Starting phenix.real_space_refine on Sat Apr 6 22:35:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/04_2024/7zoa_14845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/04_2024/7zoa_14845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/04_2024/7zoa_14845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/04_2024/7zoa_14845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/04_2024/7zoa_14845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/04_2024/7zoa_14845.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.073 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 44 5.16 5 C 5708 2.51 5 N 1570 2.21 5 O 1720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A ASP 314": "OD1" <-> "OD2" Residue "A PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "B ASP 314": "OD1" <-> "OD2" Residue "B PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9042 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Chain: "B" Number of atoms: 4422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4422 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 11, 'TRANS': 558} Chain: "D" Number of atoms: 198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 198 Unusual residues: {'BGC': 18} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 18 Time building chain proxies: 5.08, per 1000 atoms: 0.56 Number of scatterers: 9042 At special positions: 0 Unit cell: (72.775, 111.725, 135.3, 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 44 16.00 O 1720 8.00 N 1570 7.00 C 5708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 Links applied BETA1-2 " BGC D 1 " - " BGC D 2 " " BGC D 1 " - " BGC D 18 " " BGC D 2 " - " BGC D 3 " " BGC D 3 " - " BGC D 4 " " BGC D 4 " - " BGC D 5 " " BGC D 5 " - " BGC D 6 " " BGC D 6 " - " BGC D 7 " " BGC D 7 " - " BGC D 8 " " BGC D 8 " - " BGC D 9 " " BGC D 9 " - " BGC D 10 " " BGC D 10 " - " BGC D 11 " " BGC D 11 " - " BGC D 12 " " BGC D 12 " - " BGC D 13 " " BGC D 13 " - " BGC D 14 " " BGC D 14 " - " BGC D 15 " " BGC D 15 " - " BGC D 16 " " BGC D 16 " - " BGC D 17 " " BGC D 17 " - " BGC D 18 " Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 1.5 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2132 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 68.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 1 through 15 removed outlier: 3.660A pdb=" N LYS A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 47 removed outlier: 3.571A pdb=" N THR A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR A 23 " --> pdb=" O THR A 19 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 26 " --> pdb=" O ILE A 22 " (cutoff:3.500A) Proline residue: A 39 - end of helix Processing helix chain 'A' and resid 55 through 101 removed outlier: 3.808A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.701A pdb=" N HIS A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 136 removed outlier: 3.830A pdb=" N MET A 134 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN A 136 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 204 removed outlier: 3.747A pdb=" N VAL A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Proline residue: A 149 - end of helix removed outlier: 8.465A pdb=" N ARG A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 186 " --> pdb=" O ASP A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 236 through 268 removed outlier: 6.143A pdb=" N ASN A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ARG A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 267 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 318 removed outlier: 4.738A pdb=" N ALA A 304 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS A 305 " --> pdb=" O THR A 301 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP A 318 " --> pdb=" O ASP A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 403 through 410 Processing helix chain 'A' and resid 424 through 431 Processing helix chain 'A' and resid 439 through 448 removed outlier: 3.625A pdb=" N ALA A 443 " --> pdb=" O GLU A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.513A pdb=" N ALA A 456 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 473 through 489 Processing helix chain 'A' and resid 503 through 517 