Starting phenix.real_space_refine on Wed Feb 14 13:55:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/02_2024/7tyi_26180_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/02_2024/7tyi_26180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/02_2024/7tyi_26180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/02_2024/7tyi_26180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/02_2024/7tyi_26180_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/02_2024/7tyi_26180_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.087 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 67 5.16 5 C 6032 2.51 5 N 1603 2.21 5 O 1711 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "R GLU 106": "OE1" <-> "OE2" Residue "R GLU 204": "OE1" <-> "OE2" Residue "R GLU 255": "OE1" <-> "OE2" Residue "R GLU 334": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R GLU 397": "OE1" <-> "OE2" 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: 9413 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1889 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "P" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 274 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Chain: "R" Number of atoms: 3247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3247 Unusual residues: {'NAG': 2, 'PLM': 10} Classifications: {'peptide': 367, 'undetermined': 12} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 16, 'TRANS': 350, None: 12} Not linked: pdbres="PHE R 409 " pdbres="PLM R 512 " Not linked: pdbres="PLM R 512 " pdbres="NAG R 501 " Not linked: pdbres="NAG R 501 " pdbres="NAG R 502 " Not linked: pdbres="NAG R 502 " pdbres="PLM R 503 " Not linked: pdbres="PLM R 503 " pdbres="PLM R 504 " ... (remaining 7 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 5.38, per 1000 atoms: 0.57 Number of scatterers: 9413 At special positions: 0 Unit cell: (82.176, 99.296, 154.936, 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 67 16.00 O 1711 8.00 N 1603 7.00 C 6032 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, 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=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.04 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " 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 Links applied NAG-ASN " NAG R 501 " - " ASN R 130 " " NAG R 502 " - " ASN R 73 " Time building additional restraints: 3.63 Conformation dependent library (CDL) restraints added in 1.8 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 35.7% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'A' and resid 12 through 37 removed outlier: 3.517A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 removed outlier: 3.576A pdb=" N GLN A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 277 removed outlier: 3.688A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 316 removed outlier: 3.707A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.531A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.851A pdb=" N LEU A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.857A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 23 Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'R' and resid 39 through 61 removed outlier: 3.506A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS R 55 " --> pdb=" O ALA R 51 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN R 61 " --> pdb=" O ASP R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 172 removed outlier: 3.518A pdb=" N SER R 159 " --> pdb=" O GLY R 155 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE R 161 " --> pdb=" O SER R 157 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE R 165 " --> pdb=" O PHE R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 176 No H-bonds generated for 'chain 'R' and resid 174 through 176' Processing helix chain 'R' and resid 179 through 204 removed outlier: 4.013A pdb=" N LEU R 183 " --> pdb=" O GLN R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 214 Processing helix chain 'R' and resid 217 through 246 removed outlier: 3.637A pdb=" N ALA R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU R 238 " --> pdb=" O TYR R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 269 through 281 Proline residue: R 273 - end of helix removed outlier: 3.573A pdb=" N ILE R 276 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS R 277 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA R 278 " --> pdb=" O THR R 275 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE R 279 " --> pdb=" O ILE R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 296 through 328 removed outlier: 3.738A