Starting phenix.real_space_refine on Sun Apr 7 00:50:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/04_2024/7dur_30867_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/04_2024/7dur_30867.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/04_2024/7dur_30867_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/04_2024/7dur_30867_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/04_2024/7dur_30867_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/04_2024/7dur_30867.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/04_2024/7dur_30867.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/04_2024/7dur_30867_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dur_30867/04_2024/7dur_30867_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= 0.017 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: 5 Type Number sf(0) Gaussians S 54 5.16 5 Cl 2 4.86 5 C 5920 2.51 5 N 1571 2.21 5 O 1664 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 292": "OE1" <-> "OE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 348": "NH1" <-> "NH2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R GLU 387": "OE1" <-> "OE2" Residue "R GLU 418": "OE1" <-> "OE2" Residue "R ARG 421": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9211 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1957 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3264 Unusual residues: {'CLR': 6, 'HNO': 1} Classifications: {'peptide': 371, 'undetermined': 7} Link IDs: {'PTRANS': 14, 'TRANS': 356, None: 7} Not linked: pdbres="HIS R 424 " pdbres="HNO R 701 " Not linked: pdbres="HNO R 701 " pdbres="CLR R 702 " Not linked: pdbres="CLR R 702 " pdbres="CLR R 703 " Not linked: pdbres="CLR R 703 " pdbres="CLR R 704 " Not linked: pdbres="CLR R 704 " pdbres="CLR R 705 " ... (remaining 2 not shown) Chain breaks: 4 Time building chain proxies: 5.37, per 1000 atoms: 0.58 Number of scatterers: 9211 At special positions: 0 Unit cell: (94.05, 95.095, 156.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 54 16.00 O 1664 8.00 N 1571 7.00 C 5920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.01 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.49 Conformation dependent library (CDL) restraints added in 1.6 seconds 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 38.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 12 through 37 removed outlier: 3.876A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 316 No H-bonds generated for 'chain 'A' and resid 313 through 316' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.834A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 390 removed outlier: 3.757A pdb=" N VAL A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN A 377 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG A 389 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.319A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 45 removed outlier: 3.566A pdb=" N ALA G 45 " --> pdb=" O CYS G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 33 through 52 Processing helix chain 'R' and resid 90 through 93 Processing helix chain 'R' and resid 124 through 126 No H-bonds generated for 'chain 'R' and resid 124 through 126' Processing helix chain 'R' and resid 137 through 168 Processing helix chain 'R' and resid 175 through 211 removed outlier: 4.007A pdb=" N LEU R 201 " --> pdb=" O LYS R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 221 No H-bonds generated for 'chain 'R' and resid 218 through 221' Processing helix chain 'R' and resid 224 through 256 Processing helix chain 'R' and resid 264 through 291 Proline residue: R 277 - end of helix Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 303 through 336 removed outlier: 3.798A pdb=" N ILE R 308 " --> pdb=" O ASN R 304 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 346 through 360 removed outlier: 3.843A pdb=" N LYS R 351 " --> pdb=" O CYS R 347 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 367 removed outlier: 3.762A pdb=" N ILE R 366 " --> pdb=" O HIS R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 381 through 403 removed outlier: 4.162A pdb=" N THR R 391 " --> pdb=" O GLU R 387 