Starting phenix.real_space_refine on Thu Mar 14 18:03:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dty_30860/03_2024/7dty_30860_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dty_30860/03_2024/7dty_30860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dty_30860/03_2024/7dty_30860.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dty_30860/03_2024/7dty_30860.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dty_30860/03_2024/7dty_30860_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dty_30860/03_2024/7dty_30860_updated.pdb" } resolution = 2.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 6005 2.51 5 N 1649 2.21 5 O 1697 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 43": "NH1" <-> "NH2" Residue "R ARG 81": "NH1" <-> "NH2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 163": "NH1" <-> "NH2" Residue "R ARG 164": "NH1" <-> "NH2" Residue "R ARG 183": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 278": "NH1" <-> "NH2" Residue "R ARG 300": "NH1" <-> "NH2" Residue "R ARG 316": "NH1" <-> "NH2" Residue "R TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R ARG 338": "NH1" <-> "NH2" Residue "R ARG 341": "NH1" <-> "NH2" Residue "R ARG 366": "NH1" <-> "NH2" Residue "R ARG 411": "NH1" <-> "NH2" Residue "R ARG 413": "NH1" <-> "NH2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9407 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 3034 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 12, 'TRANS': 354} Chain breaks: 2 Chain: "P" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 249 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1921 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 983 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 168 Unusual residues: {'CLR': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.35, per 1000 atoms: 0.57 Number of scatterers: 9407 At special positions: 0 Unit cell: (97.461, 95.319, 155.295, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 1697 8.00 N 1649 7.00 C 6005 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 70 " distance=2.05 Simple disulfide: pdb=" SG CYS R 61 " - pdb=" SG CYS R 103 " distance=2.03 Simple disulfide: pdb=" SG CYS R 84 " - pdb=" SG CYS R 118 " distance=2.03 Simple disulfide: pdb=" SG CYS R 216 " - pdb=" SG CYS R 286 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.9 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2172 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 39.4% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'R' and resid 32 through 48 Processing helix chain 'R' and resid 116 through 118 No H-bonds generated for 'chain 'R' and resid 116 through 118' Processing helix chain 'R' and resid 125 through 161 removed outlier: 3.910A pdb=" N ASP R 129 " --> pdb=" O GLU R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 193 Processing helix chain 'R' and resid 196 through 200 Processing helix chain 'R' and resid 212 through 245 Processing helix chain 'R' and resid 254 through 280 removed outlier: 4.461A pdb=" N ARG R 257 " --> pdb=" O GLY R 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR R 258 " --> pdb=" O HIS R 255 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TRP R 264 " --> pdb=" O LEU R 261 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY R 265 " --> pdb=" O LEU R 262 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA R 266 " --> pdb=" O GLY R 263 " (cutoff:3.500A) Proline residue: R 267 - end of helix removed outlier: 4.708A pdb=" N ILE R 272 " --> pdb=" O LEU R 269 " (cutoff:3.500A) Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 293 through 327 removed outlier: 3.801A pdb=" N ILE R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 3.655A pdb=" N THR R 306 " --> pdb=" O PRO R 302 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 350 removed outlier: 4.039A pdb=" N ARG R 336 " --> pdb=" O CYS R 332 " (cutoff:3.500A) Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 355 Processing helix chain 'R' and resid 368 through 393 removed outlier: 3.961A pdb=" N ILE R 378 " --> pdb=" O LEU R 374 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY R 385 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N