removed outlier: 3.609A pdb=" N LYS A 509 " --> pdb=" O GLU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 removed outlier: 3.567A pdb=" N SER A 535 " --> pdb=" O THR A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 570 removed outlier: 3.522A pdb=" N GLY A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 15 Processing helix chain 'B' and resid 17 through 47 removed outlier: 3.572A pdb=" N THR B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N THR B 23 " --> pdb=" O THR B 19 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N MET B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYS B 25 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 26 " --> pdb=" O ILE B 22 " (cutoff:3.500A) Proline residue: B 39 - end of helix Processing helix chain 'B' and resid 55 through 101 removed outlier: 3.809A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N THR B 101 " --> pdb=" O GLU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.701A pdb=" N HIS B 107 " --> pdb=" O PRO B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 136 removed outlier: 3.830A pdb=" N MET B 134 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN B 136 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 204 removed outlier: 3.747A pdb=" N VAL B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Proline residue: B 149 - end of helix removed outlier: 8.464A pdb=" N ARG B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA B 186 " --> pdb=" O ASP B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 236 through 243 Processing helix chain 'B' and resid 244 through 268 removed outlier: 3.852A pdb=" N LYS B 267 " --> pdb=" O TYR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 318 removed outlier: 4.739A pdb=" N ALA B 304 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N LYS B 305 " --> pdb=" O THR B 301 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASP B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 424 through 431 Processing helix chain 'B' and resid 439 through 448 removed outlier: 3.625A pdb=" N ALA B 443 " --> pdb=" O GLU B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 456 removed outlier: 3.513A pdb=" N ALA B 456 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 470 Processing helix chain 'B' and resid 473 through 489 Processing helix chain 'B' and resid 503 through 517 removed outlier: 3.608A pdb=" N LYS B 509 " --> pdb=" O GLU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.566A pdb=" N SER B 535 " --> pdb=" O THR B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 570 removed outlier: 3.521A pdb=" N GLY B 570 " --> pdb=" O LEU B 566 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 6.137A pdb=" N PHE A 337 " --> pdb=" O MET A 393 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N MET A 393 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASN A 339 " --> pdb=" O ARG A 391 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ARG A 391 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA A 389 " --> pdb=" O THR A 341 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 492 through 494 removed outlier: 7.165A pdb=" N LEU A 493 " --> pdb=" O PHE A 524 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ILE A 526 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL A 367 " --> pdb=" O LEU A 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 355 through 358 removed outlier: 6.137A pdb=" N PHE B 337 " --> pdb=" O MET B 393 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET B 393 " --> pdb=" O PHE B 337 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASN B 339 " --> pdb=" O ARG B 391 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N ARG B 391 " --> pdb=" O ASN B 339 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA B 389 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 492 through 494 removed outlier: 7.165A pdb=" N LEU B 493 " --> pdb=" O PHE B 524 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N ILE B 526 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL B 367 " --> pdb=" O LEU B 540 " (cutoff:3.500A) 588 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 4.