Starting phenix.real_space_refine (version: dev) on Sun Feb 19 00:08:33 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/02_2023/7zoa_14845.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/02_2023/7zoa_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_14845/02_2023/7zoa_14845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/02_2023/7zoa_14845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/02_2023/7zoa_14845.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zoa_14845/02_2023/7zoa_14845.pdb" } resolution = 4.0 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 ------------------------------------------------------------------------------- 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 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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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 chiralities: 18 Time building chain proxies: 5.49, per 1000 atoms: 0.61 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: 3.93 Conformation dependent library (CDL) restraints added in 1.4 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: 0.41 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: 3.59 Time building geometry restraints manager: 4.22 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 1.423 1.471 -0.048 1.60e-02 3.91e+03 9.01e+00 bond pdb=" C2 BGC D 10 " pdb=" O2 BGC D 10 " ideal model delta sigma weight residual 1.423 1.468 -0.045 1.60e-02 3.91e+03 7.79e+00 bond pdb=" C1 BGC D 9 " pdb=" C2 BGC D 9 " ideal model delta sigma weight residual 1.524 1.559 -0.035 1.30e-02 5.92e+03 7.33e+00 bond pdb=" C1 BGC D 10 " pdb=" C2 BGC D 10 " ideal model delta sigma weight residual 1.524 1.557 -0.033 1.30e-02 5.92e+03 6.54e+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=" C1 BGC D 6 " pdb=" C2 BGC D 6 " pdb=" O2 BGC D 6 " ideal model delta sigma weight residual 109.48 120.33 -10.85 1.94e+00 2.67e-01 3.14e+01 angle pdb=" C3 BGC D 14 " pdb=" C2 BGC D 14 " pdb=" O2 BGC D 14 " ideal model delta sigma weight residual 110.01 99.78 10.23 1.93e+00 2.68e-01 2.81e+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 ... (remaining 12443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 4832 17.35 - 34.70: 444 34.70 - 52.04: 90 52.04 - 69.39: 14 69.39 - 86.74: 8 Dihedral angle restraints: 5388 sinusoidal: 2098 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=" CA HIS A 438 " pdb=" C HIS A 438 " pdb=" N GLU A 439 " pdb=" CA GLU A 439 " ideal model delta harmonic sigma weight residual 180.00 162.78 17.22 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5385 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 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. 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: 0.650 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: 4.000 Check model and map are aligned: 0.150 Process input model: 27.630 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 0.061 9190 Z= 0.232 Angle : 0.816 10.851 12448 Z= 0.476 Chirality : 0.073 1.512 1524 Planarity : 0.004 0.061 1560 Dihedral : 13.969 86.738 3256 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 % 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 *********************** 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 : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1947 time to fit residues: 65.3521 Evaluate side-chains 158 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.054 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3834 ------------------------------------------------------------------------------- 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: 0.0000 chunk 86 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 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: 2.1790 ------------------------------------------------------------------------------- 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 283 GLN ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7769 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 9190 Z= 0.333 Angle : 0.709 8.562 12448 Z= 0.374 Chirality : 0.043 0.250 1524 Planarity : 0.005 0.079 1560 Dihedral : 3.724 19.581 1238 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.87 % Favored : 95.77 % Rotamer Outliers : 2.45 % 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: 0.72 (0.26), residues: 1136 helix: 1.58 (0.19), residues: 726 sheet: 0.57 (0.62), residues: 78 loop : -2.12 (0.33), residues: 332 *********************** 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 194 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 188 average time/residue: 0.1923 time to fit residues: 53.1453 Evaluate side-chains 161 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1379 time to fit residues: 5.3390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 70 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 35 optimal weight: 30.0000 chunk 83 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS B 451 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9190 Z= 0.255 Angle : 0.642 8.928 12448 Z= 0.330 Chirality : 0.042 0.250 1524 Planarity : 0.004 0.063 1560 Dihedral : 3.729 17.171 1238 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.14 % Favored : 95.51 % Rotamer Outliers : 2.56 % 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: 0.96 (0.26), residues: 1136 helix: 1.74 (0.19), residues: 730 sheet: 0.73 (0.61), residues: 78 loop : -2.04 (0.34), residues: 328 *********************** 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 188 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 174 average time/residue: 0.1993 time to fit residues: 50.1412 Evaluate side-chains 151 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0876 time to fit residues: 3.5973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 69 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9190 Z= 0.226 Angle : 0.626 9.965 12448 Z= 0.319 Chirality : 0.042 0.248 1524 Planarity : 0.003 0.051 1560 Dihedral : 3.725 18.568 1238 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.79 % Favored : 95.86 % Rotamer Outliers : 2.45 % 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: 1.05 (0.26), residues: 1136 helix: 1.67 (0.19), residues: 746 sheet: 0.73 (0.60), residues: 78 loop : -1.77 (0.36), residues: 312 *********************** 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 175 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 152 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 15 residues processed: 164 average time/residue: 0.1806 time to fit residues: 43.7930 Evaluate side-chains 156 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 141 time to evaluate : 1.174 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.0902 time to fit residues: 3.8961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.0980 chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 0.0270 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 56 optimal weight: 0.0040 chunk 98 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.4050 ------------------------------------------------------------------------------- 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 