Starting phenix.real_space_refine on Wed Jun 26 05:56:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ts0_26104/06_2024/7ts0_26104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ts0_26104/06_2024/7ts0_26104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ts0_26104/06_2024/7ts0_26104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ts0_26104/06_2024/7ts0_26104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ts0_26104/06_2024/7ts0_26104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ts0_26104/06_2024/7ts0_26104.pdb" } resolution = 2.8 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= -0.000 sd= 0.006 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 63 5.16 5 C 5979 2.51 5 N 1607 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P ARG 142": "NH1" <-> "NH2" Residue "P ARG 145": "NH1" <-> "NH2" Residue "P ARG 221": "NH1" <-> "NH2" Residue "P ARG 295": "NH1" <-> "NH2" Residue "P ARG 306": "NH1" <-> "NH2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "U ARG 34": "NH1" <-> "NH2" Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 21": "NH1" <-> "NH2" Residue "A ARG 24": "NH1" <-> "NH2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "H ARG 87": "NH1" <-> "NH2" Residue "H ARG 202": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 9383 Number of models: 1 Model: "" Number of chains: 6 Chain: "P" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2459 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 8, 'TRANS': 287} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "U" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 301 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "A" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1788 Classifications: {'peptide': 224} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "H" Number of atoms: 1783 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 232, 1780 Classifications: {'peptide': 232} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 232, 1780 Classifications: {'peptide': 232} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 1820 Time building chain proxies: 6.62, per 1000 atoms: 0.71 Number of scatterers: 9383 At special positions: 0 Unit cell: (108.498, 132.834, 128.778, 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 63 16.00 O 1734 8.00 N 1607 7.00 C 5979 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS P 64 " - pdb=" SG CYS P 98 " distance=2.03 Simple disulfide: pdb=" SG CYS P 184 " - pdb=" SG CYS P 254 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.04 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 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 2.1 seconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2222 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 40.0% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'P' and resid 102 through 106 removed outlier: 4.115A pdb=" N LYS P 105 " --> pdb=" O LEU P 102 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 138 removed outlier: 4.100A pdb=" N ALA P 133 " --> pdb=" O ALA P 129 " (cutoff:3.500A) Processing helix chain 'P' and resid 146 through 171 removed outlier: 4.094A pdb=" N LEU P 171 " --> pdb=" O PHE P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 173 through 179 Processing helix chain 'P' and resid 181 through 214 removed outlier: 3.709A pdb=" N ARG P 185 " --> pdb=" O GLU P 181 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 233 Processing helix chain 'P' and resid 234 through 250 removed outlier: 4.087A pdb=" N ILE P 238 " --> pdb=" O ILE P 234 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 256 Processing helix chain 'P' and resid 265 through 298 removed outlier: 3.919A pdb=" N GLN P 269 " --> pdb=" O ASP P 265 " (cutoff:3.500A) Proline residue: P 271 - end of helix removed outlier: 3.511A pdb=" N LEU P 274 " --> pdb=" O GLY P 270 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU P 277 " --> pdb=" O ILE P 273 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET P 291 " --> pdb=" O VAL P 287 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA P 296 " --> pdb=" O THR P 292 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER P 297 " --> pdb=" O LYS P 293 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 320 removed outlier: 3.617A pdb=" N VAL P 314 " --> pdb=" O LYS P 310 " (cutoff:3.500A) Proline residue: P 317 - end of helix Processing helix chain 'P' and