PHE R 386 " --> pdb=" O SER R 382 " (cutoff:3.500A) Processing helix chain 'R' and resid 397 through 414 Processing helix chain 'P' and resid 2 through 28 Processing helix chain 'A' and resid 10 through 39 removed outlier: 4.205A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 352 removed outlier: 4.255A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.762A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 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 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 78 through 83 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.321A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.085A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.567A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.549A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.798A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.666A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.962A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.722A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1251 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: 2.69 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3069 1.35 - 1.48: 2396 1.48 - 1.61: 4081 1.61 - 1.74: 0 1.74 - 1.86: 76 Bond restraints: 9622 Sorted by residual: bond pdb=" C ALA R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.335 1.359 -0.023 1.36e-02 5.41e+03 2.90e+00 bond pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " ideal model delta sigma weight residual 1.808 1.864 -0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" C5 CLR R 603 " pdb=" C6 CLR R 603 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.53e+00 bond pdb=" C5 CLR R 602 " pdb=" C6 CLR R 602 " ideal model delta sigma weight residual 1.332 1.300 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" C5 CLR R 601 " pdb=" C6 CLR R 601 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.45e+00 ... (remaining 9617 not shown) Histogram of bond angle deviations from ideal: 99.66 - 106.55: 242 106.55 - 113.44: 5272 113.44 - 120.33: 3697 120.33 - 127.22: 3745 127.22 - 134.11: 106 Bond angle restraints: 13062 Sorted by residual: angle pdb=" CA TYR R 141 " pdb=" CB TYR R 141 " pdb=" CG TYR R 141 " ideal model delta sigma weight residual 113.90 120.25 -6.35 1.80e+00 3.09e-01 1.24e+01 angle pdb=" C HIS R 166 " pdb=" N CYS R 167 " pdb=" CA CYS R 167 " ideal model delta sigma weight residual 121.62 128.01 -6.39 1.83e+00 2.99e-01 1.22e+01 angle pdb=" C LEU R 269 " pdb=" N PHE R 270 " pdb=" CA PHE R 270 " ideal model delta sigma weight residual 122.26 116.29 5.97 1.73e+00 3.34e-01 1.19e+01 angle pdb=" C ALA P 2 " pdb=" N GLU P 3 " pdb=" CA GLU P 3 " ideal model delta sigma weight residual 120.54 124.87 -4.33 1.35e+00 5.49e-01 1.03e+01 angle pdb=" C LEU R 161 " pdb=" N PHE R 162 " pdb=" CA PHE R 162 " ideal model delta sigma weight residual 122.30 118.08 4.22 1.35e+00 5.49e-01 9.77e+00 ... (remaining 13057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 5767 15.07 - 30.14: 190 30.14 - 45.21: 49 45.21 - 60.28: 1 60.28 - 75.35: 3 Dihedral angle restraints: 6010 sinusoidal: 2649 harmonic: 3361 Sorted by residual: dihedral pdb=" CB CYS R 216 " pdb=" SG CYS R 216 " pdb=" SG CYS R 286 " pdb=" CB CYS R 286 " ideal model delta sinusoidal sigma weight residual 93.00 138.25 -45.25 1 1.00e+01 1.00e-02 2.84e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 159.05 20.95 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA LEU R 247 " pdb=" C LEU R 247 " pdb=" N VAL R 248 " pdb=" CA VAL R 248 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 6007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1270 0.082 - 0.165: 150 0.165 - 0.247: 22 0.247 - 0.330: 6 0.330 - 0.412: 6 Chirality restraints: 1454 Sorted by residual: chirality pdb=" C14 CLR R 606 " pdb=" C13 CLR R 606 " pdb=" C15 CLR R 606 " pdb=" C8 CLR R 606 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.25e+00 chirality pdb=" C14 CLR R 605 " pdb=" C13 CLR R 605 " pdb=" C15 CLR R 605 " pdb=" C8 CLR R 605 " both_signs ideal model delta sigma weight residual False -2.32 -2.73 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" C14 