Starting phenix.real_space_refine on Mon Sep 23 23:48:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gef_29968/09_2024/8gef_29968.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gef_29968/09_2024/8gef_29968.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gef_29968/09_2024/8gef_29968.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gef_29968/09_2024/8gef_29968.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gef_29968/09_2024/8gef_29968.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gef_29968/09_2024/8gef_29968.cif" } resolution = 3.8 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= -0.001 sd= 0.025 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 24 5.16 5 C 4014 2.51 5 N 1095 2.21 5 O 1083 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6216 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1835 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 138} Link IDs: {'PTRANS': 6, 'TRANS': 274} Chain breaks: 7 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 500 Unresolved non-hydrogen angles: 616 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'GLN:plan1': 12, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 16, 'PHE:plan': 1, 'GLU:plan': 21, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 309 Chain: "B" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2131 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 124} Link IDs: {'PTRANS': 5, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 396 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 304 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 11, 'ASP:plan': 26, 'ASN%COO:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 260 Chain: "G" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 287 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 54 Chain: "R" Number of atoms: 1948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 1948 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 7, 'TRANS': 273} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 319 Unresolved non-hydrogen angles: 403 Unresolved non-hydrogen dihedrals: 253 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 144 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.34, per 1000 atoms: 0.86 Number of scatterers: 6216 At special positions: 0 Unit cell: (67.84, 97.52, 130.38, 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 24 16.00 O 1083 8.00 N 1095 7.00 C 4014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.2 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1786 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 50.5% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 12 through 40 Processing helix chain 'A' and resid 52 through 61 removed outlier: 3.796A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 108 Processing helix chain 'A' and resid 129 through 135 Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.718A pdb=" N TYR A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 251 through 254 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.504A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLY A 353 " --> pdb=" O SER A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 Processing helix chain 'A' and resid 391 through 393 No H-bonds generated for 'chain 'A' and resid 391 through 393' Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.521A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.957A pdb=" N PHE R 61 " --> pdb=" O ALA R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 97 removed outlier: 3.809A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.083A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 171 removed outlier: 4.456A pdb=" N LEU R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Proline residue: R 168 - end of helix Processing helix chain 'R' and resid 172 through 175 Processing helix chain 'R' and resid 181 through 187 Processing helix chain 'R' and resid 198 through 208 Processing helix chain 'R' and resid 208 through 237 Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.670A pdb=" N THR R 274 " --> pdb=" O LYS R 270 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.326A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 317 Processing helix chain 'R' and resid 317 through 327 Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 329 through 340 Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 213 removed outlier: 