resid 321 through 326 removed outlier: 4.028A pdb=" N PHE P 326 " --> pdb=" O THR P 322 " (cutoff:3.500A) Processing helix chain 'P' and resid 334 through 362 removed outlier: 3.514A pdb=" N PHE P 350 " --> pdb=" O PHE P 346 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N GLY P 352 " --> pdb=" O GLN P 348 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N PHE P 353 " --> pdb=" O SER P 349 " (cutoff:3.500A) Processing helix chain 'P' and resid 363 through 383 removed outlier: 3.635A pdb=" N ARG P 367 " --> pdb=" O ASN P 363 " (cutoff:3.500A) Processing helix chain 'U' and resid 8 through 37 Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.189A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.525A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 removed outlier: 4.362A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASP A 218 " --> pdb=" O CYS A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.070A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 271 through 282 removed outlier: 4.179A pdb=" N LYS A 280 " --> pdb=" O GLY A 276 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 31 through 35 removed outlier: 3.704A pdb=" N THR B 34 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN B 35 " --> pdb=" O GLN B 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 31 through 35' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.554A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.608A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.589A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 67 through 68 removed outlier: 3.711A pdb=" N PHE P 68 " --> pdb=" O VAL P 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.514A pdb=" N VAL A 34 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 9.698A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE A 265 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N HIS A 322 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU A 267 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.846A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.977A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.035A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.667A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.546A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.904A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.821A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.649A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.906A pdb=" N ARG H 98 " --> pdb=" O PHE H 110 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'H' and resid 146 through 148 removed outlier: 7.045A pdb=" N LEU H 174 " --> pdb=" O TYR H 190 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N TYR H 190 " --> pdb=" O LEU H 174 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP H 176 " --> pdb=" O LEU H 188 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN H 194 " --> pdb=" O TYR H 190 " (cutoff:3.500A) 475 hydrogen bonds defined for protein. 1337 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: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3013 1.34 - 1.46: 2216 1.46 - 1.58: 4271 1.58 - 1.70: 0 1.70 - 1.82: 88 Bond restraints: 9588 Sorted by residual: bond pdb=" C ASN U 2 " pdb=" N PRO U 3 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.70e+00 bond pdb=" C ASP H 74 " pdb=" N PRO H 75 " ideal model delta sigma weight residual 1.335 1.358 -0.023 1.28e-02 6.10e+03 3.26e+00 bond pdb=" C PHE P 236 " pdb=" N PRO P 237 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.36e-02 5.41e+03 3.08e+00 bond pdb=" C LEU P 316 " pdb=" N PRO P 317 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.19e-02 7.06e+03 3.02e+00 bond pdb=" CA ASN U 2 " pdb=" C ASN U 2 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.10e-02 2.27e+03 2.32e+00 ... (remaining 9583 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.30: 132 105.30 - 112.51: 4775 112.51 - 119.71: 3155 119.71 - 126.92: 4799 126.92 - 134.12: 126 Bond angle restraints: 12987 Sorted by residual: angle pdb=" CA ARG H 218 " pdb=" CB ARG H 218 " pdb=" CG ARG H 218 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" C ARG H 191 " pdb=" N MET H 192 " pdb=" CA MET H 192 " ideal model delta sigma weight residual 124.31 131.01 -6.70 1.67e+00 3.59e-01 1.61e+01 angle pdb=" CA ARG A 210 " pdb=" CB ARG A 210 " pdb=" CG ARG A 210 " ideal model delta sigma weight residual 