pdb=" N TYR R 299 " --> pdb=" O HIS R 296 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS R 302 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY R 303 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 3.948A pdb=" N VAL R 311 " --> pdb=" O ALA R 308 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL R 320 " --> pdb=" O LEU R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 352 removed outlier: 3.518A pdb=" N ILE R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU R 348 " --> pdb=" O ALA R 344 " (cutoff:3.500A) Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 358 removed outlier: 4.280A pdb=" N VAL R 358 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 366 through 391 removed outlier: 4.021A pdb=" N PHE R 382 " --> pdb=" O SER R 378 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN R 383 " --> pdb=" O LEU R 379 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N GLY R 384 " --> pdb=" O ILE R 380 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N PHE R 385 " --> pdb=" O HIS R 381 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N PHE R 386 " --> pdb=" O PHE R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 396 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.507A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 69 through 74 removed outlier: 3.652A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.670A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.708A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.130A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.081A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.782A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.880A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 45 through 47 removed outlier: 3.696A pdb=" N VAL N 93 " --> pdb=" O GLN N 39 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 49 through 51 removed outlier: 3.585A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2488 1.33 - 1.45: 1848 1.45 - 1.58: 5184 1.58 - 1.70: 0 1.70 - 1.82: 96 Bond restraints: 9616 Sorted by residual: bond pdb=" CA SER A 286 " pdb=" CB SER A 286 " ideal model delta sigma weight residual 1.529 1.476 0.053 1.64e-02 3.72e+03 1.04e+01 bond pdb=" N THR A 285 " pdb=" CA THR A 285 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.23e-02 6.61e+03 8.49e+00 bond pdb=" N THR P 36 " pdb=" CA THR P 36 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.31e-02 5.83e+03 7.77e+00 bond pdb=" N LYS A 271 " pdb=" CA LYS A 271 " ideal model delta sigma weight residual 1.457 1.494 -0.037 1.33e-02 5.65e+03 7.71e+00 bond pdb=" N VAL P 17 " pdb=" CA VAL P 17 " ideal model delta sigma weight residual 1.461 1.494 -0.032 1.17e-02 7.31e+03 7.67e+00 ... (remaining 9611 not shown) Histogram of bond angle deviations from ideal: 100.62 - 107.30: 308 107.30 - 113.98: 5303 113.98 - 120.65: 4029 120.65 - 127.33: 3225 127.33 - 134.01: 104 Bond angle restraints: 12969 Sorted by residual: angle pdb=" N SER P 19 " pdb=" CA SER P 19 " pdb=" C SER P 19 " ideal model delta sigma weight residual 111.07 115.98 -4.91 1.07e+00 8.73e-01 2.11e+01 angle pdb=" CA ALA R 136 " pdb=" C ALA R 136 " pdb=" O ALA R 136 " ideal model delta sigma weight residual 121.94 117.03 4.91 1.15e+00 7.56e-01 1.82e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 112.96 109.04 3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N PHE R 137 " pdb=" CA PHE R 137 " pdb=" C PHE R 137 " ideal model delta sigma weight residual 113.40 107.86 5.54 1.47e+00 4.63e-01 1.42e+01 angle pdb=" CA THR R 138 " pdb=" C THR R 138 " pdb=" N PRO R 139 " ideal model delta sigma weight residual 117.44 121.65 -4.21 1.13e+00 7.83e-01 1.39e+01 ... (remaining 12964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 5300 17.92 - 35.85: 387 35.85 - 53.77: 69 53.77 - 71.70: 18 71.70 - 89.62: 7 Dihedral angle restraints: 5781 sinusoidal: 2415 harmonic: 3366 Sorted by residual: dihedral pdb=" CB CYS R 55 " pdb=" SG CYS R 55 " pdb=" SG CYS R 81 " pdb=" CB CYS R 81 " ideal model delta sinusoidal sigma weight residual -86.00 -153.21 67.21 1 1.00e+01 1.00e-02 5.88e+01 dihedral pdb=" CB CYS P 2 " pdb=" SG CYS P 2 " pdb=" SG CYS P 7 " pdb=" CB CYS P 7 " ideal model delta sinusoidal sigma weight residual 93.00 38.43 54.57 1 1.00e+01 1.00e-02 4.04e+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 -157.31 -22.69 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 5778 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1128 0.046 - 0.091: 210 0.091 - 0.137: 74 0.137 - 0.183: 3 0.183 - 0.229: 3 Chirality restraints: 1418 Sorted by residual: chirality pdb=" CA VAL