6.735A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.910A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.061A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 4.037A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.635A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.710A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.624A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 4.088A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1110 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: 2.76 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.46: 3717 1.46 - 1.71: 2589 1.71 - 1.96: 34 1.96 - 2.20: 0 2.20 - 2.45: 1 Bond restraints: 6341 Sorted by residual: bond pdb=" C PRO A 328 " pdb=" N GLU A 330 " ideal model delta sigma weight residual 1.332 2.449 -1.116 1.40e-02 5.10e+03 6.36e+03 bond pdb=" C PRO A 332 " pdb=" N ARG A 333 " ideal model delta sigma weight residual 1.335 1.247 0.088 1.31e-02 5.83e+03 4.47e+01 bond pdb=" CAI G1I R 501 " pdb=" CAJ G1I R 501 " ideal model delta sigma weight residual 1.523 1.602 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CA LEU B 168 " pdb=" C LEU B 168 " ideal model delta sigma weight residual 1.522 1.480 0.042 1.20e-02 6.94e+03 1.25e+01 bond pdb=" CAC G1I R 501 " pdb=" CAD G1I R 501 " ideal model delta sigma weight residual 1.397 1.448 -0.051 2.00e-02 2.50e+03 6.56e+00 ... (remaining 6336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.76: 8715 9.76 - 19.51: 0 19.51 - 29.27: 0 29.27 - 39.03: 1 39.03 - 48.79: 2 Bond angle restraints: 8718 Sorted by residual: angle pdb=" O PRO A 328 " pdb=" C PRO A 328 " pdb=" N GLU A 330 " ideal model delta sigma weight residual 122.64 84.01 38.63 1.35e+00 5.49e-01 8.19e+02 angle pdb=" C PRO A 328 " pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta sigma weight residual 121.54 170.33 -48.79 1.91e+00 2.74e-01 6.52e+02 angle pdb=" CA PRO A 328 " pdb=" C PRO A 328 " pdb=" N GLU A 330 " ideal model delta sigma weight residual 116.70 157.23 -40.53 2.07e+00 2.33e-01 3.83e+02 angle pdb=" O PRO A 332 " pdb=" C PRO A 332 " pdb=" N ARG A 333 " ideal model delta sigma weight residual 122.23 115.52 6.71 1.20e+00 6.94e-01 3.13e+01 angle pdb=" N GLU A 327 " pdb=" CA GLU A 327 " pdb=" C GLU A 327 " ideal model delta sigma weight residual 109.58 117.63 -8.05 1.63e+00 3.76e-01 2.44e+01 ... (remaining 8713 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.39: 3374 20.39 - 40.78: 210 40.78 - 61.17: 18 61.17 - 81.56: 1 81.56 - 101.95: 3 Dihedral angle restraints: 3606 sinusoidal: 866 harmonic: 2740 Sorted by residual: dihedral pdb=" CA PRO A 328 " pdb=" C PRO A 328 " pdb=" N GLU A 330 " pdb=" CA GLU A 330 " ideal model delta harmonic sigma weight residual -180.00 -78.05 -101.95 0 5.00e+00 4.00e-02 4.16e+02 dihedral pdb=" CAE G1I R 501 " pdb=" CAG G1I R 501 " pdb=" CAH G1I R 501 " pdb=" CAI G1I R 501 " ideal model delta sinusoidal sigma weight residual 47.24 -48.83 96.07 1 3.00e+01 1.11e-03 1.18e+01 dihedral pdb=" CA MET R 171 " pdb=" C MET R 171 " pdb=" N HIS R 172 " pdb=" CA HIS R 172 " ideal model delta harmonic sigma weight residual 180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 3603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 758 0.034 - 0.068: 218 0.068 - 0.101: 63 0.101 - 0.135: 32 0.135 - 0.169: 4 Chirality restraints: 1075 Sorted by residual: chirality pdb=" CA CYS B 166 " pdb=" N CYS B 166 " pdb=" C CYS B 166 " pdb=" CB CYS B 166 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.14e-01 chirality pdb=" CB VAL R 292 " pdb=" CA VAL R 292 " pdb=" CG1 VAL R 292 " pdb=" CG2 VAL R 292 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.86e-01 chirality pdb=" CB THR R 118 " pdb=" CA THR R 118 " pdb=" OG1 THR R 118 " pdb=" CG2 THR R 118 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.11e-01 ... (remaining 1072 not shown) Planarity restraints: 1111 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 328 " 0.031 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C PRO A 328 " -0.062 2.00e-02 2.50e+03 pdb=" O PRO A 328 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU A 330 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 297 " -0.006 2.00e-02 2.50e+03 8.22e-03 1.69e+00 pdb=" CG TRP B 297 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP B 297 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 297 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 297 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 297 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 297 