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 423 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.332A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.562A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.520A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.637A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.747A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.241A 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: 6.646A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.405A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.595A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.619A 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 122 through 124 removed outlier: 3.509A pdb=" N TRP N 36 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 82 through 84 removed outlier: 3.549A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1137 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: 3.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2886 1.34 - 1.46: 2043 1.46 - 1.58: 4430 1.58 - 1.70: 1 1.70 - 1.82: 74 Bond restraints: 9434 Sorted by residual: bond pdb=" CA GLU A 314 " pdb=" C GLU A 314 " ideal model delta sigma weight residual 1.522 1.447 0.074 1.72e-02 3.38e+03 1.87e+01 bond pdb=" N LEU R 32 " pdb=" CA LEU R 32 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.40e-02 5.10e+03 9.53e+00 bond pdb=" CA SER R 31 " pdb=" C SER R 31 " ideal model delta sigma weight residual 1.523 1.562 -0.039 1.34e-02 5.57e+03 8.34e+00 bond pdb=" C17 CLR R 705 " pdb=" C20 CLR R 705 " ideal model delta sigma weight residual 1.535 1.587 -0.052 2.00e-02 2.50e+03 6.68e+00 bond pdb=" CB TRP A 277 " pdb=" CG TRP A 277 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 4.96e+00 ... (remaining 9429 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.63: 138 104.63 - 112.14: 4644 112.14 - 119.64: 3446 119.64 - 127.15: 4468 127.15 - 134.66: 127 Bond angle restraints: 12823 Sorted by residual: angle pdb=" N LEU R 32 " pdb=" CA LEU R 32 " pdb=" C LEU R 32 " ideal model delta sigma weight residual 113.15 103.96 9.19 1.19e+00 7.06e-01 5.97e+01 angle pdb=" C12 HNO R 701 " pdb=" C14 HNO R 701 " pdb=" N15 HNO R 701 " ideal model delta sigma weight residual 101.46 118.61 -17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" N HIS R 212 " pdb=" CA HIS R 212 " pdb=" C HIS R 212 " ideal model delta sigma weight residual 111.74 104.59 7.15 1.35e+00 5.49e-01 2.80e+01 angle pdb=" N15 HNO R 701 " pdb=" C14 HNO R 701 " pdb=" N28 HNO R 701 " ideal model delta sigma weight residual 137.73 123.19 14.54 3.00e+00 1.11e-01 2.35e+01 angle pdb=" C GLY R 275 " pdb=" N VAL R 276 " pdb=" CA VAL R 276 " ideal model delta sigma weight residual 120.24 117.19 3.05 6.30e-01 2.52e+00 2.34e+01 ... (remaining 12818 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5166 17.88 - 35.75: 517 35.75 - 53.63: 131 53.63 - 71.50: 42 71.50 - 89.38: 8 Dihedral angle restraints: 5864 sinusoidal: 2579 harmonic: 3285 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual 93.00 27.19 65.81 1 1.00e+01 1.00e-02 5.67e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 151.70 -58.70 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CB CYS R 62 " pdb=" SG CYS R 62 " pdb=" SG CYS R 104 " pdb=" CB CYS R 104 " ideal model delta sinusoidal sigma weight residual -86.00 -44.74 -41.26 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 5861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1267 0.095 - 0.190: 138 0.190 - 0.285: 13 0.285 - 0.381: 6 0.381 - 0.476: 2 Chirality restraints: 1426 Sorted by residual: chirality pdb=" CG LEU R 32 " pdb=" CB LEU R 32 " pdb=" CD1 LEU R 32 " pdb=" CD2 LEU R 32 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" C14 CLR R 703 " pdb=" C13 CLR R 703 " pdb=" C15 CLR R 703 " pdb=" C8 CLR R 703 " both_signs ideal model delta sigma weight residual False -2.32 -2.70 0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" C14 CLR R 702 " pdb=" C13 CLR R 702 " pdb=" C15 CLR R 702 " pdb=" C8 CLR R 702 " both_signs ideal model delta sigma weight residual False -2.32 -2.69 0.37 2.00e-01 2.50e+01 3.39e+00 ... (remaining 1423 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 