114.10 120.98 -6.88 2.00e+00 2.50e-01 1.18e+01 angle pdb=" C ARG A 209 " pdb=" N ARG A 210 " pdb=" CA ARG A 210 " ideal model delta sigma weight residual 122.68 127.54 -4.86 1.47e+00 4.63e-01 1.09e+01 angle pdb=" C GLU A 237 " pdb=" N ASP A 238 " pdb=" CA ASP A 238 " ideal model delta sigma weight residual 123.47 128.46 -4.99 1.53e+00 4.27e-01 1.06e+01 ... (remaining 12982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 5462 15.03 - 30.06: 154 30.06 - 45.08: 47 45.08 - 60.11: 1 60.11 - 75.14: 3 Dihedral angle restraints: 5667 sinusoidal: 2223 harmonic: 3444 Sorted by residual: dihedral pdb=" CB CYS P 184 " pdb=" SG CYS P 184 " pdb=" SG CYS P 254 " pdb=" CB CYS P 254 " ideal model delta sinusoidal sigma weight residual 93.00 124.78 -31.78 1 1.00e+01 1.00e-02 1.44e+01 dihedral pdb=" CA THR B 165 " pdb=" C THR B 165 " pdb=" N CYS B 166 " pdb=" CA CYS B 166 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA SER A 310 " pdb=" C SER A 310 " pdb=" N LYS A 311 " pdb=" CA LYS A 311 " ideal model delta harmonic sigma weight residual -180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1045 0.047 - 0.095: 300 0.095 - 0.142: 85 0.142 - 0.189: 23 0.189 - 0.236: 4 Chirality restraints: 1457 Sorted by residual: chirality pdb=" CG LEU H 174 " pdb=" CB LEU H 174 " pdb=" CD1 LEU H 174 " pdb=" CD2 LEU H 174 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB THR B 223 " pdb=" CA THR B 223 " pdb=" OG1 THR B 223 " pdb=" CG2 THR B 223 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CB ILE A 185 " pdb=" CA ILE A 185 " pdb=" CG1 ILE A 185 " pdb=" CG2 ILE A 185 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 1454 not shown) Planarity restraints: 1649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 314 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C VAL P 314 " -0.051 2.00e-02 2.50e+03 pdb=" O VAL P 314 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU P 315 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 191 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" C ARG H 191 " 0.046 2.00e-02 2.50e+03 pdb=" O ARG H 191 " -0.017 2.00e-02 2.50e+03 pdb=" N MET H 192 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO B 236 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.031 5.00e-02 4.00e+02 ... (remaining 1646 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2077 2.80 - 3.32: 8259 3.32 - 3.85: 14810 3.85 - 4.37: 16991 4.37 - 4.90: 30308 Nonbonded interactions: 72445 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.273 2.440 nonbonded pdb=" OD1 ASN A 270 " pdb=" OG1 THR A 324 " model vdw 2.309 2.440 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.329 2.440 nonbonded pdb=" OD1 ASN P 120 " pdb=" OG SER P 349 " model vdw 2.336 2.440 nonbonded pdb=" O THR P 298 " pdb=" NE2 GLN P 304 " model vdw 2.344 2.520 ... (remaining 72440 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.49 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 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: 2.670 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.420 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 0.056 9588 Z= 0.232 Angle : 0.787 8.784 12987 Z= 0.456 Chirality : 0.051 0.236 1457 Planarity : 0.006 0.056 1649 Dihedral : 8.381 75.139 3433 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.10 % Allowed : 0.98 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.22), residues: 1167 helix: -0.11 (0.22), residues: 419 sheet: -0.62 (0.29), residues: 287 loop : -1.51 (0.25), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 111 HIS 0.016 0.001 HIS H 35 PHE 0.025 0.003 PHE A 190 TYR 0.020 0.002 TYR H 175 ARG 0.006 0.000 ARG P 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 298 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 265 ASP cc_start: 0.8104 (t70) cc_final: 0.7902 (t70) REVERT: P 305 TYR cc_start: 0.5611 (m-80) cc_final: 0.5388 (m-80) REVERT: P 372 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7507 (mmtt) REVERT: P 379 ASP cc_start: 0.8018 (t0) cc_final: 0.7813 (t0) REVERT: A 44 SER cc_start: 0.7860 (t) cc_final: 0.7650 (m) REVERT: A 232 ASP cc_start: 0.8365 (m-30) cc_final: 0.7949 (m-30) REVERT: A 298 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8053 (mp0) REVERT: B 205 ASP cc_start: 0.7717 (p0) cc_final: 0.7465 (p0) REVERT: H 80 PHE cc_start: 0.8193 (m-80) cc_final: 0.7931 (m-80) outliers start: 1 outliers final: 0 residues