CLR R 602 " pdb=" C13 CLR R 602 " pdb=" C15 CLR R 602 " pdb=" C8 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.95e+00 ... (remaining 1451 not shown) Planarity restraints: 1638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN P 20 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C GLN P 20 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN P 20 " 0.022 2.00e-02 2.50e+03 pdb=" N ASP P 21 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 262 " 0.016 2.00e-02 2.50e+03 3.23e-02 1.05e+01 pdb=" C LEU R 262 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU R 262 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY R 263 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN P 24 " -0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C ASN P 24 " 0.050 2.00e-02 2.50e+03 pdb=" O ASN P 24 " -0.019 2.00e-02 2.50e+03 pdb=" N TRP P 25 " -0.017 2.00e-02 2.50e+03 ... (remaining 1635 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1684 2.78 - 3.31: 8463 3.31 - 3.84: 15262 3.84 - 4.37: 17475 4.37 - 4.90: 30996 Nonbonded interactions: 73880 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.249 2.440 nonbonded pdb=" O ARG A 42 " pdb=" OG1 THR A 242 " model vdw 2.303 2.440 nonbonded pdb=" O ASN A 239 " pdb=" OG1 THR A 285 " model vdw 2.312 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.327 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.329 2.440 ... (remaining 73875 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: 0.660 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: 3.990 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 28.400 Find NCS groups from input model: 0.280 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:11.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9622 Z= 0.254 Angle : 0.775 7.728 13062 Z= 0.427 Chirality : 0.062 0.412 1454 Planarity : 0.006 0.065 1638 Dihedral : 8.413 75.348 3820 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -1.30 (0.21), residues: 1136 helix: -0.34 (0.20), residues: 447 sheet: -0.46 (0.33), residues: 236 loop : -1.50 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A 281 HIS 0.017 0.002 HIS R 409 PHE 0.024 0.002 PHE B 199 TYR 0.024 0.002 TYR P 1 ARG 0.006 0.000 ARG R 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 189 SER cc_start: 0.8431 (m) cc_final: 0.8157 (t) REVERT: R 357 PHE cc_start: 0.8966 (m-80) cc_final: 0.8679 (m-80) REVERT: R 396 ASN cc_start: 0.8852 (t0) cc_final: 0.7981 (t0) REVERT: P 10 TYR cc_start: 0.8463 (t80) cc_final: 0.8149 (t80) REVERT: A 12 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7726 (pp30) REVERT: B 36 ASN cc_start: 0.8792 (m-40) cc_final: 0.8563 (p0) REVERT: B 127 LYS cc_start: 0.8338 (tttt) cc_final: 0.8035 (ttmm) REVERT: B 155 ASN cc_start: 0.8388 (m-40) cc_final: 0.7906 (t0) REVERT: B 158 VAL cc_start: 0.9254 (t) cc_final: 0.9039 (p) REVERT: B 172 GLU cc_start: 0.8702 (tp30) cc_final: 0.8477 (tp30) REVERT: B 217 MET cc_start: 0.7850 (ptt) cc_final: 0.7620 (ptm) REVERT: G 52 THR cc_start: 0.8381 (m) cc_final: 0.8041 (p) REVERT: G 57 SER cc_start: 0.9533 (p) cc_final: 0.9255 (p) REVERT: N 11 LEU cc_start: 0.8903 (tp) cc_final: 0.8321 (tp) REVERT: N 31 ASN cc_start: 0.8716 (m-40) cc_final: 0.8457 (m-40) REVERT: N 69 THR cc_start: 0.8828 (m) cc_final: 0.8340 (p) REVERT: N 73 ASP cc_start: 0.8032 (t0) cc_final: 0.7569 (t0) REVERT: N 103 PHE cc_start: 0.9137 (m-80) cc_final: 0.8641 (m-80) REVERT: N 125 THR cc_start: 0.8830 (m) cc_final: 0.8409 (p) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 1.0950 time to fit residues: 351.9873 Evaluate side-chains 173 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 chunk 29 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 65 optimal weight: 0.0870 chunk 102 optimal weight: 4.9990 overall best weight: 0.5166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 93 HIS R 224 GLN R 242 HIS ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 91 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9622 Z= 0.173 Angle : 0.541 7.384 13062 Z= 0.281 Chirality : 0.040 0.143 1454 Planarity : 0.004 0.040 1638 Dihedral : 4.876 38.013 1668 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 