372 " 0.023 2.00e-02 2.50e+03 4.47e-02 2.00e+01 pdb=" C ILE A 372 " -0.077 2.00e-02 2.50e+03 pdb=" O ILE A 372 " 0.029 2.00e-02 2.50e+03 pdb=" N ARG A 373 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 410 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C GLN R 410 " -0.064 2.00e-02 2.50e+03 pdb=" O GLN R 410 " 0.024 2.00e-02 2.50e+03 pdb=" N LEU R 411 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 30 " 0.016 2.00e-02 2.50e+03 3.15e-02 9.89e+00 pdb=" C VAL R 30 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL R 30 " 0.021 2.00e-02 2.50e+03 pdb=" N SER R 31 " 0.018 2.00e-02 2.50e+03 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 140 2.62 - 3.19: 8476 3.19 - 3.76: 15178 3.76 - 4.33: 21186 4.33 - 4.90: 33310 Nonbonded interactions: 78290 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.048 2.440 nonbonded pdb=" O TRP R 91 " pdb=" OG SER R 94 " model vdw 2.112 2.440 nonbonded pdb=" OG SER B 275 " pdb=" O SER B 316 " model vdw 2.201 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.219 2.440 nonbonded pdb=" NZ LYS A 271 " pdb=" OD2 ASP N 50 " model vdw 2.242 2.520 ... (remaining 78285 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=1.00 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: 0.710 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: 3.980 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.950 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6850 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 : 0.007 0.074 9434 Z= 0.482 Angle : 1.117 17.150 12823 Z= 0.597 Chirality : 0.066 0.476 1426 Planarity : 0.007 0.055 1593 Dihedral : 15.693 89.376 3720 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.61 % Allowed : 7.79 % Favored : 87.60 % 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: -2.47 (0.23), residues: 1104 helix: -1.79 (0.21), residues: 433 sheet: -1.25 (0.32), residues: 201 loop : -1.46 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP R 87 HIS 0.011 0.002 HIS B 142 PHE 0.053 0.004 PHE R 280 TYR 0.034 0.004 TYR B 264 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 250 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASP cc_start: 0.9207 (OUTLIER) cc_final: 0.8891 (p0) REVERT: B 217 MET cc_start: 0.6367 (ptt) cc_final: 0.5314 (ptt) REVERT: B 264 TYR cc_start: 0.5898 (m-80) cc_final: 0.4706 (m-80) REVERT: G 38 MET cc_start: 0.8543 (ptt) cc_final: 0.7896 (ptt) REVERT: N 80 TYR cc_start: 0.6765 (m-80) cc_final: 0.6438 (m-80) REVERT: N 81 LEU cc_start: 0.8637 (tp) cc_final: 0.8373 (pp) REVERT: R 48 ARG cc_start: 0.5986 (OUTLIER) cc_final: 0.5159 (ptt90) REVERT: R 146 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8743 (tp) REVERT: R 147 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8816 (mt) REVERT: R 203 TRP cc_start: 0.9029 (OUTLIER) cc_final: 0.8599 (t60) REVERT: R 311 LEU cc_start: 0.8624 (tt) cc_final: 0.8378 (mm) REVERT: R 393 PHE cc_start: 0.8781 (m-80) cc_final: 0.8037 (m-10) REVERT: R 410 GLN cc_start: 0.8719 (mt0) cc_final: 0.8484 (mt0) REVERT: R 421 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8047 (mmp-170) outliers start: 45 outliers final: 15 residues processed: 284 average time/residue: 0.2550 time to fit residues: 94.4305 Evaluate side-chains 151 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 130 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 39 TRP Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 48 ARG Chi-restraints excluded: chain R residue 145 TYR Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 203 TRP Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 210 GLN Chi-restraints excluded: chain R residue 412 GLU Chi-restraints excluded: chain R residue 416 SER Chi-restraints excluded: chain R residue 418 GLU Chi-restraints excluded: chain R residue 421 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS B 110 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 180 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9434 Z= 0.240 Angle : 0.713 8.272 12823 Z= 0.370 Chirality : 0.045 0.176 1426 Planarity : 0.005 0.042 1593 Dihedral : 9.435 78.469 1670 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.23 % Allowed : 16.19 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.24), residues: 1104 helix: -0.41 (0.23), residues: 434 sheet: -0.71 (0.33), residues: 210 loop : -0.91 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP N 36 HIS 0.010 0.001 HIS B 225 PHE 0.031 0.002 PHE N 29 TYR 0.035 0.002 TYR N 32 ARG 0.006 0.001 ARG G 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 158 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 331 ASP cc_start: 0.9255 (OUTLIER) cc_final: 0.9028 (p0) REVERT: B 75 GLN cc_start: 0.8425 (mm110) cc_final: 0.7818 (mm110) REVERT: B 264 TYR cc_start: 0.5705 (m-80) cc_final: 0.5416 (m-80) REVERT: B 296 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7209 (m) REVERT: G 38 MET cc_start: 0.8590 (ptt) cc_final: 0.8199 (ptm) REVERT: R 221 GLN cc_start: 0.8862 (mm110) cc_final: 0.8401 (pp30) REVERT: R 269 TYR cc_start: 0.7815 (m-80) cc_final: 0.7136 (m-80) REVERT: R 294 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6072 (tp30) REVERT: R 357 ILE cc_start: 0.9074 (mm) cc_final: 0.8848 (mm) REVERT: R 393 PHE cc_start: 0.8760 (m-80) cc_final: 0.8388 (m-10) REVERT: R 418 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8389 (mm-30) outliers start: 51 outliers final: 31 residues processed: 193 average time/residue: 0.2327 time to fit residues: 61.3688 Evaluate side-chains 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 122 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 331 ASP Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain R residue 31 SER Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 38 LYS Chi-restraints excluded: chain R residue 46 CYS Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 204 MET Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 418 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN R 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9434 Z= 0.272 Angle : 0.691 12.005 12823 Z= 0.356 Chirality : 0.044 0.190 1426 Planarity : 0.005 0.045 1593 Dihedral : 8.091 70.900 1644 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 23.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.53 % Allowed : 19.36 % Favored : 75.10 % 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: -0.54 (0.25), residues: 1104 helix: 0.15 (0.24), residues: 432 sheet: -0.33 (0.34), residues: 209 loop : -0.72 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP N 36 HIS 0.004 0.001 HIS A 357 PHE 0.020 0.002 PHE R 280 TYR 0.019 0.002 TYR R 148 ARG 0.012 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 139 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 SER cc_start: 0.5767 (OUTLIER) cc_final: 0.5211 (p) REVERT: B 296 VAL cc_start: 0.7915 (OUTLIER) cc_final: 0.7463 (m) REVERT: G 32 LYS cc_start: 0.9335 (tmtt) cc_final: 0.9102 (tmmt) REVERT: G 38 MET cc_start: 0.8526 (ptt) cc_final: 0.8202 (ptm) REVERT: N 39 GLN cc_start: 0.7470 (tp-100) cc_final: 0.7252 (tp-100) REVERT: N 80 TYR cc_start: 0.6110 (m-80) cc_final: 0.5781 (m-80) REVERT: R 221 GLN cc_start: 0.8922 (mm110) cc_final: 0.8479 (pp30) REVERT: R 269 TYR cc_start: 0.7840 (m-80) cc_final: 0.7415 (m-80) REVERT: R 294 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6288 (tp30) REVERT: R 357 ILE cc_start: 0.9136 (mm) cc_final: 0.8894 (mm) REVERT: R 393 PHE cc_start: 0.8796 (m-80) cc_final: 0.8460 (m-80) outliers start: 54 outliers final: 38 residues processed: 173 average time/residue: 0.2092 time to fit residues: 50.4451 Evaluate side-chains 154 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 113 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 33 TRP Chi-restraints excluded: chain R residue 37 GLN Chi-restraints excluded: chain R residue 45 GLN Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 148 TYR Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 415 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN R 45 GLN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.4178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9434 Z= 0.197 Angle : 0.644 12.914 12823 Z= 0.328 Chirality : 0.043 0.178 1426 Planarity : 0.004 0.048 1593 Dihedral : 7.426 62.479 1630 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.33 % Allowed : 21.41 % Favored : 73.26 % 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: -0.21 (0.25), residues: 1104 helix: 0.34 (0.25), residues: 428 sheet: 0.07 (0.34), residues: 205 loop : -0.56 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 36 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.002 PHE R 230 TYR 0.021 0.002 TYR R 88 ARG 0.008 0.001 ARG R 419 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 136 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 SER cc_start: 0.5682 (OUTLIER) cc_final: 0.5168 (p) REVERT: B 296 VAL cc_start: 0.7820 (OUTLIER) cc_final: 0.7414 (m) REVERT: G 32 LYS cc_start: 0.9331 (tmtt) cc_final: 0.9092 (tmmt) REVERT: G 38 MET cc_start: 0.8600 (ptt) cc_final: 0.8232 (ptm) REVERT: N 39 GLN cc_start: 0.7393 (tp-100) cc_final: 0.7098 (tp-100) REVERT: N 81 LEU cc_start: 0.8459 (pp) cc_final: 0.8143 (pp) REVERT: R 221 GLN cc_start: 0.8934 (mm110) cc_final: 0.8541 (pp30) REVERT: R 269 TYR cc_start: 0.7694 (m-80) cc_final: 0.7276 (m-80) REVERT: R 357 ILE cc_start: 0.9130 (mm) cc_final: 0.8857 (mm) REVERT: R 393 PHE cc_start: 0.8727 (m-80) cc_final: 0.8360 (m-80) outliers start: 52 outliers final: 36 residues processed: 174 average time/residue: 0.2018 time to fit residues: 49.5954 Evaluate side-chains 155 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 117 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 354 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 7.9990 chunk 60 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 0.1980 chunk 73 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 220 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 9434 Z= 0.212 Angle : 0.634 11.745 12823 Z= 0.323 Chirality : 0.042 0.139 1426 Planarity : 0.004 0.030 1593 Dihedral : 7.015 59.959 1626 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.12 % Allowed : 22.85 % Favored : 72.03 % 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: -0.00 (0.25), residues: 1104 helix: 0.57 (0.25), residues: 423 sheet: 0.15 (0.35), residues: 195 loop : -0.47 (0.29), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 36 HIS 0.004 0.001 HIS A 220 PHE 0.022 0.002 PHE R 156 TYR 0.021 0.002 TYR B 59 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 131 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 SER cc_start: 0.5927 (OUTLIER) cc_final: 0.5448 (p) REVERT: B 296 VAL cc_start: 0.7819 (OUTLIER) cc_final: 0.7448 (p) REVERT: G 32 LYS cc_start: 0.9374 (tmtt) cc_final: 0.9124 (tmmt) REVERT: G 38 MET cc_start: 0.8583 (ptt) cc_final: 0.8282 (ptm) REVERT: N 39 GLN cc_start: 0.7180 (tp-100) cc_final: 0.6949 (tp-100) REVERT: R 221 GLN cc_start: 0.8936 (mm110) cc_final: 0.8136 (tm-30) REVERT: R 269 TYR cc_start: 0.7626 (m-80) cc_final: 0.7303 (m-80) REVERT: R 294 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6327 (tp30) REVERT: R 357 ILE cc_start: 0.9136 (mm) cc_final: 0.8876 (mm) REVERT: R 393 PHE cc_start: 0.8649 (m-80) cc_final: 0.8315 (m-80) REVERT: R 410 GLN cc_start: 0.8762 (mt0) cc_final: 0.8516 (mt0) outliers start: 50 outliers final: 40 residues processed: 164 average time/residue: 0.2073 time to fit residues: 48.3413 Evaluate side-chains 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 114 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 394 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 8 optimal weight: 0.0170 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9434 Z= 0.170 Angle : 0.648 11.703 12823 Z= 0.321 Chirality : 0.042 0.219 1426 Planarity : 0.004 0.072 1593 Dihedral : 6.789 59.931 1625 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 19.