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9190 Z= 0.178 Angle : 0.620 10.630 12448 Z= 0.307 Chirality : 0.041 0.244 1524 Planarity : 0.003 0.025 1560 Dihedral : 3.653 17.442 1238 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.49 % Favored : 95.16 % Rotamer Outliers : 2.35 % 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: 1.24 (0.26), residues: 1136 helix: 1.93 (0.19), residues: 728 sheet: 0.77 (0.62), residues: 78 loop : -1.81 (0.35), residues: 330 *********************** 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 175 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 153 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 166 average time/residue: 0.1724 time to fit residues: 42.6310 Evaluate side-chains 149 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1442 time to fit residues: 3.3662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 8.9990 chunk 99 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 110 optimal weight: 9.9990 chunk 91 optimal weight: 0.0070 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 451 HIS B 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9190 Z= 0.184 Angle : 0.635 10.962 12448 Z= 0.309 Chirality : 0.041 0.225 1524 Planarity : 0.003 0.023 1560 Dihedral : 3.595 16.936 1238 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.31 % Favored : 95.33 % Rotamer Outliers : 1.39 % 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: 1.38 (0.26), residues: 1136 helix: 2.01 (0.19), residues: 732 sheet: 0.66 (0.62), residues: 80 loop : -1.67 (0.36), residues: 324 *********************** 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 162 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 154 average time/residue: 0.1826 time to fit residues: 41.2471 Evaluate side-chains 151 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0959 time to fit residues: 3.1874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 92 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 109 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 GLN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 9190 Z= 0.277 Angle : 0.673 10.212 12448 Z= 0.338 Chirality : 0.042 0.186 1524 Planarity : 0.004 0.037 1560 Dihedral : 3.815 19.787 1238 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.35 % Allowed : 4.23 % Favored : 95.42 % Rotamer Outliers : 1.60 % 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: 1.22 (0.26), residues: 1136 helix: 1.81 (0.19), residues: 736 sheet: 0.66 (0.61), residues: 80 loop : -1.58 (0.36), residues: 320 *********************** 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 170 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 155 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 164 average time/residue: 0.1656 time to fit residues: 40.5114 Evaluate side-chains 153 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 146 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0881 time to fit residues: 2.5535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 54 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 9190 Z= 0.198 Angle : 0.652 10.571 12448 Z= 0.318 Chirality : 0.042 0.250 1524 Planarity : 0.003 0.022 1560 Dihedral : 3.737 19.554 1238 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer Outliers : 0.75 % 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: 1.36 (0.26), residues: 1136 helix: 1.83 (0.19), residues: 750 sheet: 0.64 (0.61), residues: 80 loop : -1.39 (0.37), residues: 306 *********************** 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 154 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 150 average time/residue: 0.1608 time to fit residues: 36.8432 Evaluate side-chains 145 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 142 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0874 time to fit residues: 1.9537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0970 chunk 105 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 0.7578 ------------------------------------------------------------------------------- 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 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 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: 0.7858 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 9190 Z= 0.193 Angle : 0.657 13.963 12448 Z= 0.318 Chirality : 0.042 0.272 1524 Planarity : 0.003 0.030 1560 Dihedral : 3.687 18.758 1238 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.40 % Favored : 95.33 % Rotamer Outliers : 0.64 % 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: 1.42 (0.26), residues: 1136 helix: 1.84 (0.19), residues: 752 sheet: 0.67 (0.61), residues: 80 loop : -1.30 (0.38), residues: 304 *********************** 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 150 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 144 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 147 average time/residue: 0.1684 time to fit residues: 37.2959 Evaluate side-chains 143 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0910 time to fit residues: 1.8709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 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: 0.7863 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9190 Z= 0.199 Angle : 0.668 13.445 12448 Z= 0.324 Chirality : 0.042 0.301 1524 Planarity : 0.003 0.022 1560 Dihedral : 3.662 18.670 1238 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.31 % Favored : 95.42 % Rotamer Outliers : 0.43 % 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: 1.43 (0.26), residues: 1136 helix: 1.87 (0.19), residues: 756 sheet: 0.65 (0.61), residues: 80 loop : -1.39 (0.38), residues: 300 ********************** 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 150 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 148 average time/residue: 0.1664 time to fit residues: 37.3107 Evaluate side-chains 141 residues out of total 938 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 139 time to evaluate : 1.006 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0807 time to fit residues: 1.6696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.141057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.103099 restraints weight = 22392.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.106173 restraints weight = 13239.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.108233 restraints weight = 9215.097| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.4990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 9190 Z= 0.193 Angle : 0.666 13.957 12448 Z= 0.321 Chirality : 0.042 0.286 1524 Planarity : 0.003 0.022 1560 Dihedral : 3.645 18.383 1238 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.14 % Favored : 95.60 % Rotamer Outliers : 0.53 % 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: 1.41 (0.26), residues: 1136 helix: 1.85 (0.19), residues: 756 sheet: 0.64 (0.61), residues: 80 loop : -1.40 (0.38), residues: 300 =============================================================================== Job complete usr+sys time: 1748.05 seconds wall clock time: 32 minutes 53.74 seconds (1973.74 seconds total)