3.75 % Allowed : 13.88 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.23), residues: 1136 helix: 1.38 (0.23), residues: 449 sheet: -0.11 (0.33), residues: 223 loop : -1.10 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 281 HIS 0.008 0.001 HIS R 115 PHE 0.014 0.001 PHE B 199 TYR 0.022 0.001 TYR R 335 ARG 0.008 0.001 ARG R 44 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 191 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 357 PHE cc_start: 0.9043 (m-80) cc_final: 0.8734 (m-80) REVERT: P 10 TYR cc_start: 0.8559 (t80) cc_final: 0.8296 (t80) REVERT: P 18 HIS cc_start: 0.8141 (t-170) cc_final: 0.7835 (t-170) REVERT: P 25 TRP cc_start: 0.8570 (t60) cc_final: 0.8207 (t60) REVERT: B 120 ILE cc_start: 0.9094 (mt) cc_final: 0.8753 (mm) REVERT: B 127 LYS cc_start: 0.8317 (tttt) cc_final: 0.8006 (ttmm) REVERT: B 155 ASN cc_start: 0.8368 (m-40) cc_final: 0.7829 (t0) REVERT: B 158 VAL cc_start: 0.9129 (t) cc_final: 0.8890 (p) REVERT: B 172 GLU cc_start: 0.8554 (tp30) cc_final: 0.8201 (tp30) REVERT: B 197 ARG cc_start: 0.8347 (tpp-160) cc_final: 0.8000 (mmm160) REVERT: B 217 MET cc_start: 0.8079 (ptt) cc_final: 0.7775 (ptm) REVERT: B 228 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7721 (m-30) REVERT: B 254 ASP cc_start: 0.8054 (t0) cc_final: 0.7765 (t0) REVERT: G 14 LYS cc_start: 0.9604 (tppp) cc_final: 0.9382 (tppp) REVERT: G 29 LYS cc_start: 0.9049 (mmtt) cc_final: 0.8818 (mmtm) REVERT: G 52 THR cc_start: 0.8403 (m) cc_final: 0.8036 (p) REVERT: N 11 LEU cc_start: 0.8935 (tp) cc_final: 0.8377 (tp) REVERT: N 31 ASN cc_start: 0.8783 (m-40) cc_final: 0.8572 (m-40) REVERT: N 69 THR cc_start: 0.8836 (m) cc_final: 0.8297 (p) REVERT: N 73 ASP cc_start: 0.8050 (t0) cc_final: 0.7521 (t0) REVERT: N 105 ARG cc_start: 0.8384 (mtm-85) cc_final: 0.7855 (mtm180) REVERT: N 109 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7503 (p0) REVERT: N 125 THR cc_start: 0.9008 (m) cc_final: 0.8563 (p) outliers start: 37 outliers final: 11 residues processed: 208 average time/residue: 1.1840 time to fit residues: 263.1150 Evaluate side-chains 164 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 151 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 160 SER Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.0980 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9622 Z= 0.212 Angle : 0.538 8.905 13062 Z= 0.283 Chirality : 0.040 0.151 1454 Planarity : 0.004 0.036 1638 Dihedral : 4.666 40.791 1668 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.14 % Allowed : 16.21 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.62 (0.24), residues: 1136 helix: 1.92 (0.24), residues: 457 sheet: -0.03 (0.33), residues: 221 loop : -0.90 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 281 HIS 0.007 0.001 HIS A 220 PHE 0.019 0.001 PHE B 292 TYR 0.020 0.002 TYR R 335 ARG 0.005 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 181 MET cc_start: 0.8466 (tpp) cc_final: 0.8260 (tpp) REVERT: R 376 PHE cc_start: 0.8720 (t80) cc_final: 0.8498 (t80) REVERT: P 18 HIS cc_start: 0.8230 (t-170) cc_final: 0.7970 (t-170) REVERT: P 26 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8698 (tm) REVERT: A 27 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8186 (mm-30) REVERT: A 33 ASP cc_start: 0.8539 (t70) cc_final: 0.8155 (m-30) REVERT: B 155 ASN cc_start: 0.8426 (m-40) cc_final: 0.7935 (t0) REVERT: B 158 VAL cc_start: 0.9146 (t) cc_final: 0.8883 (p) REVERT: B 172 GLU cc_start: 0.8581 (tp30) cc_final: 0.8317 (tp30) REVERT: B 254 ASP cc_start: 0.8045 (t0) cc_final: 0.7821 (t0) REVERT: G 13 ARG cc_start: 0.9017 (ptm-80) cc_final: 0.8452 (tmm160) REVERT: G 14 LYS cc_start: 0.9637 (tppp) cc_final: 0.9279 (tppt) REVERT: G 29 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8795 (mmtm) REVERT: G 52 THR cc_start: 0.8536 (m) cc_final: 0.8162 (p) REVERT: N 73 ASP cc_start: 0.8068 (t0) cc_final: 0.7569 (t0) REVERT: N 91 THR cc_start: 0.8794 (OUTLIER) cc_final: 0.8588 (t) REVERT: N 105 ARG cc_start: 0.8372 (mtm-85) cc_final: 0.7868 (mtm180) outliers start: 31 outliers final: 10 residues processed: 183 average time/residue: 1.1641 time to fit residues: 228.3470 Evaluate side-chains 155 