Starting phenix.real_space_refine on Wed Feb 14 00:25:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9x_20277/02_2024/6p9x_20277.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9x_20277/02_2024/6p9x_20277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9x_20277/02_2024/6p9x_20277.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9x_20277/02_2024/6p9x_20277.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9x_20277/02_2024/6p9x_20277.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6p9x_20277/02_2024/6p9x_20277.pdb" } resolution = 2.91 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= 0.012 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 49 5.16 5 C 5198 2.51 5 N 1435 2.21 5 O 1495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "R ARG 165": "NH1" <-> "NH2" Residue "R PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 369": "OE1" <-> "OE2" Residue "R ARG 371": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8177 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1638 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 192, 1627 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 185} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 192, 1627 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 185} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1648 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 2267 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 270, 2256 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 7, 'TRANS': 262} Conformer: "B" Number of residues, atoms: 270, 2256 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 7, 'TRANS': 262} bond proxies already assigned to first conformer: 2316 Chain: "P" Number of atoms: 265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 265 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 2, 'TRANS': 30} Chain: "A" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N AARG A 38 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 38 " occ=0.50 residue: pdb=" N SER R 301 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER R 301 " occ=0.00 residue: pdb=" N THR R 302 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR R 302 " occ=0.00 residue: pdb=" N THR R 303 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR R 303 " occ=0.00 residue: pdb=" N GLY R 335 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY R 335 " occ=0.00 residue: pdb=" N GLU R 336 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU R 336 " occ=0.00 residue: pdb=" N APHE R 362 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE R 362 " occ=0.50 Time building chain proxies: 6.18, per 1000 atoms: 0.76 Number of scatterers: 8177 At special positions: 0 Unit cell: (88.1309, 144.873, 96.5818, 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 49 16.00 O 1495 8.00 N 1435 7.00 C 5198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 188 " - pdb=" SG CYS R 258 " distance=2.03 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: 3.17 Conformation dependent library (CDL) restraints added in 2.0 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1914 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 11 sheets defined 41.5% alpha, 21.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.766A pdb=" N GLN A 19 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.624A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.517A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 391 removed outlier: 3.503A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.517A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN B 17 " --> pdb=" O GLN B 13 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 22 removed outlier: 4.217A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.856A pdb=" N ASP G 36 " --> pdb=" O LYS G 32 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.697A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.685A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 144 removed outlier: 3.820A pdb=" N HIS R 117 " --> pdb=" O LYS R 113 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE R 121 " --> pdb=" O HIS R 117 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE R 129 " --> pdb=" O LEU R 125 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE R 141 " --> pdb=" O ALA R 137 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU R 142 " --> pdb=" O PHE R 138 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 175 Processing helix chain 'R' and resid 177 through 184 removed outlier: 3.586A pdb=" N GLN R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 207 removed outlier: 3.539A pdb=" N VAL R 191 " --> pdb=" O TRP R 187 