P 32 " pdb=" N VAL P 32 " pdb=" C VAL P 32 " pdb=" CB VAL P 32 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA TYR P 37 " pdb=" N TYR P 37 " pdb=" C TYR P 37 " pdb=" CB TYR P 37 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CA PHE R 102 " pdb=" N PHE R 102 " pdb=" C PHE R 102 " pdb=" CB PHE R 102 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 1415 not shown) Planarity restraints: 1641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR R 98 " 0.007 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C TYR R 98 " -0.026 2.00e-02 2.50e+03 pdb=" O TYR R 98 " 0.010 2.00e-02 2.50e+03 pdb=" N PHE R 99 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA P 13 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C ALA P 13 " 0.024 2.00e-02 2.50e+03 pdb=" O ALA P 13 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN P 14 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO B 236 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.017 5.00e-02 4.00e+02 ... (remaining 1638 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1094 2.75 - 3.29: 9149 3.29 - 3.83: 14990 3.83 - 4.36: 18512 4.36 - 4.90: 31711 Nonbonded interactions: 75456 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.217 2.440 nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.248 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.252 2.440 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.284 2.440 nonbonded pdb=" NE2 GLN A 384 " pdb=" O ILE R 248 " model vdw 2.306 2.520 ... (remaining 75451 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=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: 0.990 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: 5.590 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.240 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 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 0.053 9616 Z= 0.257 Angle : 0.568 7.483 12969 Z= 0.367 Chirality : 0.041 0.229 1418 Planarity : 0.003 0.031 1639 Dihedral : 12.810 89.619 3586 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.50 % Allowed : 4.10 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.21), residues: 1136 helix: -2.47 (0.17), residues: 426 sheet: -0.89 (0.34), residues: 230 loop : -1.70 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 76 HIS 0.002 0.000 HIS R 121 PHE 0.010 0.001 PHE R 102 TYR 0.015 0.001 TYR R 56 ARG 0.004 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 1.037 Fit side-chains REVERT: P 16 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8419 (mt) REVERT: R 113 ASP cc_start: 0.2558 (OUTLIER) cc_final: 0.2204 (p0) REVERT: R 215 ASP cc_start: 0.6546 (p0) cc_final: 0.5963 (p0) REVERT: R 229 MET cc_start: 0.8055 (tpp) cc_final: 0.7766 (mmt) REVERT: R 359 PHE cc_start: 0.7587 (m-80) cc_final: 0.7345 (m-80) REVERT: R 396 ASN cc_start: 0.7795 (t0) cc_final: 0.7582 (t0) outliers start: 15 outliers final: 6 residues processed: 158 average time/residue: 0.2665 time to fit residues: 55.3610 Evaluate side-chains 113 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 113 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 0.0670 chunk 87 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 overall best weight: 0.3916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 340 ASN N 35 ASN N 53 GLN N 123 GLN P 3 ASN P 14 ASN R 93 GLN ** R 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 179 GLN R 288 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9616 Z= 0.149 Angle : 0.479 8.093 12969 Z= 0.250 Chirality : 0.039 0.153 1418 Planarity : 0.004 0.034 1639 Dihedral : 5.699 57.921 1453 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.20 % Allowed : 9.00 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.24), residues: 1136 helix: 0.13 (0.24), residues: 425 sheet: -0.45 (0.34), residues: 232 loop : -1.35 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.008 0.001 HIS R 336 PHE 0.010 0.001 PHE N 108 TYR 0.017 0.001 TYR A 358 ARG 0.007 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: B 270 ILE cc_start: 0.7826 (mm) cc_final: 0.7611 (mt) REVERT: P 16 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8259 (mm) REVERT: R 215 ASP cc_start: 0.6647 (p0) cc_final: 0.6064 (p0) outliers start: 22 outliers final: 14 residues processed: 124 average time/residue: 0.2159 time to fit residues: 37.7964 Evaluate side-chains 115 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 16 LEU Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 138 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.1980 chunk 31 optimal weight: 0.