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.00 % Allowed : 25.61 % Favored : 70.39 % 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: 0.11 (0.25), residues: 1104 helix: 0.69 (0.25), residues: 428 sheet: 0.13 (0.35), residues: 197 loop : -0.39 (0.30), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP N 36 HIS 0.009 0.001 HIS A 220 PHE 0.016 0.001 PHE R 156 TYR 0.017 0.001 TYR R 42 ARG 0.009 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 296 VAL cc_start: 0.7697 (OUTLIER) cc_final: 0.7316 (p) REVERT: G 32 LYS cc_start: 0.9426 (tmtt) cc_final: 0.9197 (tmmt) REVERT: R 221 GLN cc_start: 0.8904 (mm110) cc_final: 0.8123 (tm-30) REVERT: R 269 TYR cc_start: 0.7513 (m-80) cc_final: 0.7182 (m-80) REVERT: R 294 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.6000 (tp30) REVERT: R 357 ILE cc_start: 0.9117 (mm) cc_final: 0.8849 (mm) REVERT: R 393 PHE cc_start: 0.8485 (m-80) cc_final: 0.8139 (m-80) outliers start: 39 outliers final: 32 residues processed: 164 average time/residue: 0.1890 time to fit residues: 45.3568 Evaluate side-chains 152 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 118 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 228 LEU Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 294 GLU Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 0.0570 chunk 77 optimal weight: 0.1980 chunk 89 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.0302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9434 Z= 0.180 Angle : 0.661 11.619 12823 Z= 0.326 Chirality : 0.042 0.155 1426 Planarity : 0.004 0.060 1593 Dihedral : 6.554 58.619 1625 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 21.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.10 % Allowed : 26.64 % Favored : 69.26 % 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: 0.21 (0.25), residues: 1104 helix: 0.79 (0.25), residues: 428 sheet: 0.22 (0.33), residues: 213 loop : -0.39 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP N 36 HIS 0.004 0.001 HIS A 357 PHE 0.017 0.001 PHE R 280 TYR 0.025 0.002 TYR R 148 ARG 0.006 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 125 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 SER cc_start: 0.5724 (OUTLIER) cc_final: 0.5274 (p) REVERT: B 296 VAL cc_start: 0.7750 (OUTLIER) cc_final: 0.7351 (p) REVERT: R 221 GLN cc_start: 0.8939 (mm110) cc_final: 0.8180 (tm-30) REVERT: R 269 TYR cc_start: 0.7521 (m-80) cc_final: 0.7262 (m-80) REVERT: R 357 ILE cc_start: 0.9123 (mm) cc_final: 0.8872 (mm) REVERT: R 393 PHE cc_start: 0.8535 (m-80) cc_final: 0.8175 (m-80) outliers start: 40 outliers final: 35 residues processed: 154 average time/residue: 0.1885 time to fit residues: 42.7803 Evaluate side-chains 150 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 111 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.5298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9434 Z= 0.222 Angle : 0.670 11.214 12823 Z= 0.333 Chirality : 0.043 0.158 1426 Planarity : 0.004 0.042 1593 Dihedral : 6.188 57.168 1623 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.12 % Allowed : 25.82 % Favored : 69.06 % 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: 0.27 (0.25), residues: 1104 helix: 0.89 (0.25), residues: 427 sheet: 0.22 (0.34), residues: 206 loop : -0.38 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP N 36 HIS 0.010 0.001 HIS A 357 PHE 0.018 0.001 PHE R 280 TYR 0.025 0.002 TYR B 59 ARG 0.011 0.001 ARG R 380 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 121 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 SER cc_start: 0.5524 (OUTLIER) cc_final: 0.5086 (p) REVERT: B 296 VAL cc_start: 0.7898 (OUTLIER) cc_final: 0.7441 (m) REVERT: R 71 CYS cc_start: 0.3430 (OUTLIER) cc_final: 0.2867 (p) REVERT: R 221 GLN cc_start: 0.9026 (mm110) cc_final: 0.8182 (tm-30) REVERT: R 269 TYR cc_start: 0.7595 (m-80) cc_final: 0.7371 (m-80) REVERT: R 357 ILE cc_start: 0.9198 (mm) cc_final: 0.8948 (mm) REVERT: R 393 PHE cc_start: 0.8533 (m-80) cc_final: 0.8173 (m-80) outliers start: 50 outliers final: 39 residues processed: 156 average time/residue: 0.1840 time to fit residues: 42.7386 Evaluate side-chains 156 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 114 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9434 Z= 0.177 Angle : 0.672 10.930 12823 Z= 0.331 Chirality : 0.043 0.248 1426 Planarity : 0.004 0.036 1593 Dihedral : 5.966 54.350 1623 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 4.10 % Allowed : 26.95 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1104 helix: 0.94 (0.25), residues: 427 sheet: 0.24 (0.34), residues: 210 loop : -0.46 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP A 277 HIS 0.011 0.001 HIS A 357 PHE 0.020 0.001 PHE