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 347 ARG Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9622 Z= 0.338 Angle : 0.601 10.108 13062 Z= 0.315 Chirality : 0.042 0.142 1454 Planarity : 0.004 0.035 1638 Dihedral : 4.784 42.033 1668 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 4.26 % Allowed : 16.41 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 0.89 (0.25), residues: 1136 helix: 2.05 (0.24), residues: 464 sheet: 0.01 (0.32), residues: 238 loop : -0.64 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 281 HIS 0.008 0.002 HIS A 357 PHE 0.016 0.002 PHE B 199 TYR 0.020 0.002 TYR N 60 ARG 0.007 0.001 ARG R 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.033 Fit side-chains revert: symmetry clash REVERT: R 344 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7873 (mm) REVERT: R 376 PHE cc_start: 0.8819 (t80) cc_final: 0.8561 (t80) REVERT: R 397 LYS cc_start: 0.8723 (mppt) cc_final: 0.7778 (mppt) REVERT: P 18 HIS cc_start: 0.8322 (t-170) cc_final: 0.7289 (t70) REVERT: P 21 ASP cc_start: 0.9227 (m-30) cc_final: 0.8956 (p0) REVERT: A 27 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8184 (mm-30) REVERT: A 33 ASP cc_start: 0.8536 (t70) cc_final: 0.8309 (m-30) REVERT: A 392 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7810 (mm-30) REVERT: B 12 GLU cc_start: 0.9069 (tp30) cc_final: 0.8854 (tp30) REVERT: B 23 LYS cc_start: 0.9467 (mmmt) cc_final: 0.9232 (tptp) REVERT: B 155 ASN cc_start: 0.8542 (m-40) cc_final: 0.8068 (t0) REVERT: B 172 GLU cc_start: 0.8681 (tp30) cc_final: 0.8363 (tp30) REVERT: G 14 LYS cc_start: 0.9625 (tppp) cc_final: 0.9305 (tppt) REVERT: G 29 LYS cc_start: 0.9127 (mmtt) cc_final: 0.8798 (mmtm) REVERT: G 52 THR cc_start: 0.8623 (m) cc_final: 0.8230 (p) REVERT: N 11 LEU cc_start: 0.9160 (tp) cc_final: 0.8812 (mm) REVERT: N 69 THR cc_start: 0.9004 (m) cc_final: 0.8469 (p) REVERT: N 73 ASP cc_start: 0.8082 (t0) cc_final: 0.7511 (t0) REVERT: N 76 LYS cc_start: 0.9368 (ttmm) cc_final: 0.9099 (tppp) REVERT: N 78 THR cc_start: 0.8539 (m) cc_final: 0.8265 (t) REVERT: N 87 LYS cc_start: 0.8902 (mtpp) cc_final: 0.8629 (mtmm) REVERT: N 90 ASP cc_start: 0.8991 (m-30) cc_final: 0.8775 (m-30) REVERT: N 91 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8768 (t) outliers start: 42 outliers final: 17 residues processed: 175 average time/residue: 1.1184 time to fit residues: 210.4429 Evaluate side-chains 159 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 298 ILE Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 0.4980 chunk 36 optimal weight: 3.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN ** P 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9622 Z= 0.289 Angle : 0.568 8.793 13062 Z= 0.295 Chirality : 0.041 0.142 1454 Planarity : 0.004 0.043 1638 Dihedral : 4.693 46.627 1668 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.65 % Allowed : 18.44 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.00 (0.25), residues: 1136 helix: 2.16 (0.24), residues: 464 sheet: -0.06 (0.33), residues: 237 loop : -0.51 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.014 0.002 PHE A 212 TYR 0.020 0.002 TYR N 60 ARG 0.008 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: R 344 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7916 (mm) REVERT: R 376 PHE cc_start: 0.8815 (t80) cc_final: 0.8550 (t80) REVERT: R 397 LYS cc_start: 0.8502 (mppt) cc_final: 0.7695 (mppt) REVERT: P 18 HIS cc_start: 0.8331 (t-170) cc_final: 0.7484 (t70) REVERT: P 21 ASP cc_start: 0.9237 (m-30) cc_final: 0.8969 (p0) REVERT: P 26 LEU cc_start: 0.9435 (mm) cc_final: 0.8713 (tm) REVERT: A 27 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8184 (mm-30) REVERT: A 33 ASP cc_start: 0.8557 (t70) cc_final: 0.8235 (m-30) REVERT: A 392 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7786 (mm-30) REVERT: B 12 GLU cc_start: 0.9054 (tp30) cc_final: 0.8800 (tp30) REVERT: B 23 LYS cc_start: 0.9460 (mmmt) cc_final: 0.9171 (tptp) REVERT: B 78 LYS cc_start: 0.8699 (tptt) cc_final: 0.8440 (tppt) REVERT: B 155 ASN cc_start: 0.8517 (m-40) cc_final: 0.8073 (t0) REVERT: B 172 GLU cc_start: 0.8682 (tp30) cc_final: 0.8412 (tp30) REVERT: G 13 ARG cc_start: 