0.7743 (m-40) REVERT: E 247 VAL cc_start: 0.8676 (OUTLIER) cc_final: 0.8467 (t) REVERT: E 419 LYS cc_start: 0.9181 (ttpp) cc_final: 0.8858 (mtpp) REVERT: F 419 LYS cc_start: 0.7422 (mtmm) cc_final: 0.6500 (tppt) REVERT: H 5 GLN cc_start: 0.7774 (mp-120) cc_final: 0.7369 (mp10) REVERT: H 71 PHE cc_start: 0.6785 (m-10) cc_final: 0.6537 (m-10) REVERT: H 98 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7170 (t70) REVERT: H 115 MET cc_start: 0.8114 (mmm) cc_final: 0.7556 (mtt) REVERT: L 48 GLN cc_start: 0.7530 (mm-40) cc_final: 0.7316 (tp40) REVERT: L 90 ASN cc_start: 0.7704 (m-40) cc_final: 0.7456 (m-40) outliers start: 67 outliers final: 36 residues processed: 252 average time/residue: 0.0969 time to fit residues: 34.0354 Evaluate side-chains 222 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL 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 31 GLU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 264 MET 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 379 VAL Chi-restraints excluded: chain D residue 386 ILE 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 245 THR Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 292 ILE Chi-restraints excluded: chain E residue 323 THR Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 318 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 413 ILE 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 254 ASN E 302 GLN E 460 ASN F 284 GLN F 361 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.156263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.129168 restraints weight = 9676.325| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.41 r_work: 0.3495 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.6809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 9115 Z= 0.257 Angle : 0.645 8.171 12365 Z= 0.351 Chirality : 0.047 0.162 1456 Planarity : 0.004 0.044 1547 Dihedral : 5.853 54.411 1229 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 5.36 % Allowed : 20.50 % Favored : 74.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.23), residues: 1123 helix: -0.83 (0.32), residues: 239 sheet: -1.11 (0.28), residues: 312 loop : -1.90 (0.23), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 364 TYR 0.017 0.002 TYR D 417 PHE 0.016 0.002 PHE H 111 TRP 0.012 0.002 TRP H 52 HIS 0.007 0.002 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00592 ( 9095) covalent geometry : angle 0.64161 (12325) SS BOND : bond 0.00691 ( 20) SS BOND : angle 1.26660 ( 40) hydrogen bonds : bond 0.03791 ( 324) hydrogen bonds : angle 5.39764 ( 831) *********************** 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 241 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 185 time to evaluate : 0.366 Fit side-chains REVERT: B 49 ARG cc_start: 0.6959 (ttp-170) cc_final: 0.6697 (ttp-170) REVERT: D 224 GLN cc_start: 0.6144 (mm-40) cc_final: 0.5929 (mm-40) REVERT: D 236 GLU cc_start: 0.6912 (pt0) cc_final: 0.6682 (pt0) REVERT: D 256 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6926 (mt-10) REVERT: D 263 ASP cc_start: 0.7553 (t0) cc_final: 0.7095 (t0) REVERT: D 364 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7665 (mmm160) REVERT: D 394 LYS cc_start: 0.7695 (mttm) cc_final: 0.7319 (mtpt) REVERT: D 419 LYS cc_start: 0.8274 (mmmt) cc_final: 0.7854 (mptt) REVERT: E 228 ASN cc_start: 0.7918 (m-40) cc_final: 0.7674 (m-40) REVERT: E 339 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7816 (mtt180) REVERT: E 401 ASP cc_start: 0.7897 (p0) cc_final: 0.6922 (m-30) REVERT: E 404 SER cc_start: 0.8795 (m) cc_final: 0.8503 (m) REVERT: E 419 LYS cc_start: 0.9121 (ttpp) cc_final: 0.8508 (mmtt) REVERT: F 370 MET cc_start: 0.8656 (ttt) cc_final: 0.8423 (ttp) REVERT: F 419 LYS cc_start: 0.7888 (mtmm) cc_final: 0.6916 (tppt) REVERT: H 19 VAL cc_start: 0.7500 (p) cc_final: 0.7233 (m) REVERT: H 98 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7282 (t70) REVERT: H 115 MET cc_start: 0.7976 (mmm) cc_final: 0.7741 (mtt) REVERT: L 51 LYS cc_start: 0.7139 (tttp) cc_final: 0.6882 (pttm) REVERT: L 95 GLU cc_start: 0.6499 (pm20) cc_final: 0.6019 (pm20) outliers start: 56 outliers final: 42 residues processed: 231 average time/residue: 0.0952 time to fit residues: 30.7276 Evaluate side-chains 206 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 161 