N 103 TYR 0.018 0.002 TYR N 32 ARG 0.008 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 SER cc_start: 0.5502 (OUTLIER) cc_final: 0.5068 (p) REVERT: B 296 VAL cc_start: 0.7780 (OUTLIER) cc_final: 0.7339 (m) REVERT: N 93 VAL cc_start: 0.8767 (t) cc_final: 0.8557 (p) REVERT: R 71 CYS cc_start: 0.3228 (OUTLIER) cc_final: 0.2599 (p) REVERT: R 144 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9012 (pp) REVERT: R 221 GLN cc_start: 0.8987 (mm110) cc_final: 0.8215 (tm-30) REVERT: R 269 TYR cc_start: 0.7526 (m-80) cc_final: 0.7297 (m-80) REVERT: R 357 ILE cc_start: 0.9152 (mm) cc_final: 0.8901 (mm) REVERT: R 393 PHE cc_start: 0.8430 (m-80) cc_final: 0.8064 (m-80) outliers start: 40 outliers final: 32 residues processed: 151 average time/residue: 0.1909 time to fit residues: 42.5421 Evaluate side-chains 151 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain G residue 15 LEU Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 35 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 HIS B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9434 Z= 0.186 Angle : 0.693 11.105 12823 Z= 0.338 Chirality : 0.043 0.230 1426 Planarity : 0.004 0.035 1593 Dihedral : 5.779 50.478 1623 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.79 % Allowed : 27.25 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1104 helix: 0.99 (0.25), residues: 426 sheet: 0.41 (0.36), residues: 198 loop : -0.48 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP N 36 HIS 0.012 0.001 HIS A 220 PHE 0.017 0.001 PHE R 280 TYR 0.018 0.002 TYR N 94 ARG 0.005 0.000 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2208 Ramachandran restraints generated. 1104 Oldfield, 0 Emsley, 1104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 117 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 201 SER cc_start: 0.5375 (OUTLIER) cc_final: 0.4982 (p) REVERT: B 296 VAL cc_start: 0.7720 (OUTLIER) cc_final: 0.7283 (m) REVERT: R 71 CYS cc_start: 0.3259 (OUTLIER) cc_final: 0.2613 (p) REVERT: R 144 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9011 (pp) REVERT: R 221 GLN cc_start: 0.8946 (mm110) cc_final: 0.8209 (tm-30) REVERT: R 269 TYR cc_start: 0.7535 (m-80) cc_final: 0.7313 (m-80) REVERT: R 357 ILE cc_start: 0.9147 (mm) cc_final: 0.8899 (mm) REVERT: R 393 PHE cc_start: 0.8399 (m-80) cc_final: 0.8022 (m-80) outliers start: 37 outliers final: 31 residues processed: 144 average time/residue: 0.1894 time to fit residues: 40.5579 Evaluate side-chains 145 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 252 SER Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 52 GLU Chi-restraints excluded: chain R residue 65 THR Chi-restraints excluded: chain R residue 71 CYS Chi-restraints excluded: chain R residue 81 VAL Chi-restraints excluded: chain R residue 91 TRP Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 157 SER Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 282 VAL Chi-restraints excluded: chain R residue 319 VAL Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain R residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.6980 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** N 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.094245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.073781 restraints weight = 43842.910| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 7.50 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9434 Z= 0.177 Angle : 0.709 16.472 12823 Z= 0.342 Chirality : 0.043 0.222 1426 Planarity : 0.004 0.037 1593 Dihedral : 5.593 47.994 1623 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 19.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.59 % Allowed : 27.66 % Favored : 68.75 % 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: 0.30 (0.26), residues: 1104 helix: 1.03 (0.25), residues: 433 sheet: 0.33 (0.35), residues: 200 loop : -0.56 (0.30), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP N 36 HIS 0.010 0.001 HIS A 220 PHE 0.017 0.001 PHE R 280 TYR 0.016 0.002 TYR N 94 ARG 0.005 0.000 ARG A 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2192.93 seconds wall clock time: 41 minutes 4.77 seconds (2464.77 seconds total)