Starting phenix.real_space_refine (version: dev) on Mon Dec 12 06:54:19 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/12_2022/7tyi_26180_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/12_2022/7tyi_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_26180/12_2022/7tyi_26180.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/12_2022/7tyi_26180.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/12_2022/7tyi_26180_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tyi_26180/12_2022/7tyi_26180_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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 Convert atoms to be neutral 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 12 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: 5.82, per 1000 atoms: 0.62 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: 3.31 Conformation dependent library (CDL) restraints added in 1.5 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: 1.07 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: 2.57 Time building geometry restraints manager: 3.54 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: 5272 17.92 - 35.85: 385 35.85 - 53.77: 69 53.77 - 71.70: 18 71.70 - 89.62: 7 Dihedral angle restraints: 5751 sinusoidal: 2385 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 5748 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1132 0.046 - 0.091: 207 0.091 - 0.137: 73 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 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. 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: 0.840 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: 0.000 Extract box with map and model: 5.770 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 26.450 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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= 0.254 Angle : 0.563 7.483 12969 Z= 0.367 Chirality : 0.041 0.229 1418 Planarity : 0.003 0.031 1639 Dihedral : 12.857 89.619 3556 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 1.50 % 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 *********************** 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 : 1.096 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 158 average time/residue: 0.2612 time to fit residues: 55.0070 Evaluate side-chains 112 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 106 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0979 time to fit residues: 2.7132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 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: 0.3980 chunk 65 optimal weight: 1.9990 chunk 101 optimal weight: 0.0870 overall best weight: 0.2694 ------------------------------------------------------------------------------- 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 279 ASN A 371 ASN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 257 GLN R 288 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9616 Z= 0.148 Angle : 0.492 8.338 12969 Z= 0.259 Chirality : 0.039 0.159 1418 Planarity : 0.004 0.036 1639 Dihedral : 5.055 57.975 1412 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer Outliers : 1.30 % 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: -0.94 (0.24), residues: 1136 helix: 0.16 (0.24), residues: 426 sheet: -0.45 (0.34), residues: 231 loop : -1.36 (0.27), residues: 479 *********************** 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 124 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.284 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 9 residues processed: 119 average time/residue: 0.2116 time to fit residues: 35.9206 Evaluate side-chains 111 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0912 time to fit residues: 2.9207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 266 HIS N 31 ASN P 14 ASN R 296 HIS R 377 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 9616 Z= 0.229 Angle : 0.521 6.912 12969 Z= 0.275 Chirality : 0.041 0.184 1418 Planarity : 0.004 0.034 1639 Dihedral : 5.421 58.739 1412 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 1.50 % 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: -0.54 (0.25), residues: 1136 helix: 0.65 (0.25), residues: 427 sheet: -0.41 (0.35), residues: 205 loop : -1.18 (0.27), residues: 504 *********************** 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 122 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 118 average time/residue: 0.2227 time to fit residues: 36.8716 Evaluate side-chains 109 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0894 time to fit residues: 2.9679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 102 optimal weight: 0.1980 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 0.0870 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 B 268 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9616 Z= 0.137 Angle : 0.453 8.603 12969 Z= 0.238 Chirality : 0.039 0.146 1418 Planarity : 0.003 0.039 1639 Dihedral : 5.053 58.308 1412 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer Outliers : 0.80 % 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: -0.14 (0.25), residues: 1136 helix: 1.09 (0.26), residues: 421 sheet: -0.26 (0.35), residues: 205 loop : -1.00 (0.27), residues: 510 *********************** 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 118 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 1.110 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 113 average time/residue: 0.2368 time to fit residues: 37.4860 Evaluate side-chains 106 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.969 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0960 time to fit residues: 2.4202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0270 chunk 1 optimal weight: 0.6980 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 74 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.5444 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 9616 Z= 0.312 Angle : 0.548 7.673 12969 Z= 0.288 Chirality : 0.043 0.157 1418 Planarity : 0.004 0.039 1639 Dihedral : 5.900 59.430 1412 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer Outliers : 1.90 % 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: -0.34 (0.25), residues: 1136 helix: 0.81 (0.26), residues: 425 sheet: -0.55 (0.34), residues: 204 loop : -0.91 (0.27), residues: 507 *********************** 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 117 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 1.000 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 