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE R 203 " --> pdb=" O HIS R 199 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 219 Processing helix chain 'R' and resid 227 through 236 removed outlier: 3.909A pdb=" N PHE R 231 " --> pdb=" O ARG R 227 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 253 removed outlier: 3.797A pdb=" N ILE R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 256 through 260 Processing helix chain 'R' and resid 269 through 302 Proline residue: R 275 - end of helix removed outlier: 3.585A pdb=" N ALA R 300 " --> pdb=" O THR R 296 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER R 301 " --> pdb=" O LYS R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 319 removed outlier: 3.545A pdb=" N TYR R 309 " --> pdb=" O GLU R 305 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LYS R 314 " --> pdb=" O ARG R 310 " (cutoff:3.500A) Processing helix chain 'R' and resid 319 through 324 Processing helix chain 'R' and resid 325 through 330 removed outlier: 4.548A pdb=" N PHE R 330 " --> pdb=" O THR R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 337 through 354 removed outlier: 3.527A pdb=" N LEU R 351 " --> pdb=" O PHE R 347 " (cutoff:3.500A) Processing helix chain 'R' and resid 354 through 364 Processing helix chain 'R' and resid 367 through 380 Processing helix chain 'P' and resid 6 through 8 No H-bonds generated for 'chain 'P' and resid 6 through 8' Processing helix chain 'P' and resid 9 through 32 removed outlier: 3.994A pdb=" N ARG P 23 " --> pdb=" O LEU P 19 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN P 29 " --> pdb=" O GLU P 25 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 210 Processing sheet with id=AA2, first strand: chain 'A' and resid 208 through 210 removed outlier: 3.978A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.215A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.519A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.933A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.633A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.309A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.396A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.523A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 11 removed outlier: 3.553A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 401 hydrogen bonds defined for protein. 1148 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: 2.58 Time building geometry restraints manager: 3.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2672 1.35 - 1.47: 2098 1.47 - 1.59: 3507 1.59 - 1.71: 0 1.71 - 1.84: 69 Bond restraints: 8346 Sorted by residual: bond pdb=" N ILE B 229 " pdb=" CA ILE B 229 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.10e-02 8.26e+03 8.43e+00 bond pdb=" N ILE B 273 " pdb=" CA ILE B 273 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.15e+00 bond pdb=" N THR B 249 " pdb=" CA THR B 249 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.18e-02 7.18e+03 6.97e+00 bond pdb=" N HIS B 225 " pdb=" CA HIS B 225 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.31e-02 5.83e+03 6.94e+00 bond pdb=" N SER B 245 " pdb=" CA SER B 245 " ideal model delta sigma weight residual 1.454 1.486 -0.031 1.29e-02 6.01e+03 5.96e+00 ... (remaining 8341 not shown) Histogram of bond angle deviations from ideal: 99.70 - 106.58: 177 106.58 - 113.46: 4508 113.46 - 120.34: 3165 120.34 - 127.21: 3356 127.21 - 134.09: 99 Bond angle restraints: 11305 Sorted by residual: angle pdb=" N ASP B 246 " pdb=" CA ASP B 246 " pdb=" C ASP B 246 " ideal model delta sigma weight residual 113.01 109.19 3.82 1.20e+00 6.94e-01 1.01e+01 angle pdb=" N ASP B 247 " pdb=" CA ASP B 247 " pdb=" C ASP B 247 " ideal model delta sigma weight residual 113.01 109.31 3.70 1.20e+00 6.94e-01 9.53e+00 angle pdb=" CA GLY B 272 " pdb=" C GLY B 272 " pdb=" O GLY B 272 " ideal model delta sigma weight residual 122.31 118.24 4.07 1.34e+00 5.57e-01 9.21e+00 angle pdb=" N VAL R 313 " pdb=" CA VAL R 313 " pdb=" C VAL R 313 " ideal model delta sigma weight residual 111.58 108.38 3.20 1.06e+00 8.90e-01 9.13e+00 angle pdb=" CA ASP B 228 " pdb=" C ASP B 228 " pdb=" O ASP B 228 " ideal model delta sigma weight residual 121.19 118.07 3.12 1.10e+00 8.26e-01 8.03e+00 ... (remaining 11300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 4522 17.23 - 34.47: 339 34.47 - 51.70: 54 51.70 - 68.93: 8 68.93 - 86.17: 8 Dihedral angle restraints: 4931 sinusoidal: 1970 harmonic: 2961 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 0.17 -86.17 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -150.54 -29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA HIS B 142 " pdb=" C HIS B 142 " pdb=" N THR B 143 " pdb=" CA THR B 143 " ideal model delta harmonic sigma weight residual 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 4928 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 888 0.040 - 0.079: 266 0.079 - 0.119: 79 0.119 - 0.159: 10 0.159 - 0.198: 3 Chirality restraints: 1246 Sorted by residual: chirality pdb=" CA ILE B 273 " pdb=" N ILE B 273 " pdb=" C ILE B 273 " pdb=" CB ILE B 273 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA ASP B 228 " pdb=" N ASP B 228 " pdb=" C ASP B 228 " pdb=" CB ASP B 228 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.80e-01 chirality pdb=" CA ILE B 229 " pdb=" N ILE B 229 " pdb=" C ILE B 229 " pdb=" CB ILE B 229 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 1243 not shown) Planarity restraints: 1443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 238 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO R 239 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 239 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 239 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO B 236 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.011 2.00e-02 2.50e+03 1.03e-02 2.12e+00 pdb=" CG TYR B 59 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.001 2.00e-02 2.50e+03 ... (remaining 1440 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 955 2.75 - 3.29: 7757 3.29 - 3.82: 13342 3.82 - 4.36: 17688 4.36 - 4.90: 29567 Nonbonded interactions: 69309 Sorted by model distance: nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.211 2.520 nonbonded pdb=" O SER R 349 " pdb=" OG SER R 353 " model vdw 2.236 2.440 nonbonded pdb=" O ASP R 224 " pdb=" NH1 ARG R 227 " model vdw 2.256 2.520 nonbonded pdb=" OE2 GLU R 352 " pdb=" O HOH R 501 " model vdw 2.258 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.263 2.440 ... (remaining 69304 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=0.00 max=1.00 mean=0.99 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: 0.250 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: 1.660 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 27.710 Find NCS groups from input model: 0.210 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:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 0.036 8346 Z= 0.225 Angle : 0.568 5.379 11305 Z= 0.360 Chirality : 0.042 0.198 1246 Planarity : 0.003 0.041 1443 Dihedral : 12.458 79.634 3008 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.23 % Allowed : 1.48 % Favored : 98.29 % 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: -3.97 (0.22), residues: 1001 helix: -3.96 (0.14), residues: 390 sheet: -1.21 (0.33), residues: 219 loop : -1.72 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.007 0.001 HIS B 62 PHE 0.015 0.001 PHE N 108 TYR 0.025 0.001 TYR B 59 ARG 0.002 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 0.909 Fit side-chains REVERT: A 209 GLU cc_start: 0.6749 (mt-10) cc_final: 0.6481 (mt-10) REVERT: A 220 HIS cc_start: 0.7940 (t-170) cc_final: 0.7686 (t70) REVERT: A 280 LYS cc_start: 0.8645 (ptmt) cc_final: 0.8360 (ptpt) REVERT: A 283 ARG cc_start: 0.7498 (mtt180) cc_final: 0.7089 (mtt-85) REVERT: A 339 TYR cc_start: 0.8360 (m-80) cc_final: 0.7784 (m-80) REVERT: A 344 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7943 (mm-30) REVERT: B 23 LYS cc_start: 0.8098 (ttpp) cc_final: 0.7860 (tppt) REVERT: B 46 ARG cc_start: 0.7540 (mtm180) cc_final: 0.7071 (mmm-85) REVERT: B 76 ASP cc_start: 0.8810 (p0) cc_final: 0.8440 (p0) REVERT: B 138 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7607 (mt-10) REVERT: B 245 SER cc_start: 0.9034 (t) cc_final: 0.8735 (t) REVERT: B 246 ASP cc_start: 0.8221 (m-30) cc_final: 0.7968 (m-30) REVERT: B 312 ASP cc_start: 0.7919 (m-30) cc_final: 0.7714 (m-30) REVERT: G 20 LYS cc_start: 0.8080 (mttm) cc_final: 0.7704 (mtmm) REVERT: G 32 LYS cc_start: 0.8608 (tmtt) cc_final: 0.8228 (tptm) REVERT: N 5 GLN cc_start: 0.7728 (tp-100) cc_final: 0.7492 (mm110) REVERT: N 34 MET cc_start: 0.8941 (mmm) cc_final: 0.8444 (mmm) REVERT: N 83 MET cc_start: 0.9050 (mtp) cc_final: 0.8422 (mtp) REVERT: R 225 ARG cc_start: 0.7507 (mtp180) cc_final: 0.7292 (mtp180) REVERT: R 234 ILE cc_start: 0.8596 (mt) cc_final: 0.8385 (mm) REVERT: R 333 ASN cc_start: 0.7704 (t0) cc_final: 0.7434 (t0) outliers start: 2 outliers final: 0 residues processed: 153 average time/residue: 1.3586 time to fit residues: 219.0764 Evaluate side-chains 116 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 218 ASN A 264 ASN A 279 ASN A 377 ASN B 75 GLN B 110 ASN B 119 ASN B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 127 HIS R 166 ASN R 173 GLN R 182 GLN R 379 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8346 Z= 0.279 