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL 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 29 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 91 THR 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 247 VAL 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 364 ARG Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 403 SER 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 456 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 287 SER 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 413 ILE 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 5 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 444 ASN H 5 GLN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.161135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.135005 restraints weight = 9694.755| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.30 r_work: 0.3540 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.7179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9115 Z= 0.155 Angle : 0.550 7.826 12365 Z= 0.298 Chirality : 0.044 0.140 1456 Planarity : 0.003 0.035 1547 Dihedral : 5.504 58.525 1229 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.79 % Allowed : 21.84 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.91 (0.24), residues: 1123 helix: -0.53 (0.34), residues: 241 sheet: -0.86 (0.29), residues: 304 loop : -1.81 (0.23), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 75 TYR 0.014 0.001 TYR L 55 PHE 0.012 0.002 PHE H 111 TRP 0.009 0.001 TRP F 314 HIS 0.004 0.002 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 9095) covalent geometry : angle 0.54712 (12325) SS BOND : bond 0.00298 ( 20) SS BOND : angle 1.07309 ( 40) hydrogen bonds : bond 0.03127 ( 324) hydrogen bonds : angle 5.03526 ( 831) *********************** 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 222 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.410 Fit side-chains REVERT: B 49 ARG cc_start: 0.6990 (ttp-170) cc_final: 0.6773 (ttp-170) REVERT: C 42 LYS cc_start: 0.7818 (mtmt) cc_final: 0.7567 (mtmt) REVERT: D 236 GLU cc_start: 0.6878 (pt0) cc_final: 0.6421 (tt0) REVERT: D 256 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7094 (mt-10) REVERT: D 394 LYS cc_start: 0.7528 (mttm) cc_final: 0.7160 (mtmt) REVERT: E 228 ASN cc_start: 0.7886 (m-40) cc_final: 0.7496 (m-40) REVERT: E 339 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7917 (mtt180) REVERT: E 368 ASP cc_start: 0.8075 (p0) cc_final: 0.7736 (p0) REVERT: E 401 ASP cc_start: 0.7906 (p0) cc_final: 0.7032 (m-30) REVERT: E 404 SER cc_start: 0.8818 (m) cc_final: 0.8531 (m) REVERT: E 419 LYS cc_start: 0.8986 (ttpp) cc_final: 0.8564 (mmtt) REVERT: E 444 ASN cc_start: 0.8605 (OUTLIER) cc_final: 0.8371 (p0) REVERT: E 462 GLN cc_start: 0.8405 (mm-40) cc_final: 0.8147 (mm110) REVERT: F 370 MET cc_start: 0.8585 (ttt) cc_final: 0.8199 (ttp) REVERT: F 419 LYS cc_start: 0.7925 (mtmm) cc_final: 0.6964 (tppt) REVERT: H 19 VAL cc_start: 0.7657 (p) cc_final: 0.7413 (m) REVERT: H 98 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7312 (t70) REVERT: L 51 LYS cc_start: 0.7129 (tttp) cc_final: 0.6835 (mttm) outliers start: 50 outliers final: 39 residues processed: 210 average time/residue: 0.0914 time to fit residues: 27.3761 Evaluate side-chains 193 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 151 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain D residue 219 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 375 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 403 SER Chi-restraints excluded: chain D residue 423 THR Chi-restraints excluded: chain D residue 451 SER Chi-restraints excluded: chain E residue 285 SER 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 444 ASN Chi-restraints excluded: chain E residue 456 LEU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 309 ILE 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 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 23 CYS Chi-restraints excluded: chain L residue 71 VAL 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 73 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 98 optimal weight: 0.2980 chunk 110 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 224 GLN E 444 ASN E 462 GLN H 5 GLN H 120 GLN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.161603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.135788 restraints weight = 9652.868| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.28 r_work: 0.3546 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9115 Z= 0.140 Angle : 0.543 7.520 12365 Z= 0.295 Chirality : 0.044 0.140 1456 Planarity : 0.003 0.032 1547 Dihedral : 5.362 59.829 1228 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 5.94 % Allowed : 20.