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1466 1.30 - 1.43: 2382 1.43 - 1.56: 5256 1.56 - 1.69: 0 1.69 - 1.82: 86 Bond restraints: 9190 Sorted by residual: bond pdb=" C GLN A 184 " pdb=" O GLN A 184 " ideal model delta sigma weight residual 1.237 1.176 0.061 1.17e-02 7.31e+03 2.72e+01 bond pdb=" C2 BGC D 9 " pdb=" O2 BGC D 9 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C2 BGC D 10 " pdb=" O2 BGC D 10 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.50e+00 bond pdb=" C2 BGC D 5 " pdb=" O2 BGC D 5 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" C2 BGC D 6 " pdb=" O2 BGC D 6 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.98e+00 ... (remaining 9185 not shown) Histogram of bond angle deviations from ideal: 98.34 - 105.47: 114 105.47 - 112.60: 5058 112.60 - 119.73: 3019 119.73 - 126.86: 4169 126.86 - 133.99: 88 Bond angle restraints: 12448 Sorted by residual: angle pdb=" N SER B 243 " pdb=" CA SER B 243 " pdb=" CB SER B 243 " ideal model delta sigma weight residual 110.56 120.60 -10.04 1.38e+00 5.25e-01 5.29e+01 angle pdb=" C LEU B 241 " pdb=" N ALA B 242 " pdb=" CA ALA B 242 " ideal model delta sigma weight residual 120.29 111.86 8.43 1.42e+00 4.96e-01 3.53e+01 angle pdb=" CA ARG B 408 " pdb=" CB ARG B 408 " pdb=" CG ARG B 408 " ideal model delta sigma weight residual 114.10 103.69 10.41 2.00e+00 2.50e-01 2.71e+01 angle pdb=" CA ARG A 408 " pdb=" CB ARG A 408 " pdb=" CG ARG A 408 " ideal model delta sigma weight residual 114.10 103.70 10.40 2.00e+00 2.50e-01 2.71e+01 angle pdb=" C ALA B 242 " pdb=" N SER B 243 " pdb=" CA SER B 243 " ideal model delta sigma weight residual 122.65 114.37 8.28 1.66e+00 3.63e-01 2.49e+01 ... (remaining 12443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.70: 5201 24.70 - 49.41: 337 49.41 - 74.11: 69 74.11 - 98.81: 68 98.81 - 123.52: 55 Dihedral angle restraints: 5730 sinusoidal: 2440 harmonic: 3290 Sorted by residual: dihedral pdb=" N SER B 243 " pdb=" C SER B 243 " pdb=" CA SER B 243 " pdb=" CB SER B 243 " ideal model delta harmonic sigma weight residual 122.80 148.62 -25.82 0 2.50e+00 1.60e-01 1.07e+02 dihedral pdb=" C SER B 243 " pdb=" N SER B 243 " pdb=" CA SER B 243 " pdb=" CB SER B 243 " ideal model delta harmonic sigma weight residual -122.60 -147.84 25.24 0 2.50e+00 1.60e-01 1.02e+02 dihedral pdb=" C3 BGC D 18 " pdb=" C1 BGC D 18 " pdb=" C2 BGC D 18 " pdb=" O5 BGC D 18 " ideal model delta sinusoidal sigma weight residual -58.08 65.44 -123.52 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 5727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.302: 1516 0.302 - 0.605: 5 0.605 - 0.907: 1 0.907 - 1.210: 1 1.210 - 1.512: 1 Chirality restraints: 1524 Sorted by residual: chirality pdb=" C1 BGC D 7 " pdb=" O2 BGC D 6 " pdb=" C2 BGC D 7 " pdb=" O5 BGC D 7 " both_signs ideal model delta sigma weight residual False -2.40 -0.89 -1.51 2.00e-02 2.50e+03 5.72e+03 chirality pdb=" C1 BGC D 3 " pdb=" O2 BGC D 2 " pdb=" C2 BGC D 3 " pdb=" O5 BGC D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.58 -0.82 2.00e-02 2.50e+03 1.68e+03 chirality pdb=" C1 BGC D 1 " pdb=" C2 BGC D 1 " pdb=" O5 BGC D 1 " pdb=" O2 BGC D 18 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-02 2.50e+03 5.70e+02 ... (remaining 1521 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 241 " 0.018 2.00e-02 2.50e+03 3.61e-02 1.30e+01 pdb=" C LEU B 241 " -0.062 2.00e-02 2.50e+03 pdb=" O LEU B 241 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA B 242 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 187 " 0.013 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C VAL A 187 " -0.043 2.00e-02 2.50e+03 pdb=" O VAL A 187 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 188 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " -0.134 9.50e-02 1.11e+02 6.06e-02 3.32e+00 pdb=" NE ARG A 408 " 0.002 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " 0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " -0.011 2.00e-02 2.50e+03 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 399 2.72 - 3.27: 9600 3.27 - 3.81: 14913 3.81 - 4.36: 15850 4.36 - 4.90: 27760 Nonbonded interactions: 68522 Sorted by model distance: nonbonded pdb=" ND2 ASN A 422 " pdb=" OE2 GLU B 196 " model vdw 2.176 2.520 nonbonded pdb=" NE2 GLN A 478 " pdb=" O