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 297 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 297 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 297 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 326 " -0.006 2.00e-02 2.50e+03 1.14e-02 1.31e+00 pdb=" C PRO A 326 " 0.020 2.00e-02 2.50e+03 pdb=" O PRO A 326 " -0.007 2.00e-02 2.50e+03 pdb=" N GLU A 327 " -0.007 2.00e-02 2.50e+03 ... (remaining 1108 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2027 2.82 - 3.34: 5939 3.34 - 3.86: 10232 3.86 - 4.38: 10224 4.38 - 4.90: 18745 Nonbonded interactions: 47167 Sorted by model distance: nonbonded pdb=" O LYS B 57 " pdb=" OG SER B 74 " model vdw 2.302 3.040 nonbonded pdb=" NH1 ARG A 385 " pdb=" OE1 GLN R 229 " model vdw 2.322 3.120 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.330 3.040 nonbonded pdb=" O ASP B 186 " pdb=" N CYS B 204 " model vdw 2.336 3.120 nonbonded pdb=" OH TYR R 209 " pdb=" O PHE R 290 " model vdw 2.356 3.040 ... (remaining 47162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.860 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 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 : 0.014 1.116 6341 Z= 0.521 Angle : 0.957 48.785 8718 Z= 0.558 Chirality : 0.040 0.169 1075 Planarity : 0.003 0.037 1111 Dihedral : 13.648 101.948 1817 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.42 % Allowed : 17.02 % Favored : 81.56 % 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: 2.13 (0.29), residues: 911 helix: 3.07 (0.25), residues: 415 sheet: 0.62 (0.43), residues: 160 loop : -0.34 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 297 HIS 0.004 0.001 HIS B 225 PHE 0.012 0.001 PHE A 340 TYR 0.013 0.001 TYR A 360 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.542 Fit side-chains REVERT: B 169 TRP cc_start: 0.8171 (m100) cc_final: 0.7909 (m100) outliers start: 6 outliers final: 5 residues processed: 72 average time/residue: 0.1303 time to fit residues: 13.2702 Evaluate side-chains 66 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 218 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.0670 chunk 47 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 44 optimal weight: 0.0000 chunk 54 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.4922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 6341 Z= 0.144 Angle : 0.439 5.321 8718 Z= 0.244 Chirality : 0.039 0.162 1075 Planarity : 0.003 0.028 1111 Dihedral : 4.441 37.708 1000 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.84 % Allowed : 17.02 % Favored : 80.14 % 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: 2.23 (0.29), residues: 913 helix: 3.19 (0.25), residues: 413 sheet: 0.65 (0.43), residues: 160 loop : -0.30 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 297 HIS 0.003 0.001 HIS B 142 PHE 0.010 0.001 PHE B 199 TYR 0.010 0.001 TYR R 199 ARG 0.003 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.670 Fit side-chains REVERT: R 296 HIS cc_start: 0.8389 (OUTLIER) cc_final: 0.8146 (p-80) outliers start: 12 outliers final: 4 residues processed: 86 average time/residue: 0.1316 time to fit residues: 16.4760 Evaluate side-chains 65 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 60 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 23 optimal weight: 0.0370 chunk 84 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6341 Z= 0.166 Angle : 0.433 5.442 8718 Z= 0.240 Chirality : 0.039 0.149 1075 Planarity : 0.003 0.028 1111 Dihedral : 4.247 38.431 995 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.36 % Allowed : 19.39 % Favored : 78.25 % 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: 2.26 (0.29), residues: 913 helix: 3.24 (0.25), residues: 420 sheet: 0.81 (0.43), residues: 155 loop : -0.47 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.022 0.001 PHE A 340 TYR 0.011 0.001 TYR R 199 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.596 Fit side-chains REVERT: R 296 HIS cc_start: 0.8457 (OUTLIER) cc_final: 0.8244 (p-80) outliers start: 10 outliers final: 6 residues processed: 71 average time/residue: 0.1365 time to fit residues: 13.9534 Evaluate side-chains 64 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 83 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 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 371 ASN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6341 Z= 0.192 Angle : 0.436 5.551 8718 Z= 0.243 Chirality : 0.039 0.148 1075 Planarity : 0.003 0.028 1111 Dihedral : 4.325 39.504 