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.89 (0.24), residues: 1123 helix: -0.37 (0.34), residues: 241 sheet: -1.12 (0.28), residues: 332 loop : -1.71 (0.24), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 75 TYR 0.013 0.001 TYR L 55 PHE 0.011 0.002 PHE H 111 TRP 0.010 0.001 TRP L 41 HIS 0.004 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 9095) covalent geometry : angle 0.54087 (12325) SS BOND : bond 0.00278 ( 20) SS BOND : angle 0.98627 ( 40) hydrogen bonds : bond 0.03049 ( 324) hydrogen bonds : angle 4.95212 ( 831) *********************** 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: 62 poor density : 163 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: D 236 GLU cc_start: 0.7001 (pt0) cc_final: 0.6618 (tt0) REVERT: D 256 GLU cc_start: 0.7397 (mt-10) cc_final: 0.7041 (mt-10) REVERT: D 263 ASP cc_start: 0.7272 (t0) cc_final: 0.6780 (t0) REVERT: D 364 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7685 (mmm160) REVERT: D 394 LYS cc_start: 0.7574 (mttm) cc_final: 0.7178 (mtmt) REVERT: E 228 ASN cc_start: 0.7860 (m-40) cc_final: 0.7577 (m-40) REVERT: E 339 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7913 (mtt180) REVERT: E 368 ASP cc_start: 0.8097 (p0) cc_final: 0.7730 (p0) REVERT: E 401 ASP cc_start: 0.7956 (p0) cc_final: 0.7035 (m-30) REVERT: E 404 SER cc_start: 0.8798 (m) cc_final: 0.8521 (m) REVERT: E 419 LYS cc_start: 0.8991 (ttpp) cc_final: 0.8570 (mmtt) REVERT: E 462 GLN cc_start: 0.8256 (mm110) cc_final: 0.8018 (mm110) REVERT: F 217 ILE cc_start: 0.5570 (OUTLIER) cc_final: 0.5306 (pt) REVERT: F 228 ASN cc_start: 0.8710 (m110) cc_final: 0.7709 (m110) REVERT: F 232 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6121 (mp0) REVERT: F 370 MET cc_start: 0.8398 (ttt) cc_final: 0.8032 (ttp) REVERT: F 419 LYS cc_start: 0.7914 (mtmm) cc_final: 0.7013 (tppt) REVERT: H 19 VAL cc_start: 0.7736 (p) cc_final: 0.7448 (m) outliers start: 62 outliers final: 48 residues processed: 209 average time/residue: 0.0894 time to fit residues: 26.7670 Evaluate side-chains 204 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 152 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 61 LEU 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 219 THR Chi-restraints excluded: chain D residue 220 VAL 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 324 THR Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 451 SER 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 339 ARG 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 278 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 309 ILE 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 394 LYS 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 120 GLN 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 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 75 optimal weight: 4.9990 chunk 72 optimal weight: 0.0980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 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 388 ASN H 5 GLN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.161575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136117 restraints weight = 9603.237| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.26 r_work: 0.3546 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.7520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9115 Z= 0.141 Angle : 0.537 7.574 12365 Z= 0.291 Chirality : 0.044 0.158 1456 Planarity : 0.004 0.056 1547 Dihedral : 5.316 59.842 1228 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 5.56 % Allowed : 21.46 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.76 (0.24), residues: 1123 helix: -0.25 (0.34), residues: 241 sheet: -1.05 (0.29), residues: 329 loop : -1.61 (0.24), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 49 TYR 0.012 0.001 TYR L 55 PHE 0.012 0.001 PHE H 111 TRP 0.009 0.001 TRP L 41 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 9095) covalent