ALA A 498 " model vdw 2.181 2.520 nonbonded pdb=" NE2 GLN B 478 " pdb=" O ALA B 498 " model vdw 2.181 2.520 nonbonded pdb=" O VAL A 431 " pdb=" NH1 ARG B 213 " model vdw 2.194 2.520 nonbonded pdb=" O ARG A 433 " pdb=" NH2 ARG B 213 " model vdw 2.209 2.520 ... (remaining 68517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.680 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: 3.350 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.930 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 0.065 9190 Z= 0.277 Angle : 0.811 10.411 12448 Z= 0.422 Chirality : 0.073 1.512 1524 Planarity : 0.004 0.061 1560 Dihedral : 24.010 123.517 3598 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.26 % Favored : 96.39 % Rotamer: Outliers : 0.11 % Allowed : 0.00 % Favored : 99.89 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1136 helix: 1.98 (0.20), residues: 708 sheet: 0.38 (0.66), residues: 78 loop : -2.35 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 62 HIS 0.006 0.001 HIS B 191 PHE 0.018 0.001 PHE B 421 TYR 0.017 0.001 TYR A 96 ARG 0.018 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LYS cc_start: 0.7015 (ptpp) cc_final: 0.6551 (mmtt) REVERT: A 61 MET cc_start: 0.7946 (ppp) cc_final: 0.7279 (ppp) REVERT: A 201 THR cc_start: 0.8335 (t) cc_final: 0.7995 (t) REVERT: B 12 GLN cc_start: 0.8581 (tt0) cc_final: 0.8381 (tp40) REVERT: B 171 MET cc_start: 0.8132 (mtp) cc_final: 0.7474 (ttp) REVERT: B 248 MET cc_start: 0.8838 (mmm) cc_final: 0.8602 (mmm) REVERT: B 298 GLN cc_start: 0.8743 (tt0) cc_final: 0.8496 (mm-40) REVERT: B 394 ILE cc_start: 0.7766 (tp) cc_final: 0.7361 (mm) REVERT: B 546 HIS cc_start: 0.7192 (m-70) cc_final: 0.6914 (m-70) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1901 time to fit residues: 63.4875 Evaluate side-chains 163 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 0.0010 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 212 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9190 Z= 0.379 Angle : 0.867 8.801 12448 Z= 0.414 Chirality : 0.048 0.348 1524 Planarity : 0.006 0.095 1560 Dihedral : 20.618 107.727 1580 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.79 % Favored : 95.86 % Rotamer: Outliers : 2.35 % Allowed : 16.31 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.25), residues: 1136 helix: 1.37 (0.19), residues: 730 sheet: 0.59 (0.62), residues: 78 loop : -2.18 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 238 HIS 0.010 0.002 HIS A 197 PHE 0.025 0.002 PHE B 133 TYR 0.020 0.002 TYR B 461 ARG 0.010 0.001 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8377 (ppp) cc_final: 0.7977 (ppp) REVERT: A 71 MET cc_start: 0.8203 (mmm) cc_final: 0.7847 (tpt) REVERT: A 92 MET cc_start: 0.8747 (tpp) cc_final: 0.8486 (tpp) REVERT: A 201 THR cc_start: 0.9136 (t) cc_final: 0.8774 (t) REVERT: A 236 LEU cc_start: 0.9231 (mt) cc_final: 0.8498 (pt) REVERT: A 243 SER cc_start: 0.9070 (p) cc_final: 0.8826 (p) REVERT: B 68 PHE cc_start: 0.8518 (t80) cc_final: 0.7979 (t80) REVERT: B 96 TYR cc_start: 0.8423 (t80) cc_final: 0.8192 (t80) REVERT: B 130 TRP cc_start: 0.9031 (m-10) cc_final: 0.8397 (m-90) REVERT: B 152 MET cc_start: 0.8187 (ttp) cc_final: 0.7335 (tpt) REVERT: B 171 MET cc_start: 0.8664 (mtp) cc_final: 0.7974 (ttp) REVERT: B 223 ASP cc_start: 0.8642 (m-30) cc_final: 0.8101 (t0) REVERT: B 248 MET cc_start: 0.9154 (mmm) cc_final: 0.8885 (mmm) REVERT: B 298 GLN cc_start: 0.8838 (tt0) cc_final: 0.8505 (mm-40) REVERT: B 461 TYR cc_start: 0.7092 (p90) cc_final: 0.6831 (p90) REVERT: B 543 ASP cc_start: 0.8295 (p0) cc_final: 0.7615 (p0) outliers start: 22 outliers final: 19 residues processed: 185 average time/residue: 0.1769 time to fit residues: 47.6436 Evaluate side-chains 167 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 13 TYR Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 453 PHE Chi-restraints excluded: chain B residue 463 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN B 438 HIS B 451 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9190 Z= 0.243 Angle : 0.728 8.789 12448 Z= 0.334 Chirality : 0.044 0.249 1524 Planarity : 0.004 0.059 1560 Dihedral : 17.295 106.840 1580 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.05 % Favored : 95.60 % Rotamer: Outliers : 3.94 % Allowed : 20.04 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1136 helix: 1.73 (0.19), residues: 730 sheet: 0.82 (0.62), residues: 78 loop : -2.15 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 238 HIS 0.011 0.001 HIS B 451 PHE 0.017 0.002 PHE B 264 TYR 0.022 0.002 TYR B 342 ARG 0.006 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 163 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9050 (mt) cc_final: 0.8420 (mt) REVERT: A 61 MET cc_start: 0.8394 (ppp) cc_final: 0.8057 (ppp) REVERT: A 71 MET cc_start: 0.8296 (mmm) cc_final: 0.7798 (tpt) REVERT: A 92 MET cc_start: 0.8732 (tpp) cc_final: 0.8307 (tpp) REVERT: A 155 ASP cc_start: 0.7525 (t70) cc_final: 0.5841 (m-30) REVERT: A 201 THR cc_start: 0.9100 (t) cc_final: 0.8193 (t) REVERT: A 236 LEU cc_start: 0.9269 (mt) cc_final: 0.8626 (pt) REVERT: A 243 SER cc_start: 0.9021 (p) cc_final: 0.8814 (p) REVERT: B 68 PHE cc_start: 0.8519 (t80) cc_final: 0.8316 (t80) REVERT: B 71 MET cc_start: 0.7695 (mmp) cc_final: 0.6755 (mtt) REVERT: B 97 GLU cc_start: 0.8766 (tp30) cc_final: 0.8324 (pt0) REVERT: B 130 TRP cc_start: 0.8996 (m-10) cc_final: 0.8489 (m-90) REVERT: B 152 MET cc_start: 0.8275 (ttp) cc_final: 0.7249 (tpt) REVERT: B 171 MET cc_start: 0.8637 (mtp) cc_final: 0.7983 (ttp) REVERT: B 223 ASP cc_start: 0.8580 (m-30) cc_final: 0.8068 (t0) REVERT: B 298 GLN cc_start: 0.8830 (tt0) cc_final: 0.8471 (mm-40) REVERT: B 342 TYR cc_start: 0.8035 (t80) cc_final: 0.7528 (t80) REVERT: B 461 TYR cc_start: 0.7152 (p90) cc_final: 0.6784 (p90) REVERT: B 462 ASP cc_start: 0.8658 (m-30) cc_final: 0.8405 (m-30) outliers start: 37 outliers final: 27 residues processed: 185 average time/residue: 0.1779 time to fit residues: 48.4355 Evaluate side-chains 175 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 420 LEU Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 110 optimal weight: 20.0000 chunk 54 optimal weight: 0.3980 chunk 98 optimal weight: 0.0980 chunk 29 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 320 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9190 Z= 0.230 Angle : 0.687 8.815 12448 Z= 0.315 Chirality : 0.043 0.237 1524 Planarity : 0.003 0.053 1560 Dihedral : 15.534 104.080 1580 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.35 % Favored : 96.30 % Rotamer: Outliers : 4.37 % Allowed : 21.00 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1136 helix: 1.83 (0.19), residues: 734 sheet: 0.84 (0.62), residues: 78 loop : -1.90 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 238 HIS 0.007 0.001 HIS B 451 PHE 0.015 0.001 PHE B 453 TYR 0.014 0.002 TYR A 461 ARG 0.008 0.001 ARG A 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 150 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9053 (mt) cc_final: 0.8358 (mt) REVERT: A 61 MET cc_start: 0.8435 (ppp) cc_final: 0.8109 (ppp) REVERT: A 71 MET cc_start: 0.8325 (mmm) cc_final: 0.7802 (tpt) REVERT: A 92 MET cc_start: 0.8669 (tpp) cc_final: 0.8313 (tpp) REVERT: A 155 ASP cc_start: 0.7548 (t70) cc_final: 0.5880 (m-30) REVERT: A 156 MET cc_start: 0.6076 (pmm) cc_final: 0.5791 (pmm) REVERT: A 243 SER cc_start: 0.9050 (p) cc_final: 0.8843 (p) REVERT: B 24 MET cc_start: 0.8405 (tpp) cc_final: 0.8104 (tpp) REVERT: B 130 TRP cc_start: 0.9043 (m-10) cc_final: 0.8833 (m-10) REVERT: B 152 MET cc_start: 0.8318 (ttp) cc_final: 0.7224 (tpt) REVERT: B 171 MET cc_start: 0.8659 (mtp) cc_final: 0.8001 (ttp) REVERT: B 223 ASP cc_start: 0.8652 (m-30) cc_final: 0.8110 (t0) REVERT: B 298 GLN cc_start: 0.8880 (tt0) cc_final: 0.8583 (mm-40) REVERT: B 320 GLN cc_start: 0.5526 (OUTLIER) cc_final: 0.5307 (tm-30) REVERT: B 342 TYR cc_start: 0.8056 (t80) cc_final: 0.7527 (t80) REVERT: B 461 TYR cc_start: 0.7093 (p90) cc_final: 0.6649 (p90) REVERT: B 462 ASP cc_start: 0.8715 (m-30) cc_final: 0.8386 (m-30) outliers start: 41 outliers final: 30 residues processed: 178 average time/residue: 0.1747 time to fit residues: 45.6211 Evaluate side-chains 172 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 237 ASN Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 320 GLN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.1980 chunk 62 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 