995 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 3.31 % Allowed : 20.80 % Favored : 75.89 % 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: 2.21 (0.29), residues: 913 helix: 3.24 (0.25), residues: 420 sheet: 0.61 (0.43), residues: 157 loop : -0.47 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.001 PHE A 340 TYR 0.015 0.001 TYR R 174 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 65 time to evaluate : 0.719 Fit side-chains outliers start: 14 outliers final: 10 residues processed: 76 average time/residue: 0.1386 time to fit residues: 15.2394 Evaluate side-chains 68 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 76 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6341 Z= 0.176 Angle : 0.431 5.488 8718 Z= 0.238 Chirality : 0.039 0.156 1075 Planarity : 0.003 0.028 1111 Dihedral : 4.294 39.552 995 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 3.55 % Allowed : 21.75 % Favored : 74.70 % 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: 2.24 (0.29), residues: 913 helix: 3.37 (0.25), residues: 414 sheet: 0.53 (0.43), residues: 159 loop : -0.50 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 235 TYR 0.018 0.001 TYR R 174 ARG 0.002 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 67 time to evaluate : 0.731 Fit side-chains REVERT: R 275 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8663 (mm) REVERT: R 296 HIS cc_start: 0.8436 (OUTLIER) cc_final: 0.7921 (p-80) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.1339 time to fit residues: 15.6362 Evaluate side-chains 72 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 30 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 47 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6341 Z= 0.184 Angle : 0.434 5.536 8718 Z= 0.240 Chirality : 0.039 0.166 1075 Planarity : 0.003 0.028 1111 Dihedral : 4.315 39.789 995 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.31 % Allowed : 23.17 % Favored : 73.52 % 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: 2.19 (0.29), residues: 913 helix: 3.39 (0.25), residues: 414 sheet: 0.22 (0.42), residues: 166 loop : -0.44 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.001 PHE B 235 TYR 0.019 0.001 TYR R 174 ARG 0.001 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.657 Fit side-chains REVERT: R 275 LEU cc_start: 0.9106 (OUTLIER) cc_final: 0.8657 (mm) REVERT: R 296 HIS cc_start: 0.8458 (OUTLIER) cc_final: 0.7897 (p-80) outliers start: 14 outliers final: 11 residues processed: 80 average time/residue: 0.1484 time to fit residues: 16.5948 Evaluate side-chains 72 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 86 optimal weight: 0.0020 chunk 10 optimal weight: 0.0570 chunk 51 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 89 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6341 Z= 0.124 Angle : 0.414 6.153 8718 Z= 0.227 Chirality : 0.038 0.170 1075 Planarity : 0.002 0.027 1111 Dihedral : 4.114 38.426 995 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.07 % Allowed : 23.17 % Favored : 73.76 % 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: 2.22 (0.29), residues: 913 helix: 3.42 (0.25), residues: 414 sheet: 0.05 (0.40), residues: 179 loop : -0.33 (0.35), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 PHE 0.013 0.001 PHE A 340 TYR 0.021 0.001 TYR R 174 ARG 0.001 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.893 Fit side-chains REVERT: A 349 SER cc_start: 0.9357 (p) cc_final: 0.9009 (t) REVERT: R 275 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8595 (mm) REVERT: R 296 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7708 (p-80) outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.1356 time to fit residues: 15.9300 Evaluate side-chains 71 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 296 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 35 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 8 optimal weight: 50.0000 chunk 70 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6341 Z= 0.188 Angle : 0.442 6.329 8718 Z= 0.243 Chirality : 0.039 0.176 1075 Planarity : 0.003 0.034 1111 Dihedral : 4.248 39.587 995 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.07 % Allowed : 23.64 % Favored : 73.29 % 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: 2.18 (0.29), residues: 913 helix: 3.41 (0.25), residues: 414 sheet: 0.03 (0.41), residues: 174 loop : -0.38 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 277 HIS 0.006 0.001 HIS B 225 PHE 