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 110 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN N 31 ASN P 14 ASN R 257 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9616 Z= 0.172 Angle : 0.471 6.455 12969 Z= 0.248 Chirality : 0.040 0.152 1418 Planarity : 0.003 0.034 1639 Dihedral : 5.417 57.905 1450 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.40 % Allowed : 10.90 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.25), residues: 1136 helix: 0.81 (0.26), residues: 427 sheet: -0.43 (0.34), residues: 216 loop : -1.12 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.005 0.001 HIS R 336 PHE 0.018 0.001 PHE N 108 TYR 0.017 0.001 TYR A 358 ARG 0.005 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.059 Fit side-chains REVERT: A 384 GLN cc_start: 0.8186 (tt0) cc_final: 0.7979 (tt0) REVERT: B 45 MET cc_start: 0.6999 (mtm) cc_final: 0.6653 (mtp) REVERT: B 270 ILE cc_start: 0.7919 (mm) cc_final: 0.7713 (mt) REVERT: R 215 ASP cc_start: 0.6791 (p0) cc_final: 0.6168 (p0) outliers start: 24 outliers final: 17 residues processed: 129 average time/residue: 0.2137 time to fit residues: 38.8307 Evaluate side-chains 118 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 138 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 7.9990 chunk 52 optimal weight: 0.0000 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 0.0020 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9616 Z= 0.125 Angle : 0.434 9.181 12969 Z= 0.227 Chirality : 0.038 0.142 1418 Planarity : 0.003 0.037 1639 Dihedral : 5.079 56.968 1448 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.20 % Allowed : 12.90 % Favored : 84.90 % 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 (0.25), residues: 1136 helix: 1.19 (0.26), residues: 421 sheet: -0.24 (0.35), residues: 205 loop : -0.98 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS A 220 PHE 0.010 0.001 PHE N 108 TYR 0.012 0.001 TYR B 59 ARG 0.003 0.000 ARG R 362 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.088 Fit side-chains REVERT: A 29 GLN cc_start: 0.7437 (tp40) cc_final: 0.7110 (mm-40) REVERT: B 45 MET cc_start: 0.7024 (mtm) cc_final: 0.6722 (mtp) REVERT: B 70 LEU cc_start: 0.7953 (pp) cc_final: 0.7712 (pp) REVERT: B 270 ILE cc_start: 0.7891 (mm) cc_final: 0.7681 (mt) REVERT: P 37 TYR cc_start: 0.5929 (OUTLIER) cc_final: 0.3985 (p90) REVERT: R 215 ASP cc_start: 0.6836 (p0) cc_final: 0.6221 (p0) REVERT: R 237 MET cc_start: 0.8289 (mtt) cc_final: 0.8047 (mtt) outliers start: 22 outliers final: 15 residues processed: 124 average time/residue: 0.2147 time to fit residues: 37.8983 Evaluate side-chains 114 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 98 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 133 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 30.0000 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN ** N 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 HIS R 377 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9616 Z= 0.371 Angle : 0.589 8.116 12969 Z= 0.310 Chirality : 0.044 0.149 1418 Planarity : 0.004 0.049 1639 Dihedral : 6.461 59.024 1448 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.60 % Allowed : 12.20 % Favored : 84.20 % 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: -0.42 (0.25), residues: 1136 helix: 0.71 (0.25), residues: 429 sheet: -0.54 (0.34), residues: 213 loop : -0.95 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 236 HIS 0.008 0.001 HIS B 54 PHE 0.024 0.002 PHE N 108 TYR 0.022 0.002 TYR B 59 ARG 0.008 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 95 time to evaluate : 1.180 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7805 (mtt90) cc_final: 0.7567 (mtm110) REVERT: B 45 MET cc_start: 0.7465 (mtm) cc_final: 0.7187 (mtp) REVERT: N 65 LYS cc_start: 0.8284 (tptt) cc_final: 0.8011 (tttm) REVERT: N 117 TYR cc_start: 0.8503 (m-80) cc_final: 0.8255 (m-80) REVERT: P 37 TYR cc_start: 0.6018 (OUTLIER) cc_final: 0.3953 (p90) REVERT: R 215 ASP cc_start: 0.6934 (p0) cc_final: 0.6383 (p0) outliers start: 36 outliers final: 27 residues processed: 123 average time/residue: 0.2665 time to fit residues: 43.5993 Evaluate side-chains 117 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 89 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 52 SER 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 N residue 122 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 112 CYS Chi-restraints excluded: chain R residue 133 MET Chi-restraints excluded: chain R residue 246 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 104 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 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9616 