processed: 299 average time/residue: 1.0218 time to fit residues: 328.0316 Evaluate side-chains 187 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.0670 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 69 ASN P 106 GLN P 198 ASN P 251 ASN ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 GLN A 189 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9588 Z= 0.260 Angle : 0.583 8.101 12987 Z= 0.308 Chirality : 0.043 0.173 1457 Planarity : 0.004 0.045 1649 Dihedral : 4.072 22.953 1290 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 4.79 % Allowed : 12.13 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.67 (0.24), residues: 1167 helix: 2.05 (0.24), residues: 424 sheet: -0.06 (0.29), residues: 288 loop : -0.72 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP H 111 HIS 0.006 0.002 HIS B 142 PHE 0.018 0.002 PHE A 190 TYR 0.021 0.002 TYR A 231 ARG 0.006 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 198 time to evaluate : 1.082 Fit side-chains REVERT: P 365 GLU cc_start: 0.7371 (mt-10) cc_final: 0.7085 (mt-10) REVERT: P 372 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7516 (mmtt) REVERT: B 150 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8403 (mmt90) REVERT: G 20 LYS cc_start: 0.8351 (mtmt) cc_final: 0.8114 (mttm) REVERT: H 80 PHE cc_start: 0.8680 (m-80) cc_final: 0.8295 (m-80) REVERT: H 85 SER cc_start: 0.8319 (m) cc_final: 0.8110 (t) outliers start: 49 outliers final: 16 residues processed: 224 average time/residue: 1.1422 time to fit residues: 273.5505 Evaluate side-chains 180 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 163 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 303 ILE Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 71 optimal weight: 0.0470 chunk 29 optimal weight: 0.8980 chunk 105 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 152 HIS ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9588 Z= 0.151 Angle : 0.488 8.245 12987 Z= 0.255 Chirality : 0.039 0.155 1457 Planarity : 0.003 0.039 1649 Dihedral : 3.728 19.139 1290 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.94 % Allowed : 17.32 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.29 (0.25), residues: 1167 helix: 2.71 (0.25), residues: 424 sheet: 0.16 (0.29), residues: 289 loop : -0.44 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.006 0.001 HIS P 174 PHE 0.013 0.001 PHE P 256 TYR 0.027 0.001 TYR A 231 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.071 Fit side-chains REVERT: P 372 LYS cc_start: 0.8089 (mtpt) cc_final: 0.7489 (mmmt) REVERT: A 273 ASP cc_start: 0.8187 (p0) cc_final: 0.7593 (p0) REVERT: A 277 GLU cc_start: 0.8099 (mt-10) cc_final: 0.7489 (mm-30) REVERT: G 46 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8350 (tppt) REVERT: H 80 PHE cc_start: 0.8660 (m-80) cc_final: 0.8293 (m-80) REVERT: H 85 SER cc_start: 0.8440 (m) cc_final: 0.8226 (t) outliers start: 30 outliers final: 12 residues processed: 183 average time/residue: 1.1735 time to fit residues: 230.1127 Evaluate side-chains 167 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 154 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 9588 Z= 0.470 Angle : 0.669 8.683 12987 Z= 0.354 Chirality : 0.047 0.233 1457 Planarity : 0.005 0.045 1649 Dihedral : 4.480 18.728 1290 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.31 % Allowed : 15.36 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.15 (0.25), residues: 1167 helix: 2.49 (0.25), residues: 415 sheet: 0.23 (0.30), residues: 271 loop : -0.42 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 111 HIS 0.008 0.002 HIS B 142 PHE 0.018 0.002 PHE H 110 TYR 0.047 0.003 TYR B 85 ARG 0.005 0.001 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 163 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: P 178 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6760 (mm-30) REVERT: P 215 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7407 (tpt) REVERT: P 371 ARG cc_start: 0.7369 (ttm-80) cc_final: 0.7140 (mmt180) REVERT: P 372 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7470 (mmtt) REVERT: P 377 TRP cc_start: 0.8308 (t-100) cc_final: 0.8064 (t60) REVERT: A 246 GLU cc_start: 0.8617 (tt0) cc_final: 0.8045 (tp30) REVERT: A 273 ASP cc_start: 0.8147 (p0) cc_final: 0.7539 (p0) REVERT: A 277 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7352 (mm-30) REVERT: A 298 GLU cc_start: 0.8376 (mt-10) cc_final: 