geometry : angle 0.53519 (12325) SS BOND : bond 0.00273 ( 20) SS BOND : angle 1.01381 ( 40) hydrogen bonds : bond 0.03001 ( 324) hydrogen bonds : angle 4.85612 ( 831) *********************** 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 220 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 162 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: D 236 GLU cc_start: 0.7129 (pt0) cc_final: 0.6626 (tt0) REVERT: D 256 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7091 (mt-10) REVERT: D 364 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.7702 (mmm160) REVERT: D 394 LYS cc_start: 0.7573 (mttm) cc_final: 0.7184 (mtmt) REVERT: D 440 ASP cc_start: 0.8163 (t0) cc_final: 0.7870 (t0) REVERT: E 228 ASN cc_start: 0.7555 (m-40) cc_final: 0.7276 (m-40) REVERT: E 295 GLU cc_start: 0.7688 (pm20) cc_final: 0.7454 (pm20) REVERT: E 339 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7988 (mtt180) REVERT: E 368 ASP cc_start: 0.8041 (p0) cc_final: 0.7750 (p0) REVERT: E 401 ASP cc_start: 0.7980 (p0) cc_final: 0.7042 (m-30) REVERT: E 404 SER cc_start: 0.8778 (m) cc_final: 0.8496 (m) REVERT: E 419 LYS cc_start: 0.8958 (ttpp) cc_final: 0.8607 (mmtt) REVERT: E 428 ASN cc_start: 0.8028 (t0) cc_final: 0.7739 (t0) REVERT: E 448 ASP cc_start: 0.7251 (t0) cc_final: 0.6971 (t0) REVERT: E 462 GLN cc_start: 0.8303 (mm110) cc_final: 0.7997 (mm110) REVERT: F 217 ILE cc_start: 0.5482 (OUTLIER) cc_final: 0.5222 (pt) REVERT: F 228 ASN cc_start: 0.8737 (m110) cc_final: 0.7646 (m-40) REVERT: F 232 GLU cc_start: 0.7485 (OUTLIER) cc_final: 0.6045 (mp0) REVERT: F 370 MET cc_start: 0.8396 (ttt) cc_final: 0.8042 (ttp) REVERT: F 419 LYS cc_start: 0.7985 (mtmm) cc_final: 0.7064 (tppt) REVERT: H 19 VAL cc_start: 0.7822 (p) cc_final: 0.7543 (m) outliers start: 58 outliers final: 43 residues processed: 204 average time/residue: 0.0875 time to fit residues: 25.7349 Evaluate side-chains 200 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 153 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL 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 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 324 THR Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 451 SER 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 337 THR Chi-restraints excluded: chain E residue 339 ARG 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 287 SER 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 393 CYS Chi-restraints excluded: chain F residue 394 LYS 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 71 VAL Chi-restraints excluded: chain L residue 101 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 103 optimal weight: 0.0870 chunk 52 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 83 optimal weight: 0.4980 chunk 58 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN L 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.164671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139066 restraints weight = 9588.887| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.28 r_work: 0.3587 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9115 Z= 0.105 Angle : 0.508 7.407 12365 Z= 0.276 Chirality : 0.043 0.147 1456 Planarity : 0.003 0.034 1547 Dihedral : 5.113 58.478 1228 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.02 % Allowed : 22.80 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.54 (0.24), residues: 1123 helix: -0.08 (0.34), residues: 243 sheet: -0.78 (0.29), residues: 342 loop : -1.58 (0.25), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 49 TYR 0.011 0.001 TYR E 342 PHE 0.009 0.001 PHE E 223 TRP 0.011 0.001 TRP L 41 HIS 0.003 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9095) covalent geometry : angle 0.50685 (12325) SS BOND : bond 0.00230 ( 20) SS BOND : angle 0.87506 ( 40) hydrogen bonds : bond 0.02727 ( 324) hydrogen bonds : angle 4.67412 ( 831) *********************** 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 212 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 91 THR cc_start: 0.7084 (m) cc_final: 0.6853 (p) REVERT: B 62 SER cc_start: 0.6261 (t) cc_final: 0.5969 (p) REVERT: D 236 GLU cc_start: 0.7037 (pt0) cc_final: 0.6736 (tt0) REVERT: D 256 GLU cc_start: 0.7402 (mt-10) cc_final: 0.7044 (mt-10) REVERT: D 311 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7842 (p) REVERT: D 