Z= 0.189 Angle : 0.492 8.381 12969 Z= 0.258 Chirality : 0.040 0.193 1418 Planarity : 0.003 0.039 1639 Dihedral : 5.957 59.172 1448 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.20 % Allowed : 12.80 % Favored : 84.00 % 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: -0.14 (0.25), residues: 1136 helix: 1.03 (0.26), residues: 424 sheet: -0.55 (0.34), residues: 203 loop : -0.80 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.013 0.001 PHE N 108 TYR 0.012 0.001 TYR R 391 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 265 ARG cc_start: 0.7783 (mtt90) cc_final: 0.7567 (mtm110) REVERT: B 45 MET cc_start: 0.7471 (mtm) cc_final: 0.7222 (mtp) REVERT: B 217 MET cc_start: 0.8426 (pmm) cc_final: 0.7973 (ptt) REVERT: N 65 LYS cc_start: 0.8281 (tptt) cc_final: 0.8009 (tttm) REVERT: P 37 TYR cc_start: 0.6000 (OUTLIER) cc_final: 0.4149 (p90) REVERT: R 101 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6201 (m-30) REVERT: R 215 ASP cc_start: 0.6945 (p0) cc_final: 0.6393 (p0) REVERT: R 359 PHE cc_start: 0.8053 (m-10) cc_final: 0.7808 (m-80) outliers start: 32 outliers final: 26 residues processed: 124 average time/residue: 0.2567 time to fit residues: 43.3693 Evaluate side-chains 122 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 94 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR 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 N residue 122 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 112 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.0470 chunk 79 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9616 Z= 0.173 Angle : 0.490 9.109 12969 Z= 0.253 Chirality : 0.040 0.179 1418 Planarity : 0.003 0.039 1639 Dihedral : 5.734 58.461 1448 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.30 % Allowed : 13.00 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1136 helix: 1.17 (0.26), residues: 424 sheet: -0.42 (0.34), residues: 209 loop : -0.78 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE N 108 TYR 0.011 0.001 TYR N 94 ARG 0.007 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 1.087 Fit side-chains REVERT: A 60 MET cc_start: 0.4252 (mmp) cc_final: 0.1935 (ttt) REVERT: A 265 ARG cc_start: 0.7777 (mtt90) cc_final: 0.7563 (mtm110) REVERT: B 45 MET cc_start: 0.7455 (mtm) cc_final: 0.7186 (mtp) REVERT: B 59 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7561 (t80) REVERT: B 217 MET cc_start: 0.8380 (pmm) cc_final: 0.8021 (ptt) REVERT: N 59 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7558 (p) REVERT: P 37 TYR cc_start: 0.6001 (OUTLIER) cc_final: 0.4304 (p90) REVERT: R 101 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6176 (m-30) REVERT: R 215 ASP cc_start: 0.6950 (p0) cc_final: 0.6407 (p0) REVERT: R 359 PHE cc_start: 0.7945 (m-10) cc_final: 0.7686 (m-80) outliers start: 33 outliers final: 25 residues processed: 120 average time/residue: 0.2803 time to fit residues: 45.0283 Evaluate side-chains 122 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER 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 N residue 122 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 112 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9616 Z= 0.167 Angle : 0.478 7.581 12969 Z= 0.249 Chirality : 0.040 0.171 1418 Planarity : 0.003 0.047 1639 Dihedral : 5.624 58.227 1448 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.20 % Allowed : 13.40 % Favored : 83.40 % 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 (0.25), residues: 1136 helix: 1.27 (0.26), residues: 424 sheet: -0.35 (0.34), residues: 209 loop : -0.79 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE N 108 TYR 0.011 0.001 TYR N 94 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 94 time to evaluate : 1.076 Fit side-chains REVERT: B 45 MET cc_start: 0.7485 (mtm) cc_final: 0.7215 (mtp) REVERT: B 59 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7558 (t80) REVERT: B 217 MET cc_start: 0.8387 (pmm) cc_final: 0.8005 (ptt) REVERT: N 59 SER cc_start: 0.8023 (OUTLIER) cc_final: 0.7487 (p) REVERT: P 37 TYR cc_start: 0.5972 (OUTLIER) cc_final: 0.4261 (p90) REVERT: R 101 ASP cc_start: 0.6970 (OUTLIER) cc_final: 0.6172 (m-30) REVERT: R 215 ASP cc_start: 0.6952 (p0) cc_final: 0.6400 (p0) REVERT: R 359 PHE cc_start: 0.7858 (m-10) cc_final: 0.7586 (m-80) outliers start: 32 outliers final: 26 residues processed: 118 average time/residue: 0.2409 time to fit residues: 39.1250 Evaluate side-chains 123 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER 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 N residue 122 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 