Angle : 0.590 15.218 11305 Z= 0.310 Chirality : 0.044 0.155 1246 Planarity : 0.005 0.046 1443 Dihedral : 4.714 27.458 1119 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.05 % Allowed : 9.00 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.24), residues: 1001 helix: -1.49 (0.23), residues: 400 sheet: -0.65 (0.33), residues: 227 loop : -1.29 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 339 HIS 0.009 0.002 HIS A 357 PHE 0.019 0.002 PHE N 108 TYR 0.017 0.002 TYR B 105 ARG 0.010 0.001 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 128 time to evaluate : 0.947 Fit side-chains REVERT: A 16 GLU cc_start: 0.6938 (tt0) cc_final: 0.6560 (tt0) REVERT: A 25 LYS cc_start: 0.8140 (ttmm) cc_final: 0.7592 (tttp) REVERT: A 280 LYS cc_start: 0.8823 (ptmt) cc_final: 0.8578 (ptpt) REVERT: A 283 ARG cc_start: 0.7463 (mtt180) cc_final: 0.7134 (mtt-85) REVERT: A 284 ASP cc_start: 0.8211 (m-30) cc_final: 0.7963 (m-30) REVERT: A 389 ARG cc_start: 0.7413 (ttp-110) cc_final: 0.6984 (mtp180) REVERT: B 13 GLN cc_start: 0.7868 (mm-40) cc_final: 0.7226 (tt0) REVERT: B 23 LYS cc_start: 0.8169 (ttpp) cc_final: 0.7928 (tppt) REVERT: B 46 ARG cc_start: 0.7560 (mtm180) cc_final: 0.7072 (mmm-85) REVERT: B 76 ASP cc_start: 0.8902 (p0) cc_final: 0.8475 (p0) REVERT: B 134 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6480 (mmp80) REVERT: B 153 ASP cc_start: 0.8385 (m-30) cc_final: 0.8025 (m-30) REVERT: B 262 MET cc_start: 0.8723 (ttm) cc_final: 0.8436 (tpp) REVERT: G 20 LYS cc_start: 0.7985 (mttm) cc_final: 0.7680 (mtmm) REVERT: G 32 LYS cc_start: 0.8677 (tmtt) cc_final: 0.8347 (tptm) REVERT: N 5 GLN cc_start: 0.7692 (tp-100) cc_final: 0.7459 (mm110) REVERT: N 19 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8205 (ttt180) REVERT: N 34 MET cc_start: 0.9003 (mmm) cc_final: 0.8485 (mmm) REVERT: N 83 MET cc_start: 0.9101 (mtp) cc_final: 0.8755 (mtp) REVERT: N 89 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: R 206 MET cc_start: 0.8526 (mtm) cc_final: 0.8107 (mtm) REVERT: R 225 ARG cc_start: 0.7568 (mtp180) cc_final: 0.7302 (mtp85) REVERT: R 333 ASN cc_start: 0.7726 (t0) cc_final: 0.7383 (t0) REVERT: P 21 MET cc_start: 0.7442 (ttm) cc_final: 0.7129 (ttp) outliers start: 18 outliers final: 10 residues processed: 137 average time/residue: 1.3899 time to fit residues: 200.7426 Evaluate side-chains 131 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 118 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 177 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 142 HIS B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8346 Z= 0.168 Angle : 0.503 13.368 11305 Z= 0.263 Chirality : 0.042 0.135 1246 Planarity : 0.004 0.047 1443 Dihedral : 4.406 23.718 1119 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.39 % Allowed : 10.93 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.25), residues: 1001 helix: -0.12 (0.25), residues: 398 sheet: -0.41 (0.33), residues: 227 loop : -0.97 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.015 0.001 PHE R 260 TYR 0.010 0.001 TYR R 363 ARG 0.011 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.986 Fit side-chains REVERT: A 16 GLU cc_start: 0.6967 (tt0) cc_final: 0.6593 (tt0) REVERT: A 25 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7593 (tttp) REVERT: A 283 ARG cc_start: 0.7415 (mtt180) cc_final: 0.7056 (mtt-85) REVERT: A 389 ARG cc_start: 0.7377 (ttp-110) cc_final: 0.7078 (mtp180) REVERT: B 23 LYS cc_start: 0.8210 (ttpp) cc_final: 0.7963 (tppt) REVERT: B 46 ARG cc_start: 0.7587 (mtm180) cc_final: 0.7066 (mmm-85) REVERT: B 76 ASP cc_start: 0.8832 (p0) cc_final: 0.8490 (p0) REVERT: B 134 ARG cc_start: 0.7135 (OUTLIER) cc_final: 0.6429 (mmp80) REVERT: B 186 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7328 (m-30) REVERT: B 219 ARG cc_start: 0.7721 (mtp85) cc_final: 0.7515 (mmt90) REVERT: G 20 LYS cc_start: 0.7994 (mttm) cc_final: 0.7702 (mtmm) REVERT: G 32 LYS cc_start: 0.8612 (tmtt) cc_final: 0.8339 (tptm) REVERT: N 5 GLN cc_start: 0.7593 (tp-100) cc_final: 0.7302 (mm110) REVERT: N 19 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8199 (ttt180) REVERT: N 25 SER cc_start: 0.8555 (OUTLIER) cc_final: 0.8073 (p) REVERT: N 34 MET cc_start: 0.8978 (mmm) cc_final: 0.8557 (mmm) REVERT: R 206 MET cc_start: 0.8580 (mtm) cc_final: 0.8365 (mtp) REVERT: R 225 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7330 (mtp85) REVERT: R 333 ASN cc_start: 0.7657 (t0) cc_final: 0.7378 (t0) outliers start: 21 outliers final: 10 residues processed: 144 average time/residue: 1.4143 time to fit residues: 214.5338 Evaluate side-chains 134 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 177 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN B 142 HIS B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN N 31 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8346 Z= 0.156 Angle : 0.485 12.822 11305 Z= 0.254 Chirality : 0.041 0.135 1246 Planarity : 0.004 0.044 1443 Dihedral : 4.246 21.172 1119 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.62 % Allowed : 13.33 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.26), residues: 1001 helix: 0.49 (0.26), residues: 402 sheet: -0.24 (0.33), residues: 220 loop : -0.80 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.007 0.001 HIS A 220 PHE 0.015 0.001 PHE R 260 TYR 0.010 0.001 TYR N 80 ARG 0.011 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 125 time to evaluate : 0.955 Fit side-chains REVERT: A 16 GLU cc_start: 0.6932 (tt0) cc_final: 0.6567 (tt0) REVERT: A 25 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7608 (tttp) REVERT: A 283 ARG cc_start: 0.7413 (mtt180) cc_final: 0.7073 (mtt-85) REVERT: A 389 ARG cc_start: 0.7440 (ttp-110) cc_final: 0.7110 (mtp180) REVERT: B 23 LYS cc_start: 0.8207 (ttpp) cc_final: 0.7968 (tppt) REVERT: B 46 ARG cc_start: 0.7587 (mtm180) cc_final: 0.7050 (mmm-85) REVERT: B 76 ASP cc_start: 0.8796 (p0) cc_final: 0.8423 (p0) REVERT: B 86 THR cc_start: 0.8681 (m) cc_final: 0.8240 (p) REVERT: B 134 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6491 (mmp80) REVERT: B 186 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7346 (m-30) REVERT: B 217 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8012 (ppp) REVERT: B 291 ASP cc_start: 0.7680 (p0) cc_final: 0.7407 (p0) REVERT: G 20 LYS cc_start: 0.8182 (mttm) cc_final: 0.7866 (mtmm) REVERT: G 32 LYS cc_start: 0.8554 (tmtt) cc_final: 0.8263 (tptm) REVERT: N 5 GLN cc_start: 0.7544 (tp-100) cc_final: 0.7241 (mm110) REVERT: N 19 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8140 (ttt180) REVERT: N 25 SER cc_start: 0.8595 (OUTLIER) cc_final: 0.8111 (p) REVERT: N 34 MET cc_start: 0.8967 (mmm) cc_final: 0.8528 (mmm) REVERT: N 89 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6990 (pm20) REVERT: R 225 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7395 (mtp85) REVERT: R 333 ASN cc_start: 0.7656 (t0) cc_final: 0.7389 (t0) outliers start: 23 outliers final: 11 residues processed: 137 average time/residue: 1.4580 time to fit residues: 210.2156 Evaluate side-chains 136 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 177 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 36 ASN B 142 HIS B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8346 Z= 0.197 Angle : 0.505 13.898 11305 Z= 0.262 Chirality : 0.042 0.134 1246 Planarity : 0.004 0.044 1443 Dihedral : 4.329 20.580 1119 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.30 % Allowed : 13.33 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1001 helix: 0.79 (0.26), residues: 398 sheet: -0.20 (0.33), residues: 225 loop : -0.70 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 339 HIS 0.008 0.001 HIS A 220 PHE 0.015 0.001 PHE N 108 TYR 0.011 0.001 TYR A 339 ARG 0.010 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 1.169 Fit side-chains REVERT: A 25 LYS cc_start: 0.8152 (ttmm) cc_final: 0.7622 (tttp) REVERT: A 283 ARG cc_start: 0.7388 (mtt180) cc_final: 0.7033 (mtt-85) REVERT: A 389 ARG cc_start: 0.7449 (ttp-110) cc_final: 0.7111 (mtp180) REVERT: B 23 LYS cc_start: 0.8220 (ttpp) cc_final: 0.7975 (tppt) REVERT: B 46 ARG cc_start: 0.7595 (mtm180) cc_final: 0.7239 (mmt-90) REVERT: B 76 ASP cc_start: 0.8766 (p0) cc_final: 0.8344 (p0) REVERT: B 86 THR cc_start: 0.8665 (m) cc_final: 0.8266 (p) REVERT: B 134 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6459 (mmp80) REVERT: B 186 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: B 214 ARG cc_start: 0.7862 (mmt180) cc_final: 0.7592 (mpp-170) REVERT: B 291 ASP cc_start: 0.7686 (p0) cc_final: 0.7420 (p0) REVERT: B 312 ASP cc_start: 0.7953 (m-30) cc_final: 0.7746 (m-30) REVERT: G 20 LYS cc_start: 0.8074 (mttm) cc_final: 0.7782 (mtmm) REVERT: G 32 LYS cc_start: 0.8548 (tmtt) cc_final: 0.8242 (tptm) REVERT: N 5 GLN cc_start: 0.7581 (tp-100) cc_final: 0.7285 (mm110) REVERT: N 19 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.8187 (ttt180) REVERT: N 25 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8073 (p) REVERT: N 34 MET cc_start: 0.8960 (mmm) cc_final: 0.8508 (mmm) REVERT: N 89 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7019 (pm20) REVERT: R 206 MET cc_start: 0.8636 (mtm) cc_final: 0.7970 (mtm) REVERT: R 225 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7408 (mtp85) REVERT: R 333 ASN cc_start: 0.7741 (t0) cc_final: 0.7460 (t0) outliers start: 29 outliers final: 16 residues processed: 137 average