364 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7549 (mmm160) REVERT: D 394 LYS cc_start: 0.7493 (mttm) cc_final: 0.7204 (mtmt) REVERT: E 228 ASN cc_start: 0.7417 (m-40) cc_final: 0.7123 (m-40) REVERT: E 295 GLU cc_start: 0.7745 (pm20) cc_final: 0.7301 (pm20) REVERT: E 339 ARG cc_start: 0.8395 (OUTLIER) cc_final: 0.7952 (mtt180) REVERT: E 368 ASP cc_start: 0.7952 (p0) cc_final: 0.7671 (p0) REVERT: E 401 ASP cc_start: 0.7831 (p0) cc_final: 0.7059 (m-30) REVERT: E 419 LYS cc_start: 0.8823 (ttpp) cc_final: 0.8532 (mmtt) REVERT: E 427 LYS cc_start: 0.7627 (ttmm) cc_final: 0.7402 (ttmm) REVERT: E 428 ASN cc_start: 0.8088 (t0) cc_final: 0.7851 (t0) REVERT: E 462 GLN cc_start: 0.8392 (mm110) cc_final: 0.8099 (mm110) REVERT: F 228 ASN cc_start: 0.8694 (m110) cc_final: 0.7586 (m-40) REVERT: F 232 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.5628 (mp0) REVERT: F 370 MET cc_start: 0.8197 (ttt) cc_final: 0.7962 (ttp) REVERT: H 19 VAL cc_start: 0.7826 (p) cc_final: 0.7547 (m) outliers start: 42 outliers final: 31 residues processed: 203 average time/residue: 0.0938 time to fit residues: 26.9746 Evaluate side-chains 189 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 ILE 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 364 ARG Chi-restraints excluded: chain D residue 375 LEU 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 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 456 LEU Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 394 LYS Chi-restraints excluded: chain F residue 420 THR Chi-restraints excluded: chain F residue 443 SER 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 71 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 21 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN H 5 GLN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 92 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.154753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127963 restraints weight = 9720.619| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.40 r_work: 0.3476 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.7953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 9115 Z= 0.238 Angle : 0.609 7.094 12365 Z= 0.328 Chirality : 0.046 0.164 1456 Planarity : 0.004 0.050 1547 Dihedral : 5.376 56.713 1226 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 5.36 % Allowed : 22.03 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.72 (0.24), residues: 1123 helix: -0.16 (0.34), residues: 241 sheet: -1.09 (0.29), residues: 324 loop : -1.57 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 49 TYR 0.014 0.002 TYR F 458 PHE 0.014 0.002 PHE E 351 TRP 0.009 0.002 TRP B 52 HIS 0.006 0.002 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00560 ( 9095) covalent geometry : angle 0.60554 (12325) SS BOND : bond 0.00387 ( 20) SS BOND : angle 1.23295 ( 40) hydrogen bonds : bond 0.03432 ( 324) hydrogen bonds : angle 5.11490 ( 831) *********************** 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 217 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 161 time to evaluate : 0.384 Fit side-chains REVERT: D 236 GLU cc_start: 0.7139 (pt0) cc_final: 0.6808 (tt0) REVERT: D 263 ASP cc_start: 0.7327 (t0) cc_final: 0.6777 (t0) REVERT: D 364 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7645 (mmm160) REVERT: D 394 LYS cc_start: 0.7463 (mttm) cc_final: 0.7060 (mtmt) REVERT: E 228 ASN cc_start: 0.7470 (m-40) cc_final: 0.7194 (m-40) REVERT: E 295 GLU cc_start: 0.7893 (pm20) cc_final: 0.7517 (pm20) REVERT: E 339 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7976 (mtt180) REVERT: E 368 ASP cc_start: 0.8094 (p0) cc_final: 0.7874 (p0) REVERT: E 401 ASP cc_start: 0.7895 (p0) cc_final: 0.6888 (m-30) REVERT: E 419 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8542 (mmtt) REVERT: E 428 ASN cc_start: 0.8150 (t0) cc_final: 0.7902 (t0) REVERT: E 448 ASP cc_start: 0.7572 (t0) cc_final: 0.7254 (t0) REVERT: E 462 GLN cc_start: 0.8512 (mm110) cc_final: 0.8015 (mm110) REVERT: F 228 ASN cc_start: 0.8596 (m110) cc_final: 0.7346 (m110) REVERT: F 232 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.5529 (mp0) REVERT: F 370 MET cc_start: 0.8509 (ttt) cc_final: 0.8200 (ttp) REVERT: H 19 VAL cc_start: 0.7641 (p) cc_final: 0.7373 (m) REVERT: L 18 ARG cc_start: 0.7639 (mtp-110) cc_final: 0.7249 (tpp80) outliers start: 56 outliers final: 48 residues processed: 205 average time/residue: 0.0941 time to fit residues: 27.2510 Evaluate side-chains 207 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 ILE Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 91 THR 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 324 THR Chi-restraints excluded: chain D residue 364 ARG Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 386 ILE Chi-restraints excluded: chain D residue 451 SER 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 456 LEU Chi-restraints excluded: chain F residue 217 ILE Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 309 ILE 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 394 LYS Chi-restraints excluded: chain F residue 419 LYS 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 56 ILE 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 71 VAL Chi-restraints excluded: chain L residue 101 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: 0.8980 chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 GLN H 5 GLN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.159879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.134164 restraints weight = 9661.477| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.26 r_work: 0.3531 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.8025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9115 Z= 0.151 Angle : 0.548 7.223 12365 Z= 0.297 Chirality : 0.044 0.150 1456 Planarity : 0.004 0.041 1547 Dihedral : 5.251 57.863 1226 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.31 % Allowed : 23.18 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.24), residues: 1123 helix: -0.06 (0.34), residues: 241 sheet: -1.03 (0.29), residues: 324 loop : -1.60 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 49 TYR 0.014 0.001 TYR L 55 PHE 0.011 0.002 PHE E 223 TRP 0.009 0.001 TRP L 41 HIS 0.004 0.001 HIS D 317 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9095) covalent geometry : angle 0.54615 (12325) SS BOND : bond 0.00271 ( 20) SS BOND : angle 0.97731 ( 40) hydrogen bonds : bond 0.03044 ( 324) hydrogen bonds : angle 4.92228 ( 831) *********************** 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: 45 poor density : 160 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 91 THR cc_start: 0.7035 (m) cc_final: 0.6824 (p) REVERT: D 224 GLN cc_start: 0.6116 (mm110) cc_final: 0.5726 (mm-40) REVERT: D 236 GLU cc_start: 0.7255 (pt0) cc_final: 0.6931 (tt0) REVERT: D 256 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7074 (mt-10) REVERT: D 263 ASP cc_start: 0.7199 (t0) cc_final: 0.6687 (t0) REVERT: D 394 LYS cc_start: 0.7496 (mttm) cc_final: 0.7221 (mtmt) REVERT: E 228 ASN cc_start: 0.7407 (m-40) cc_final: 0.7134 (m-40) REVERT: E 295 GLU cc_start: 0.7965 (pm20) cc_final: 0.7583 (pm20) REVERT: E 339 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7895 (mtt180) REVERT: E 401 ASP cc_start: 0.7859 (p0) cc_final: 0.6966 (m-30) REVERT: E 419 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8537 (mmtt) REVERT: E 427 LYS cc_start: 0.7615 (ttmm) cc_final: 0.7405 (ttmm) REVERT: E 428 ASN cc_start: 0.8129 (t0) cc_final: 0.7900 (t0) REVERT: E 462 GLN cc_start: 0.8528 (mm110) cc_final: 0.8225 (mm-40) REVERT: F 228 ASN cc_start: 0.8698 (m110) cc_final: 0.7641 (m-40) REVERT: F 232 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.5642 (mp0) REVERT: H 19 VAL cc_start: 0.7809 (p) cc_final: 0.7576 (m) REVERT: L 18 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7256 (tpp80) outliers start: 45 outliers final: 41 residues processed: 197 average time/residue: 0.0950 time to fit residues: 26.4743 Evaluate side-chains 199 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 ILE 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 319 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 451 SER 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 456 LEU Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 394 LYS 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 56 ILE 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 71 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 48 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.161440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135946 restraints weight = 