112 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 0.0770 chunk 78 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9616 Z= 0.164 Angle : 0.481 9.245 12969 Z= 0.248 Chirality : 0.039 0.164 1418 Planarity : 0.003 0.043 1639 Dihedral : 5.550 58.182 1448 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.10 % Allowed : 13.50 % Favored : 83.40 % 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: 0.12 (0.25), residues: 1136 helix: 1.31 (0.26), residues: 425 sheet: -0.31 (0.34), residues: 209 loop : -0.77 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE N 108 TYR 0.011 0.001 TYR N 94 ARG 0.010 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 94 time to evaluate : 1.101 Fit side-chains REVERT: B 45 MET cc_start: 0.7473 (mtm) cc_final: 0.7203 (mtp) REVERT: B 217 MET cc_start: 0.8363 (pmm) cc_final: 0.8011 (ptt) REVERT: N 59 SER cc_start: 0.8022 (OUTLIER) cc_final: 0.7490 (p) REVERT: P 37 TYR cc_start: 0.5987 (OUTLIER) cc_final: 0.4285 (p90) REVERT: R 101 ASP cc_start: 0.6985 (OUTLIER) cc_final: 0.6141 (m-30) REVERT: R 215 ASP cc_start: 0.6939 (p0) cc_final: 0.6397 (p0) REVERT: R 359 PHE cc_start: 0.7722 (m-10) cc_final: 0.7380 (m-80) outliers start: 31 outliers final: 27 residues processed: 116 average time/residue: 0.2445 time to fit residues: 39.1186 Evaluate side-chains 123 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 93 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER 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 N residue 122 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 112 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN P 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9616 Z= 0.166 Angle : 0.475 7.273 12969 Z= 0.247 Chirality : 0.039 0.147 1418 Planarity : 0.003 0.042 1639 Dihedral : 5.458 58.072 1448 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.20 % Allowed : 13.50 % Favored : 83.30 % 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: 0.15 (0.25), residues: 1136 helix: 1.34 (0.26), residues: 425 sheet: -0.28 (0.34), residues: 209 loop : -0.76 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 211 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE N 108 TYR 0.010 0.001 TYR R 338 ARG 0.009 0.000 ARG B 219 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 93 time to evaluate : 1.045 Fit side-chains REVERT: B 217 MET cc_start: 0.8352 (pmm) cc_final: 0.7998 (ptt) REVERT: N 59 SER cc_start: 0.8035 (OUTLIER) cc_final: 0.7510 (p) REVERT: P 37 TYR cc_start: 0.5958 (OUTLIER) cc_final: 0.4204 (p90) REVERT: R 101 ASP cc_start: 0.7031 (OUTLIER) cc_final: 0.5977 (m-30) REVERT: R 213 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6525 (ttp80) REVERT: R 215 ASP cc_start: 0.7058 (p0) cc_final: 0.6533 (p0) REVERT: R 359 PHE cc_start: 0.7644 (m-10) cc_final: 0.7323 (m-80) outliers start: 32 outliers final: 29 residues processed: 116 average time/residue: 0.2298 time to fit residues: 37.0071 Evaluate side-chains 124 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 92 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 34 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 155 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER 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 N residue 122 THR Chi-restraints excluded: chain P residue 36 THR Chi-restraints excluded: chain P residue 37 TYR Chi-restraints excluded: chain R residue 48 MET Chi-restraints excluded: chain R residue 101 ASP Chi-restraints excluded: chain R residue 112 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 91 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 30.0000 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.191986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141862 restraints weight = 10337.979| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.14 r_work: 0.3412 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 9616 Z= 0.304 Angle : 0.871 59.145 12969 Z= 0.518 Chirality : 0.050 1.133 1418 Planarity : 0.003 0.041 1639 Dihedral : 5.536 58.058 1448 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.40 % Allowed : 13.40 % Favored : 83.20 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.12 (0.25), residues: 1136 helix: 1.33 (0.26), residues: 425 sheet: -0.31 (0.34), residues: 209 loop : -0.79 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 211 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE N 108 TYR 0.015 0.001 TYR R 338 ARG 0.010 0.000 ARG B 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2331.94 seconds wall clock time: 43 minutes 1.85 seconds (2581.85 seconds total)