94 optimal weight: 20.0000 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9190 Z= 0.179 Angle : 0.690 10.772 12448 Z= 0.308 Chirality : 0.042 0.218 1524 Planarity : 0.003 0.023 1560 Dihedral : 14.934 103.425 1580 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.87 % Favored : 95.77 % Rotamer: Outliers : 4.26 % Allowed : 23.13 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.26), residues: 1136 helix: 1.98 (0.19), residues: 736 sheet: 0.76 (0.62), residues: 80 loop : -1.86 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 238 HIS 0.004 0.001 HIS B 191 PHE 0.010 0.001 PHE A 68 TYR 0.011 0.001 TYR B 461 ARG 0.011 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9043 (mt) cc_final: 0.8374 (mt) REVERT: A 61 MET cc_start: 0.8408 (ppp) cc_final: 0.8098 (ppp) REVERT: A 71 MET cc_start: 0.8325 (mmm) cc_final: 0.7767 (tpt) REVERT: A 243 SER cc_start: 0.9061 (p) cc_final: 0.8845 (p) REVERT: B 24 MET cc_start: 0.8258 (tpp) cc_final: 0.7996 (tpp) REVERT: B 68 PHE cc_start: 0.8451 (t80) cc_final: 0.7936 (t80) REVERT: B 97 GLU cc_start: 0.8763 (tp30) cc_final: 0.8317 (pt0) REVERT: B 130 TRP cc_start: 0.8987 (m-10) cc_final: 0.8761 (m-10) REVERT: B 152 MET cc_start: 0.8279 (ttp) cc_final: 0.7225 (tpt) REVERT: B 171 MET cc_start: 0.8647 (mtp) cc_final: 0.7789 (tmm) REVERT: B 223 ASP cc_start: 0.8621 (m-30) cc_final: 0.8119 (t0) REVERT: B 248 MET cc_start: 0.8819 (tpp) cc_final: 0.8612 (tpp) REVERT: B 298 GLN cc_start: 0.8922 (tt0) cc_final: 0.8590 (mm-40) REVERT: B 311 GLN cc_start: 0.8914 (tp40) cc_final: 0.8509 (tm-30) REVERT: B 342 TYR cc_start: 0.8114 (t80) cc_final: 0.7520 (t80) REVERT: B 461 TYR cc_start: 0.7213 (p90) cc_final: 0.6741 (p90) REVERT: B 462 ASP cc_start: 0.8713 (m-30) cc_final: 0.8365 (m-30) outliers start: 40 outliers final: 23 residues processed: 177 average time/residue: 0.1779 time to fit residues: 45.5235 Evaluate side-chains 167 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 478 GLN Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 0.1980 chunk 91 optimal weight: 0.0170 chunk 51 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9190 Z= 0.171 Angle : 0.699 10.545 12448 Z= 0.310 Chirality : 0.042 0.212 1524 Planarity : 0.003 0.025 1560 Dihedral : 14.365 101.958 1580 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.96 % Favored : 95.77 % Rotamer: Outliers : 3.30 % Allowed : 24.52 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.26), residues: 1136 helix: 2.12 (0.19), residues: 732 sheet: 0.81 (0.62), residues: 80 loop : -1.79 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 238 HIS 0.005 0.001 HIS B 191 PHE 0.009 0.001 PHE A 68 TYR 0.025 0.001 TYR A 96 ARG 0.012 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LEU cc_start: 0.9028 (mt) cc_final: 0.8664 (mt) REVERT: A 61 MET cc_start: 0.8372 (ppp) cc_final: 0.8142 (ppp) REVERT: A 243 SER cc_start: 0.9044 (p) cc_final: 0.8797 (p) REVERT: A 542 MET cc_start: 0.3569 (tpt) cc_final: 0.3334 (tpt) REVERT: B 11 MET cc_start: 0.8609 (tpp) cc_final: 0.8370 (mmp) REVERT: B 24 MET cc_start: 0.8288 (tpp) cc_final: 0.8029 (tpp) REVERT: B 97 GLU cc_start: 0.8714 (tp30) cc_final: 0.8108 (pt0) REVERT: B 152 MET cc_start: 0.8275 (ttp) cc_final: 0.7237 (tpt) REVERT: B 171 MET cc_start: 0.8654 (mtp) cc_final: 0.7954 (ttp) REVERT: B 223 ASP cc_start: 0.8612 (m-30) cc_final: 0.8108 (t0) REVERT: B 298 GLN cc_start: 0.8915 (tt0) cc_final: 0.8584 (mm-40) REVERT: B 342 TYR cc_start: 0.8049 (t80) cc_final: 0.7387 (t80) REVERT: B 461 TYR cc_start: 0.7242 (p90) cc_final: 0.6864 (p90) REVERT: B 462 ASP cc_start: 0.8717 (m-30) cc_final: 0.8352 (m-30) outliers start: 31 outliers final: 24 residues processed: 176 average time/residue: 0.1725 time to fit residues: 44.9140 Evaluate side-chains 171 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 147 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 66 optimal weight: 0.4980 chunk 50 optimal weight: 0.0020 chunk 67 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9190 Z= 0.175 Angle : 0.689 11.209 12448 Z= 0.309 Chirality : 0.041 0.200 1524 Planarity : 0.003 0.028 1560 Dihedral : 14.059 100.751 1580 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.96 % Favored : 95.77 % Rotamer: Outliers : 3.09 % Allowed : 24.73 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.26), residues: 1136 helix: 2.14 (0.19), residues: 732 sheet: 0.74 (0.62), residues: 80 loop : -1.72 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 130 HIS 0.004 0.001 HIS A 191 PHE 0.009 0.001 PHE A 68 TYR 0.023 0.001 TYR A 96 ARG 0.007 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 145 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 MET cc_start: 0.8522 (tpp) cc_final: 0.8247 (tpp) REVERT: A 177 MET cc_start: 0.8307 (tpp) cc_final: 0.8024 (tmm) REVERT: A 243 SER cc_start: 0.9052 (p) cc_final: 0.8787 (p) REVERT: A 542 MET cc_start: 0.3421 (tpt) cc_final: 0.3166 (tpt) REVERT: B 11 MET cc_start: 0.8562 (tpp) cc_final: 0.8310 (mmp) REVERT: B 68 PHE cc_start: 0.8491 (t80) cc_final: 0.7917 (t80) REVERT: B 71 MET cc_start: 0.7791 (mmp) cc_final: 0.6665 (mtt) REVERT: B 97 GLU cc_start: 0.8690 (tp30) cc_final: 0.8109 (pt0) REVERT: B 152 MET cc_start: 0.8297 (ttp) cc_final: 0.7257 (tpt) REVERT: B 171 MET cc_start: 0.8709 (mtp) cc_final: 0.7965 (ttp) REVERT: B 223 ASP cc_start: 0.8631 (m-30) cc_final: 0.8171 (t0) REVERT: B 298 GLN cc_start: 0.8921 (tt0) cc_final: 0.8598 (mm-40) REVERT: B 342 TYR cc_start: 0.7999 (t80) cc_final: 0.7260 (t80) REVERT: B 461 TYR cc_start: 0.7151 (p90) cc_final: 0.6767 (p90) outliers start: 29 outliers final: 26 residues processed: 168 average time/residue: 0.1706 time to fit residues: 42.4369 Evaluate side-chains 166 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 140 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 192 HIS Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 10 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.4417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9190 Z= 0.177 Angle : 0.695 10.252 12448 Z= 0.309 Chirality : 0.042 0.206 1524 Planarity : 0.003 0.026 1560 Dihedral : 13.732 99.037 1580 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.96 % Favored : 95.77 % Rotamer: Outliers : 3.20 % Allowed : 25.27 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1136 helix: 2.19 (0.19), residues: 732 sheet: 0.77 (0.62), residues: 80 loop : -1.66 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 130 HIS 0.004 0.001 HIS A 191 PHE 0.008 0.001 PHE A 68 TYR 0.020 0.001 TYR A 96 ARG 0.006 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.8298 (tpp) cc_final: 0.8011 (tmm) REVERT: A 243 SER cc_start: 0.9003 (p) cc_final: 0.8738 (p) REVERT: A 542 MET cc_start: 0.3288 (tpt) cc_final: 0.3050 (tpt) REVERT: B 11 MET cc_start: 0.8563 (tpp) cc_final: 0.8313 (mmp) REVERT: B 68 PHE cc_start: 0.8504 (t80) cc_final: 0.7929 (t80) REVERT: B 71 MET cc_start: 0.7832 (mmp) cc_final: 0.6662 (mtt) REVERT: B 92 MET cc_start: 0.8945 (tpp) cc_final: 0.8441 (tpp) REVERT: B 97 GLU cc_start: 0.8685 (tp30) cc_final: 0.8040 (pt0) REVERT: B 152 MET cc_start: 0.8292 (ttp) cc_final: 0.7247 (tpt) REVERT: B 171 MET cc_start: 0.8725 (mtp) cc_final: 0.8000 (ttp) REVERT: B 223 ASP cc_start: 0.8638 (m-30) cc_final: 0.8184 (t0) REVERT: B 239 TRP cc_start: 0.7886 (m100) cc_final: 0.7656 (m100) REVERT: B 298 GLN cc_start: 0.8916 (tt0) cc_final: 0.8627 (mm-40) REVERT: B 342 TYR cc_start: 0.8001 (t80) cc_final: 0.7320 (t80) REVERT: B 461 TYR cc_start: 0.7165 (p90) cc_final: 0.6734 (p90) outliers start: 30 outliers final: 27 residues processed: 168 average time/residue: 0.1738 time to fit residues: 43.2457 Evaluate side-chains 166 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 67 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9190 Z= 0.190 Angle : 0.699 11.405 12448 Z= 0.313 Chirality : 0.042 0.244 1524 Planarity : 0.003 0.023 1560 Dihedral : 13.540 97.774 1580 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.04 % Rotamer: Outliers : 3.30 % Allowed : 25.59 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1136 helix: 2.19 (0.19), residues: 732 sheet: 0.73 (0.61), residues: 80 loop : -1.64 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 130 HIS 0.004 0.001 HIS A 191 PHE 0.015 0.001 PHE B 453 TYR 0.009 0.001 TYR B 461 ARG 0.009 0.000 ARG B 408 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8568 (ppp) cc_final: 0.8233 (ppp) REVERT: A 177 