107 average time/residue: 0.2608 time to fit residues: 37.9751 Evaluate side-chains 101 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 88 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1054 time to fit residues: 3.7972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.1980 chunk 56 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 9616 Z= 0.144 Angle : 0.461 7.441 12969 Z= 0.242 Chirality : 0.039 0.155 1418 Planarity : 0.003 0.040 1639 Dihedral : 5.346 59.655 1412 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1136 helix: 1.19 (0.26), residues: 423 sheet: -0.40 (0.34), residues: 211 loop : -0.77 (0.28), residues: 502 *********************** 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 117 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 1.086 Fit side-chains outliers start: 16 outliers final: 8 residues processed: 112 average time/residue: 0.2533 time to fit residues: 38.7836 Evaluate side-chains 103 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 1.036 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0920 time to fit residues: 2.9469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 40.0000 chunk 91 optimal weight: 0.4980 chunk 60 optimal weight: 0.0980 chunk 107 optimal weight: 0.0170 chunk 67 optimal weight: 0.2980 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.059 9616 Z= 0.138 Angle : 0.462 7.470 12969 Z= 0.242 Chirality : 0.039 0.159 1418 Planarity : 0.003 0.040 1639 Dihedral : 5.041 58.997 1412 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 0.80 % 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: 0.17 (0.25), residues: 1136 helix: 1.37 (0.26), residues: 423 sheet: -0.24 (0.35), residues: 206 loop : -0.78 (0.28), residues: 507 *********************** 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 113 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.999 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 110 average time/residue: 0.2504 time to fit residues: 37.7161 Evaluate side-chains 102 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.998 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0915 time to fit residues: 2.6105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.0970 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 20 optimal weight: 0.0470 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 84 optimal weight: 20.0000 chunk 98 optimal weight: 0.1980 chunk 103 optimal weight: 0.1980 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 9616 Z= 0.125 Angle : 0.452 9.213 12969 Z= 0.235 Chirality : 0.038 0.150 1418 Planarity : 0.003 0.040 1639 Dihedral : 4.749 57.372 1412 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer Outliers : 0.50 % 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: 0.36 (0.26), residues: 1136 helix: 1.62 (0.26), residues: 416 sheet: -0.24 (0.35), residues: 210 loop : -0.67 (0.28), residues: 510 *********************** 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 108 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 1.142 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 107 average time/residue: 0.2518 time to fit residues: 36.8840 Evaluate side-chains 97 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 94 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0920 time to fit residues: 2.0344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.0980 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 106 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 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: 0.7950 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 9616 Z= 0.140 Angle : 0.457 7.492 12969 Z= 0.240 Chirality : 0.039 0.150 1418 Planarity : 0.003 0.040 1639 Dihedral : 4.818 57.343 1412 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.10 % 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: 0.41 (0.26), residues: 1136 helix: 1.65 (0.26), residues: 416 sheet: -0.08 (0.35), residues: 205 loop : -0.69 (0.28), residues: 515 *********************** 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 99 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 1.142 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.2597 time to fit residues: 34.8621 Evaluate side-chains 96 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 95 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0875 time to fit residues: 1.7244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 111 optimal weight: 0.3980 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 70 optimal weight: 0.5980 chunk 94 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9616 Z= 0.158 Angle : 0.473 10.361 12969 Z= 0.245 Chirality : 0.039 0.148 1418 Planarity : 0.003 0.040 1639 Dihedral : 4.893 57.588 1412 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 0.40 % 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: 0.37 (0.26), residues: 1136 helix: 1.60 (0.26), residues: 416 sheet: -0.11 (0.35), residues: 205 loop : -0.69 (0.28), residues: 515 ********************** 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 103 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 1.086 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.2631 time to fit residues: 36.6295 Evaluate side-chains 98 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 95 time to evaluate : 1.116 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0922 time to fit residues: 2.1356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.0070 chunk 37 optimal weight: 4.9990 chunk 91 optimal weight: 0.1980 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 overall best weight: 0.9078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.191782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.141419 restraints weight = 10305.298| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.11 r_work: 0.3410 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9616 Z= 0.202 Angle : 0.496 7.538 12969 Z= 0.260 Chirality : 0.040 0.148 1418 Planarity : 0.003 0.040 1639 Dihedral : 5.268 59.558 1412 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer Outliers : 0.00 % 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: 0.24 (0.25), residues: 1136 helix: 1.36 (0.26), residues: 425 sheet: -0.25 (0.35), residues: 211 loop : -0.66 (0.28), residues: 500 =============================================================================== Job complete usr+sys time: 2181.86 seconds wall clock time: 40 minutes 17.55 seconds (2417.55 seconds total)