time/residue: 1.3816 time to fit residues: 199.5739 Evaluate side-chains 138 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 117 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 177 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 142 HIS B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8346 Z= 0.212 Angle : 0.511 14.116 11305 Z= 0.265 Chirality : 0.042 0.133 1246 Planarity : 0.004 0.044 1443 Dihedral : 4.364 20.747 1119 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.30 % Allowed : 13.55 % Favored : 83.14 % 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: 0.07 (0.26), residues: 1001 helix: 0.91 (0.26), residues: 398 sheet: -0.15 (0.34), residues: 225 loop : -0.63 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.008 0.001 HIS A 220 PHE 0.015 0.001 PHE N 108 TYR 0.011 0.001 TYR A 339 ARG 0.009 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.906 Fit side-chains REVERT: A 16 GLU cc_start: 0.6775 (tt0) cc_final: 0.6484 (tp30) REVERT: A 25 LYS cc_start: 0.8065 (ttmm) cc_final: 0.7553 (tttp) REVERT: A 283 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6975 (mtt-85) REVERT: A 389 ARG cc_start: 0.7437 (ttp-110) cc_final: 0.7022 (mtp180) REVERT: B 23 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7977 (tppt) REVERT: B 46 ARG cc_start: 0.7525 (mtm180) cc_final: 0.7213 (mmt-90) REVERT: B 76 ASP cc_start: 0.8776 (p0) cc_final: 0.8365 (p0) REVERT: B 134 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6507 (mmp80) REVERT: B 214 ARG cc_start: 0.7949 (mmt180) cc_final: 0.7689 (mpp-170) REVERT: B 217 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7217 (ppp) REVERT: B 291 ASP cc_start: 0.7690 (p0) cc_final: 0.7423 (p0) REVERT: B 312 ASP cc_start: 0.7961 (m-30) cc_final: 0.7739 (m-30) REVERT: G 20 LYS cc_start: 0.8065 (mttm) cc_final: 0.7780 (mtmm) REVERT: G 32 LYS cc_start: 0.8499 (tmtt) cc_final: 0.8206 (tptm) REVERT: N 5 GLN cc_start: 0.7616 (tp-100) cc_final: 0.7272 (mm110) REVERT: N 19 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8194 (ttt180) REVERT: N 34 MET cc_start: 0.8945 (mmm) cc_final: 0.8529 (mmm) REVERT: N 89 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7023 (pm20) REVERT: R 225 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7434 (mtp85) REVERT: R 333 ASN cc_start: 0.7764 (t0) cc_final: 0.7472 (t0) outliers start: 29 outliers final: 16 residues processed: 130 average time/residue: 1.4199 time to fit residues: 194.4622 Evaluate side-chains 129 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 177 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 58 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 155 ASN B 220 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8346 Z= 0.270 Angle : 0.550 15.772 11305 Z= 0.284 Chirality : 0.044 0.140 1246 Planarity : 0.004 0.044 1443 Dihedral : 4.541 22.513 1119 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.76 % Allowed : 13.55 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1001 helix: 0.88 (0.26), residues: 398 sheet: -0.15 (0.34), residues: 229 loop : -0.62 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 47 HIS 0.010 0.002 HIS A 220 PHE 0.018 0.002 PHE N 108 TYR 0.012 0.002 TYR A 339 ARG 0.009 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 112 time to evaluate : 0.884 Fit side-chains REVERT: A 16 GLU cc_start: 0.6864 (tt0) cc_final: 0.6614 (tp30) REVERT: A 25 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7617 (tttp) REVERT: A 283 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6975 (mtt-85) REVERT: A 389 ARG cc_start: 0.7451 (ttp-110) cc_final: 0.7019 (mtp180) REVERT: B 13 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7308 (tp40) REVERT: B 23 LYS cc_start: 0.8095 (ttpp) cc_final: 0.7787 (tppt) REVERT: B 46 ARG cc_start: 0.7537 (mtm180) cc_final: 0.7229 (mmt-90) REVERT: B 76 ASP cc_start: 0.8785 (p0) cc_final: 0.8345 (p0) REVERT: B 134 ARG cc_start: 0.7078 (OUTLIER) cc_final: 0.6447 (mmp80) REVERT: B 214 ARG cc_start: 0.7953 (mmt180) cc_final: 0.7722 (mpp-170) REVERT: B 217 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7154 (ppp) REVERT: B 291 ASP cc_start: 0.7716 (p0) cc_final: 0.7442 (p0) REVERT: B 312 ASP cc_start: 0.7973 (m-30) cc_final: 0.7743 (m-30) REVERT: G 20 LYS cc_start: 0.8065 (mttm) cc_final: 0.7691 (mtmm) REVERT: G 32 LYS cc_start: 0.8481 (tmtt) cc_final: 0.8136 (tptm) REVERT: N 5 GLN cc_start: 0.7636 (tp-100) cc_final: 0.7295 (mm110) REVERT: N 19 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8213 (ttt180) REVERT: N 34 MET cc_start: 0.8945 (mmm) cc_final: 0.8558 (mmm) REVERT: N 89 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7031 (pm20) REVERT: R 333 ASN cc_start: 0.7815 (t0) cc_final: 0.7476 (t0) outliers start: 33 outliers final: 16 residues processed: 131 average time/residue: 1.3437 time to fit residues: 185.6616 Evaluate side-chains 129 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 140 LEU Chi-restraints excluded: chain R residue 177 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.1980 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.0000 chunk 75 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 8346 Z= 0.123 Angle : 0.461 11.620 11305 Z= 0.242 Chirality : 0.041 0.133 1246 Planarity : 0.003 0.045 1443 Dihedral : 4.143 18.938 1119 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.19 % Allowed : 14.58 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 1001 helix: 1.29 (0.27), residues: 396 sheet: 0.04 (0.35), residues: 215 loop : -0.49 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.001 PHE R 260 TYR 0.009 0.001 TYR R 363 ARG 0.009 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 0.950 Fit side-chains REVERT: A 16 GLU cc_start: 0.6763 (tt0) cc_final: 0.6474 (tp30) REVERT: A 283 ARG cc_start: 0.7381 (mtt180) cc_final: 0.7009 (mtt-85) REVERT: A 389 ARG cc_start: 0.7412 (ttp-110) cc_final: 0.7109 (mtp180) REVERT: B 13 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7297 (tp-100) REVERT: B 23 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7845 (tppt) REVERT: B 46 ARG cc_start: 0.7609 (mtm180) cc_final: 0.7254 (mmt-90) REVERT: B 76 ASP cc_start: 0.8694 (p0) cc_final: 0.8276 (p0) REVERT: B 134 ARG cc_start: 0.7069 (OUTLIER) cc_final: 0.6473 (mmp80) REVERT: B 214 ARG cc_start: 0.7999 (mmt180) cc_final: 0.7737 (mpp-170) REVERT: B 217 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8046 (ppp) REVERT: B 291 ASP cc_start: 0.7594 (p0) cc_final: 0.7319 (p0) REVERT: B 312 ASP cc_start: 0.7932 (m-30) cc_final: 0.7691 (m-30) REVERT: G 20 LYS cc_start: 0.8073 (mttm) cc_final: 0.7713 (mtmm) REVERT: G 32 LYS cc_start: 0.8483 (tmtt) cc_final: 0.8191 (tptm) REVERT: N 5 GLN cc_start: 0.7562 (tp-100) cc_final: 0.7179 (mm110) REVERT: N 19 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8222 (ttt180) REVERT: N 34 MET cc_start: 0.8934 (mmm) cc_final: 0.8538 (mmm) REVERT: N 52 SER cc_start: 0.8488 (OUTLIER) cc_final: 0.8270 (p) REVERT: N 87 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7685 (ptpp) REVERT: N 89 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6795 (pm20) REVERT: R 333 ASN cc_start: 0.7718 (t0) cc_final: 0.7439 (t0) outliers start: 28 outliers final: 17 residues processed: 138 average time/residue: 1.2580 time to fit residues: 183.9375 Evaluate side-chains 142 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 177 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8346 Z= 0.209 Angle : 0.514 13.714 11305 Z= 0.267 Chirality : 0.042 0.141 1246 Planarity : 0.004 0.045 1443 Dihedral : 4.272 19.752 1119 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.42 % Allowed : 14.58 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.26), residues: 1001 helix: 1.28 (0.26), residues: 393 sheet: 0.06 (0.35), residues: 216 loop : -0.45 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 47 HIS 0.009 0.001 HIS A 220 PHE 0.015 0.001 PHE N 108 TYR 0.011 0.001 TYR A 339 ARG 0.008 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 113 time to evaluate : 1.032 Fit side-chains REVERT: A 16 GLU cc_start: 0.6789 (tt0) cc_final: 0.6406 (tp30) REVERT: A 20 ARG cc_start: 0.7341 (mtm110) cc_final: 0.6865 (mtm110) REVERT: A 25 LYS cc_start: 0.8076 (ttmm) cc_final: 0.7593 (tttp) REVERT: A 283 ARG cc_start: 0.7398 (mtt180) cc_final: 0.7025 (mtt-85) REVERT: A 389 ARG cc_start: 0.7455 (ttp-110) cc_final: 0.7110 (mtp180) REVERT: A 392 GLU cc_start: 0.7400 (mm-30) cc_final: 0.7026 (mm-30) REVERT: B 13 GLN cc_start: 0.7679 (OUTLIER) cc_final: 0.7305 (tp-100) REVERT: B 23 LYS cc_start: 0.8103 (ttpp) cc_final: 0.7777 (tppt) REVERT: B 46 ARG cc_start: 0.7585 (mtm180) cc_final: 0.7268 (mmt-90) REVERT: B 76 ASP cc_start: 0.8747 (p0) cc_final: 0.8298 (p0) REVERT: B 134 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6402 (mmp80) REVERT: B 214 ARG cc_start: 0.7966 (mmt180) cc_final: 0.7709 (mpp-170) REVERT: B 217 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8071 (ppp) REVERT: B 291 ASP cc_start: 0.7697 (p0) cc_final: 0.7419 (p0) REVERT: B 312 ASP cc_start: 0.7953 (m-30) cc_final: 0.7713 (m-30) REVERT: G 20 LYS cc_start: 0.8001 (mttm) cc_final: 0.7625 (mtmm) REVERT: G 32 LYS cc_start: 0.8467 (tmtt) cc_final: 0.8176 (tptm) REVERT: N 5 GLN cc_start: 0.7583 (tp-100) cc_final: 0.7192 (mm110) REVERT: N 19 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8235 (ttt180) REVERT: N 34 MET cc_start: 0.8955 (mmm) cc_final: 