MET cc_start: 0.8351 (tpp) cc_final: 0.8049 (tmm) REVERT: A 243 SER cc_start: 0.9049 (p) cc_final: 0.8776 (p) REVERT: A 542 MET cc_start: 0.3372 (tpt) cc_final: 0.3129 (tpt) REVERT: B 11 MET cc_start: 0.8560 (tpp) cc_final: 0.8334 (mmp) REVERT: B 71 MET cc_start: 0.7832 (mmp) cc_final: 0.6663 (mtt) REVERT: B 97 GLU cc_start: 0.8685 (tp30) cc_final: 0.8046 (pt0) REVERT: B 152 MET cc_start: 0.8332 (ttp) cc_final: 0.7277 (tpt) REVERT: B 171 MET cc_start: 0.8741 (mtp) cc_final: 0.8007 (ttp) REVERT: B 223 ASP cc_start: 0.8594 (m-30) cc_final: 0.8139 (t0) REVERT: B 298 GLN cc_start: 0.8914 (tt0) cc_final: 0.8625 (mm-40) REVERT: B 342 TYR cc_start: 0.8035 (t80) cc_final: 0.7344 (t80) REVERT: B 461 TYR cc_start: 0.7054 (p90) cc_final: 0.6564 (p90) outliers start: 31 outliers final: 28 residues processed: 160 average time/residue: 0.2011 time to fit residues: 47.9740 Evaluate side-chains 166 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 138 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9190 Z= 0.189 Angle : 0.702 11.338 12448 Z= 0.314 Chirality : 0.042 0.251 1524 Planarity : 0.003 0.032 1560 Dihedral : 13.276 96.162 1580 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.70 % Favored : 96.04 % Rotamer: Outliers : 3.30 % Allowed : 26.01 % Favored : 70.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1136 helix: 2.21 (0.19), residues: 732 sheet: 0.72 (0.61), residues: 80 loop : -1.57 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 130 HIS 0.004 0.001 HIS A 191 PHE 0.025 0.001 PHE B 68 TYR 0.009 0.001 TYR B 461 ARG 0.009 0.000 ARG B 408 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 61 MET cc_start: 0.8535 (ppp) cc_final: 0.8215 (ppp) REVERT: A 177 MET cc_start: 0.8363 (tpp) cc_final: 0.8061 (tmm) REVERT: A 243 SER cc_start: 0.9056 (p) cc_final: 0.8786 (p) REVERT: A 542 MET cc_start: 0.3231 (tpt) cc_final: 0.2990 (tpt) REVERT: B 11 MET cc_start: 0.8569 (tpp) cc_final: 0.8350 (mmp) REVERT: B 68 PHE cc_start: 0.8535 (t80) cc_final: 0.8019 (t80) REVERT: B 71 MET cc_start: 0.7921 (mmp) cc_final: 0.6786 (mtt) REVERT: B 96 TYR cc_start: 0.8493 (t80) cc_final: 0.8264 (t80) REVERT: B 97 GLU cc_start: 0.8666 (tp30) cc_final: 0.8056 (pt0) REVERT: B 152 MET cc_start: 0.8369 (ttp) cc_final: 0.7153 (tpp) REVERT: B 171 MET cc_start: 0.8736 (mtp) cc_final: 0.7995 (ttp) REVERT: B 223 ASP cc_start: 0.8604 (m-30) cc_final: 0.8132 (t0) REVERT: B 298 GLN cc_start: 0.8905 (tt0) cc_final: 0.8626 (mm-40) REVERT: B 342 TYR cc_start: 0.7915 (t80) cc_final: 0.7211 (t80) REVERT: B 461 TYR cc_start: 0.6931 (p90) cc_final: 0.6477 (p90) outliers start: 31 outliers final: 28 residues processed: 168 average time/residue: 0.1692 time to fit residues: 42.5761 Evaluate side-chains 170 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 100 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain B residue 274 ASP Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 433 ARG Chi-restraints excluded: chain B residue 437 THR Chi-restraints excluded: chain B residue 463 THR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 525 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 93 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.147730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.108936 restraints weight = 22083.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.112152 restraints weight = 12841.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.114337 restraints weight = 8854.438| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9190 Z= 0.187 Angle : 0.702 11.234 12448 Z= 0.314 Chirality : 0.042 0.251 1524 Planarity : 0.003 0.022 1560 Dihedral : 13.116 95.169 1580 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.61 % Favored : 96.13 % Rotamer: Outliers : 2.99 % Allowed : 26.55 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1136 helix: 2.16 (0.19), residues: 738 sheet: 0.63 (0.61), residues: 80 loop : -1.68 (0.36), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 130 HIS 0.004 0.001 HIS A 191 PHE 0.020 0.001 PHE B 68 TYR 0.010 0.001 TYR A 342 ARG 0.008 0.000 ARG B 408 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.10 seconds wall clock time: 34 minutes 9.96 seconds (2049.96 seconds total)