0.7797 (tp30) REVERT: A 341 ASP cc_start: 0.7929 (m-30) cc_final: 0.7698 (m-30) REVERT: B 150 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8372 (mmt90) REVERT: B 217 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.8603 (pmt) REVERT: G 46 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8424 (tppt) REVERT: H 85 SER cc_start: 0.8774 (m) cc_final: 0.8485 (t) outliers start: 44 outliers final: 29 residues processed: 189 average time/residue: 1.2840 time to fit residues: 258.2696 Evaluate side-chains 173 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 263 LEU Chi-restraints excluded: chain U residue 6 SER Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 145 SER Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 206 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 177 HIS P 198 ASN ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9588 Z= 0.207 Angle : 0.522 8.519 12987 Z= 0.275 Chirality : 0.041 0.162 1457 Planarity : 0.004 0.042 1649 Dihedral : 3.980 17.462 1290 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.91 % Allowed : 16.93 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.40 (0.25), residues: 1167 helix: 2.90 (0.25), residues: 415 sheet: 0.31 (0.29), residues: 276 loop : -0.48 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.008 0.001 HIS P 174 PHE 0.015 0.001 PHE P 256 TYR 0.025 0.002 TYR A 231 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 155 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: P 205 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7394 (tt0) REVERT: P 215 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7170 (tpt) REVERT: P 372 LYS cc_start: 0.8109 (mtpt) cc_final: 0.7448 (mmmt) REVERT: P 377 TRP cc_start: 0.8308 (t-100) cc_final: 0.8044 (t60) REVERT: A 198 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.6667 (mtm-85) REVERT: B 150 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8409 (mmt90) REVERT: G 46 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8397 (tppt) REVERT: H 85 SER cc_start: 0.8722 (m) cc_final: 0.8432 (t) REVERT: H 145 SER cc_start: 0.7666 (t) cc_final: 0.7398 (t) outliers start: 40 outliers final: 21 residues processed: 182 average time/residue: 1.1989 time to fit residues: 233.0690 Evaluate side-chains 164 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 177 HIS ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 HIS A 242 ASN A 295 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9588 Z= 0.213 Angle : 0.508 8.619 12987 Z= 0.268 Chirality : 0.040 0.163 1457 Planarity : 0.004 0.042 1649 Dihedral : 3.889 17.527 1290 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.11 % Allowed : 17.12 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.49 (0.25), residues: 1167 helix: 3.03 (0.25), residues: 415 sheet: 0.27 (0.29), residues: 281 loop : -0.43 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.008 0.001 HIS P 174 PHE 0.016 0.001 PHE P 256 TYR 0.012 0.001 TYR H 59 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: P 178 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6742 (mm-30) REVERT: P 205 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: P 215 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7162 (tpt) REVERT: P 372 LYS cc_start: 0.8121 (mtpt) cc_final: 0.7431 (mmtt) REVERT: P 377 TRP cc_start: 0.8293 (t-100) cc_final: 0.8025 (t60) REVERT: A 198 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.6676 (mtm-85) REVERT: B 150 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8400 (mmt90) REVERT: G 46 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8396 (tppt) REVERT: H 85 SER cc_start: 0.8755 (m) cc_final: 0.8464 (t) REVERT: H 145 SER cc_start: 0.7646 (t) cc_final: 0.7359 (t) outliers start: 42 outliers final: 23 residues processed: 178 average time/residue: 1.2734 time to fit residues: 241.3330 Evaluate side-chains 173 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 205 GLU Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 0.0870 chunk 111 optimal weight: 0.4980 chunk 69 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 295 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9588 Z= 0.158 Angle : 0.489 8.532 12987 Z= 0.255 Chirality : 0.039 0.164 1457 Planarity : 0.003 0.041 1649 Dihedral : 3.732 16.983 1290 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.52 % Allowed : 18.20 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.65 (0.25), residues: 1167 helix: 3.16 (0.25), residues: 415 sheet: 0.42 (0.29), residues: 284 loop : -0.39 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.008 0.001 HIS P 174 PHE 0.016 0.001 PHE P 256 TYR 0.011 0.001 TYR H 59 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: P 215 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7203 (tpt) REVERT: P 372 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7452 (mmtt) REVERT: P 377 TRP cc_start: 0.8273 (t-100) cc_final: 0.8067 (t60) REVERT: A 198 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.6640 (mtm-85) REVERT: A 277 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7883 (mt-10) REVERT: A 295 ASN cc_start: 0.7908 (OUTLIER) cc_final: 0.7688 (t0) REVERT: B 150 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8461 (mmt90) REVERT: B 217 MET cc_start: 0.8854 (pmt) cc_final: 0.8593 (pmt) REVERT: G 46 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8368 (tppt) REVERT: H 80 PHE cc_start: 0.8884 (m-80) cc_final: 0.8476 (m-80) REVERT: H 85 SER cc_start: 0.8781 (m) cc_final: 0.8516 (t) REVERT: H 145 SER cc_start: 0.7655 (t) cc_final: 0.7372 (t) outliers start: 36 outliers final: 20 residues processed: 178 average time/residue: 1.2130 time to fit residues: 230.3124 Evaluate side-chains 172 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 251 ASN ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 295 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 9588 Z= 0.426 Angle : 0.637 9.131 12987 Z= 0.332 Chirality : 0.045 0.178 1457 Planarity : 0.005 0.043 1649 Dihedral : 4.292 18.436 1290 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.50 % Allowed : 17.51 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.23 (0.25), residues: 1167 helix: 2.72 (0.25), residues: 416 sheet: 0.16 (0.29), residues: 283 loop : -0.51 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 111 HIS 0.008 0.002 HIS P 174 PHE 0.016 0.002 PHE B 151 TYR 0.023 0.002 TYR H 175 ARG 0.006 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 147 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: P 109 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.4853 (p90) REVERT: P 178 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.6793 (mm-30) REVERT: P 215 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7402 (tpt) REVERT: P 372 LYS cc_start: 0.8172 (mtpt) cc_final: 0.7480 (mmtt) REVERT: P 377 TRP cc_start: 0.8319 (t-100) cc_final: 0.8035 (t60) REVERT: A 198 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.6882 (mtm-85) REVERT: A 246 GLU cc_start: 0.8693 (tt0) cc_final: 0.8140 (tp30) REVERT: A 295 ASN cc_start: 0.8040 (OUTLIER) cc_final: 0.7743 (t0) REVERT: B 150 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8347 (mmt90) REVERT: B 217 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8588 (pmt) REVERT: G 46 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8435 (tppt) REVERT: H 85 SER cc_start: 0.8814 (m) cc_final: 0.8519 (t) REVERT: H 145 SER cc_start: 0.7735 (t) cc_final: 0.7466 (t) outliers start: 46 outliers final: 29 residues processed: 173 average time/residue: 1.3009 time to fit residues: 239.6160 Evaluate side-chains 182 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 145 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 109 TYR Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 178 GLU Chi-restraints excluded: chain P residue 182 VAL Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 219 THR Chi-restraints excluded: chain P residue 240 VAL Chi-restraints excluded: chain P residue 244 ILE Chi-restraints excluded: chain P residue 258 LYS Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 208 SER Chi-restraints excluded: chain H residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 0.0000 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 170 GLN P 198 ASN ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 295 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN B 75 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9588 Z= 0.152 Angle : 0.503 8.634 12987 Z= 0.262 Chirality : 0.040 0.158 1457 Planarity : 0.003 0.040 1649 Dihedral : 3.863 17.762 1290 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.64 % Allowed : 19.47 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1167 helix: 3.22 (0.25), residues: 409 sheet: 0.41 (0.29), residues: 283 loop : -0.55 