0.8552 (mmm) REVERT: N 89 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: R 333 ASN cc_start: 0.7767 (t0) cc_final: 0.7438 (t0) outliers start: 30 outliers final: 18 residues processed: 132 average time/residue: 1.3385 time to fit residues: 186.8942 Evaluate side-chains 135 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain P residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 78 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 17 GLN B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8346 Z= 0.152 Angle : 0.485 12.121 11305 Z= 0.254 Chirality : 0.041 0.142 1246 Planarity : 0.004 0.045 1443 Dihedral : 4.177 19.170 1119 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.96 % Allowed : 14.69 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.27), residues: 1001 helix: 1.37 (0.27), residues: 396 sheet: 0.13 (0.35), residues: 215 loop : -0.39 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.008 0.001 HIS A 220 PHE 0.016 0.001 PHE R 260 TYR 0.009 0.001 TYR R 363 ARG 0.008 0.000 ARG R 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 0.906 Fit side-chains REVERT: A 16 GLU cc_start: 0.6777 (tt0) cc_final: 0.6375 (tp30) REVERT: A 20 ARG cc_start: 0.7374 (mtm110) cc_final: 0.6893 (mtm110) REVERT: A 25 LYS cc_start: 0.8057 (ttmm) cc_final: 0.7615 (tttp) REVERT: A 283 ARG cc_start: 0.7391 (mtt180) cc_final: 0.7017 (mtt-85) REVERT: A 389 ARG cc_start: 0.7452 (ttp-110) cc_final: 0.7117 (mtp180) REVERT: A 392 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7149 (mm-30) REVERT: B 13 GLN cc_start: 0.7786 (OUTLIER) cc_final: 0.7438 (tp-100) REVERT: B 23 LYS cc_start: 0.8056 (ttpp) cc_final: 0.7772 (tppt) REVERT: B 46 ARG cc_start: 0.7604 (mtm180) cc_final: 0.7253 (mmt-90) REVERT: B 59 TYR cc_start: 0.8912 (OUTLIER) cc_final: 0.8647 (m-80) REVERT: B 76 ASP cc_start: 0.8714 (p0) cc_final: 0.8268 (p0) REVERT: B 134 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6455 (mmp80) REVERT: B 214 ARG cc_start: 0.7997 (mmt180) cc_final: 0.7729 (mpp-170) REVERT: B 217 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8048 (ppp) REVERT: B 291 ASP cc_start: 0.7637 (p0) cc_final: 0.7375 (p0) REVERT: B 312 ASP cc_start: 0.7926 (m-30) cc_final: 0.7669 (m-30) REVERT: B 325 MET cc_start: 0.8481 (tpp) cc_final: 0.8252 (mmm) REVERT: G 20 LYS cc_start: 0.8013 (mttm) cc_final: 0.7649 (mtmm) REVERT: G 32 LYS cc_start: 0.8470 (tmtt) cc_final: 0.8181 (tptm) REVERT: N 5 GLN cc_start: 0.7560 (tp-100) cc_final: 0.7173 (mm110) REVERT: N 19 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8243 (ttt180) REVERT: N 34 MET cc_start: 0.8945 (mmm) cc_final: 0.8536 (mmm) REVERT: N 52 SER cc_start: 0.8495 (OUTLIER) cc_final: 0.8248 (p) REVERT: N 89 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: R 333 ASN cc_start: 0.7755 (t0) cc_final: 0.7430 (t0) outliers start: 26 outliers final: 18 residues processed: 129 average time/residue: 1.3890 time to fit residues: 189.1663 Evaluate side-chains 141 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 46 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 19 ARG Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 89 GLU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain R residue 125 LEU Chi-restraints excluded: chain R residue 177 SER Chi-restraints excluded: chain P residue 7 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 32 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 56 optimal weight: 0.0970 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 ASN B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 355 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.135422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.103139 restraints weight = 17154.977| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.48 r_work: 0.2878 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 35 | |-----------------------------------------------------------------------------| r_final: 0.2861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 8346 Z= 0.192 Angle : 0.898 59.194 11305 Z= 0.524 Chirality : 0.045 0.617 1246 Planarity : 0.004 0.045 1443 Dihedral : 4.236 24.104 1119 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.42 % Allowed : 14.24 % Favored : 82.35 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.27), residues: 1001 helix: 1.34 (0.27), residues: 396 sheet: 0.14 (0.35), residues: 215 loop : -0.39 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 339 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.001 PHE R 260 TYR 0.009 0.001 TYR A 339 ARG 0.006 0.000 ARG R 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3578.27 seconds wall clock time: 64 minutes 18.38 seconds (3858.38 seconds total)