9580.357| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.25 r_work: 0.3547 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.8069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9115 Z= 0.130 Angle : 0.539 7.454 12365 Z= 0.291 Chirality : 0.044 0.153 1456 Planarity : 0.003 0.037 1547 Dihedral : 5.148 58.384 1226 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 4.41 % Allowed : 23.56 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.65 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.59 (0.24), residues: 1123 helix: 0.01 (0.34), residues: 241 sheet: -0.96 (0.29), residues: 325 loop : -1.55 (0.24), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.012 0.001 TYR L 55 PHE 0.011 0.001 PHE E 366 TRP 0.010 0.001 TRP L 41 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 9095) covalent geometry : angle 0.53698 (12325) SS BOND : bond 0.00248 ( 20) SS BOND : angle 0.93920 ( 40) hydrogen bonds : bond 0.02906 ( 324) hydrogen bonds : angle 4.81575 ( 831) ********************** 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 206 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 160 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 236 GLU cc_start: 0.7141 (pt0) cc_final: 0.6858 (tt0) REVERT: D 394 LYS cc_start: 0.7543 (mttm) cc_final: 0.7229 (mtmt) REVERT: E 228 ASN cc_start: 0.7226 (m-40) cc_final: 0.6953 (m-40) REVERT: E 295 GLU cc_start: 0.7988 (pm20) cc_final: 0.7618 (pm20) REVERT: E 339 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7851 (mtt180) REVERT: E 401 ASP cc_start: 0.7937 (p0) cc_final: 0.6977 (m-30) REVERT: E 419 LYS cc_start: 0.8770 (ttpp) cc_final: 0.8521 (mmtt) REVERT: E 427 LYS cc_start: 0.7658 (ttmm) cc_final: 0.7445 (ttmm) REVERT: E 428 ASN cc_start: 0.8107 (t0) cc_final: 0.7882 (t0) REVERT: E 462 GLN cc_start: 0.8514 (mm110) cc_final: 0.8201 (mm110) REVERT: L 18 ARG cc_start: 0.7580 (mtp-110) cc_final: 0.7261 (tpp80) outliers start: 46 outliers final: 45 residues processed: 196 average time/residue: 0.0921 time to fit residues: 25.7403 Evaluate side-chains 200 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 59 ILE 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 319 SER Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 451 SER 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 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 456 LEU Chi-restraints excluded: chain F residue 232 GLU Chi-restraints excluded: chain F residue 278 VAL Chi-restraints excluded: chain F residue 287 SER Chi-restraints excluded: chain F residue 309 ILE Chi-restraints excluded: chain F residue 311 THR Chi-restraints excluded: chain F residue 335 THR Chi-restraints excluded: chain F residue 393 CYS Chi-restraints excluded: chain F residue 394 LYS 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 56 ILE 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 71 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 94 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 0.4980 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 chunk 63 optimal weight: 0.8980 chunk 101 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 5 GLN ** 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 = 0.3963 r_free = 0.3963 target = 0.162972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137756 restraints weight = 9419.384| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.23 r_work: 0.3561 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.8114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9115 Z= 0.118 Angle : 0.535 7.446 12365 Z= 0.289 Chirality : 0.044 0.185 1456 Planarity : 0.003 0.033 1547 Dihedral : 5.081 58.991 1226 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.24), residues: 1123 helix: 0.04 (0.34), residues: 240 sheet: -0.90 (0.29), residues: 325 loop : -1.45 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 49 TYR 0.011 0.001 TYR L 55 PHE 0.010 0.001 PHE E 223 TRP 0.010 0.001 TRP L 41 HIS 0.003 0.001 HIS E 317 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9095) covalent geometry : angle 0.53382 (12325) SS BOND : bond 0.00238 ( 20) SS BOND : angle 0.89272 ( 40) hydrogen bonds : bond 0.02810 ( 324) hydrogen bonds : angle 4.76531 ( 831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.23 seconds wall clock time: 43 minutes 29.94 seconds (2609.94 seconds total)