0.014 0.001 PHE B 235 TYR 0.019 0.001 TYR R 174 ARG 0.001 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 63 time to evaluate : 0.701 Fit side-chains REVERT: R 275 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8666 (mm) REVERT: R 296 HIS cc_start: 0.8421 (OUTLIER) cc_final: 0.7841 (p-80) outliers start: 13 outliers final: 10 residues processed: 74 average time/residue: 0.1294 time to fit residues: 14.2019 Evaluate side-chains 73 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 61 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 0.0870 chunk 85 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 6341 Z= 0.128 Angle : 0.412 5.828 8718 Z= 0.226 Chirality : 0.038 0.136 1075 Planarity : 0.003 0.032 1111 Dihedral : 4.088 38.332 995 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.84 % Allowed : 23.64 % Favored : 73.52 % 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: 2.25 (0.29), residues: 913 helix: 3.45 (0.25), residues: 413 sheet: 0.05 (0.40), residues: 178 loop : -0.31 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 277 HIS 0.006 0.001 HIS B 225 PHE 0.010 0.001 PHE B 199 TYR 0.024 0.001 TYR R 174 ARG 0.001 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.713 Fit side-chains REVERT: R 275 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8630 (mm) REVERT: R 296 HIS cc_start: 0.8250 (OUTLIER) cc_final: 0.7675 (p-80) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.1264 time to fit residues: 14.4035 Evaluate side-chains 73 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 62 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 53 optimal weight: 0.0970 chunk 41 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 0.3980 chunk 85 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 0.0470 chunk 78 optimal weight: 1.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 6341 Z= 0.124 Angle : 0.412 6.926 8718 Z= 0.225 Chirality : 0.038 0.170 1075 Planarity : 0.003 0.030 1111 Dihedral : 3.987 37.607 995 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 3.07 % Allowed : 23.40 % Favored : 73.52 % 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: 2.29 (0.29), residues: 913 helix: 3.46 (0.25), residues: 413 sheet: 0.11 (0.40), residues: 178 loop : -0.28 (0.35), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 277 HIS 0.005 0.001 HIS B 225 PHE 0.010 0.001 PHE A 340 TYR 0.024 0.001 TYR R 174 ARG 0.001 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1826 Ramachandran restraints generated. 913 Oldfield, 0 Emsley, 913 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 0.714 Fit side-chains REVERT: A 385 ARG cc_start: 0.8701 (mtm-85) cc_final: 0.8462 (ttp-110) REVERT: R 275 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8587 (mm) REVERT: R 296 HIS cc_start: 0.8191 (OUTLIER) cc_final: 0.7581 (p-80) outliers start: 13 outliers final: 8 residues processed: 79 average time/residue: 0.1339 time to fit residues: 15.3963 Evaluate side-chains 72 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 62 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 275 LEU Chi-restraints excluded: chain R residue 296 HIS Chi-restraints excluded: chain R residue 321 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 93 random chunks: chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 9 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 64 optimal weight: 0.0570 chunk 4 optimal weight: 0.0980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.112871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.097394 restraints weight = 13219.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099404 restraints weight = 7944.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.100718 restraints weight = 5505.019| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6341 Z= 0.118 Angle : 0.410 6.436 8718 Z= 0.223 Chirality : 0.038 0.135 1075 Planarity : 0.002 0.030 1111 Dihedral : 3.887 37.000 995 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.60 % Allowed : 24.11 % Favored : 73.29 % 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: 2.36 (0.29), residues: 913 helix: 3.45 (0.24), residues: 420 sheet: 0.14 (0.40), residues: 181 loop : -0.23 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 277 HIS 0.005 0.001 HIS B 225 PHE 0.010 0.001 PHE A 340 TYR 0.024 0.001 TYR R 174 ARG 0.001 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1355.13 seconds wall clock time: 32 minutes 59.13 seconds (1979.13 seconds total)