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.008 0.001 HIS P 174 PHE 0.015 0.001 PHE P 256 TYR 0.012 0.001 TYR P 359 ARG 0.004 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.025 Fit side-chains REVERT: P 215 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7246 (tpt) REVERT: P 372 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7441 (mmtt) REVERT: A 198 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.6598 (mtm-85) REVERT: A 277 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7701 (mt-10) REVERT: A 295 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7694 (t0) REVERT: A 332 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8165 (mt) REVERT: B 150 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8390 (mmt90) REVERT: B 217 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8525 (pmt) REVERT: G 46 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8390 (tppt) REVERT: H 85 SER cc_start: 0.8805 (m) cc_final: 0.8567 (t) REVERT: H 145 SER cc_start: 0.7676 (t) cc_final: 0.7401 (t) outliers start: 27 outliers final: 15 residues processed: 161 average time/residue: 1.2994 time to fit residues: 222.9729 Evaluate side-chains 163 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 141 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.2980 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN A 242 ASN A 295 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9588 Z= 0.172 Angle : 0.510 8.820 12987 Z= 0.264 Chirality : 0.040 0.157 1457 Planarity : 0.004 0.041 1649 Dihedral : 3.815 18.070 1290 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.35 % Allowed : 19.37 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.60 (0.25), residues: 1167 helix: 3.26 (0.25), residues: 409 sheet: 0.28 (0.28), residues: 289 loop : -0.42 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.008 0.001 HIS P 174 PHE 0.017 0.001 PHE P 256 TYR 0.011 0.001 TYR H 59 ARG 0.005 0.000 ARG B 197 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 142 time to evaluate : 1.158 Fit side-chains REVERT: P 215 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7256 (tpt) REVERT: P 372 LYS cc_start: 0.8137 (mtpt) cc_final: 0.7447 (mmtt) REVERT: A 198 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.6600 (mtm-85) REVERT: A 295 ASN cc_start: 0.8079 (OUTLIER) cc_final: 0.7792 (t0) REVERT: A 332 ILE cc_start: 0.8570 (OUTLIER) cc_final: 0.8180 (mt) REVERT: B 150 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8396 (mmt90) REVERT: B 217 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8549 (pmt) REVERT: G 46 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8389 (tppt) REVERT: H 85 SER cc_start: 0.8732 (m) cc_final: 0.8479 (t) REVERT: H 145 SER cc_start: 0.7700 (t) cc_final: 0.7431 (t) outliers start: 24 outliers final: 15 residues processed: 158 average time/residue: 1.2865 time to fit residues: 216.6331 Evaluate side-chains 166 residues out of total 1028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 144 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 215 MET Chi-restraints excluded: chain P residue 328 VAL Chi-restraints excluded: chain U residue 10 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 198 ARG Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain H residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 0.0030 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 chunk 66 optimal weight: 0.0980 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN A 295 ASN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.144643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.099592 restraints weight = 13511.491| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.54 r_work: 0.2994 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9588 Z= 0.223 Angle : 0.528 8.757 12987 Z= 0.275 Chirality : 0.041 0.161 1457 Planarity : 0.004 0.042 1649 Dihedral : 3.894 18.625 1290 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.15 % Allowed : 19.57 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 1.54 (0.25), residues: 1167 helix: 3.20 (0.25), residues: 409 sheet: 0.25 (0.28), residues: 289 loop : -0.44 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.008 0.001 HIS P 174 PHE 0.016 0.001 PHE P 256 TYR 0.012 0.001 TYR P 359 ARG 0.005 0.000 ARG B 197 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4629.31 seconds wall clock time: 80 minutes 57.39 seconds (4857.39 seconds total)