0.8998 (ptm-80) cc_final: 0.8423 (tmm160) REVERT: G 14 LYS cc_start: 0.9617 (tppp) cc_final: 0.9189 (tppt) REVERT: G 29 LYS cc_start: 0.9152 (mmtt) cc_final: 0.8849 (mmtm) REVERT: G 52 THR cc_start: 0.8683 (m) cc_final: 0.8345 (p) REVERT: N 73 ASP cc_start: 0.8057 (t0) cc_final: 0.7489 (t0) REVERT: N 78 THR cc_start: 0.8589 (m) cc_final: 0.8280 (t) REVERT: N 86 LEU cc_start: 0.9056 (mm) cc_final: 0.8849 (mm) REVERT: N 91 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8696 (t) outliers start: 36 outliers final: 15 residues processed: 169 average time/residue: 1.0463 time to fit residues: 191.0297 Evaluate side-chains 157 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 260 LEU Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.0060 chunk 21 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN P 20 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9622 Z= 0.186 Angle : 0.535 7.371 13062 Z= 0.277 Chirality : 0.039 0.137 1454 Planarity : 0.003 0.047 1638 Dihedral : 4.475 48.490 1668 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.95 % Allowed : 18.24 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.18 (0.25), residues: 1136 helix: 2.32 (0.24), residues: 464 sheet: 0.05 (0.33), residues: 232 loop : -0.46 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.021 0.001 TYR N 60 ARG 0.003 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 145 time to evaluate : 1.275 Fit side-chains revert: symmetry clash REVERT: R 344 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7911 (mm) REVERT: R 376 PHE cc_start: 0.8846 (t80) cc_final: 0.8566 (t80) REVERT: R 397 LYS cc_start: 0.8588 (mppt) cc_final: 0.7889 (mppt) REVERT: R 398 GLU cc_start: 0.8435 (tm-30) cc_final: 0.8223 (tm-30) REVERT: P 18 HIS cc_start: 0.8318 (t-170) cc_final: 0.7458 (t70) REVERT: P 21 ASP cc_start: 0.9216 (m-30) cc_final: 0.8967 (p0) REVERT: P 26 LEU cc_start: 0.9431 (mm) cc_final: 0.8777 (tm) REVERT: A 27 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8158 (mm-30) REVERT: A 33 ASP cc_start: 0.8539 (t70) cc_final: 0.8199 (m-30) REVERT: A 392 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7771 (mm-30) REVERT: B 12 GLU cc_start: 0.9070 (tp30) cc_final: 0.8769 (tp30) REVERT: B 23 LYS cc_start: 0.9445 (mmmt) cc_final: 0.9180 (tptp) REVERT: B 78 LYS cc_start: 0.8686 (tptt) cc_final: 0.8414 (tppt) REVERT: B 155 ASN cc_start: 0.8494 (m-40) cc_final: 0.8058 (t0) REVERT: B 158 VAL cc_start: 0.8959 (t) cc_final: 0.8679 (p) REVERT: B 172 GLU cc_start: 0.8652 (tp30) cc_final: 0.8353 (tp30) REVERT: G 13 ARG cc_start: 0.8976 (ptm-80) cc_final: 0.8529 (tmm160) REVERT: G 14 LYS cc_start: 0.9598 (tppp) cc_final: 0.9272 (tppt) REVERT: G 29 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8782 (mmtm) REVERT: G 52 THR cc_start: 0.8732 (m) cc_final: 0.8458 (p) REVERT: N 73 ASP cc_start: 0.8031 (t0) cc_final: 0.7450 (t0) REVERT: N 78 THR cc_start: 0.8497 (m) cc_final: 0.8003 (p) REVERT: N 86 LEU cc_start: 0.9038 (mm) cc_final: 0.8824 (mm) REVERT: N 87 LYS cc_start: 0.8991 (mtpm) cc_final: 0.8701 (mtmm) REVERT: N 91 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8649 (t) outliers start: 39 outliers final: 16 residues processed: 169 average time/residue: 1.1210 time to fit residues: 203.4503 Evaluate side-chains 162 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 144 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 43 optimal weight: 0.0670 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 230 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.4620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9622 Z= 0.233 Angle : 0.555 8.234 13062 Z= 0.287 Chirality : 0.040 0.137 1454 Planarity : 0.004 0.048 1638 Dihedral : 4.505 48.989 1668 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.14 % Allowed : 19.55 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1136 helix: 2.37 (0.24), residues: 464 sheet: -0.00 (0.33), residues: 241 loop : -0.37 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.021 0.002 TYR N 60 ARG 0.010 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 203 ASP cc_start: 0.8752 (m-30) cc_final: 0.8047 (t0) REVERT: R 376 PHE cc_start: 0.8843 (t80) cc_final: 0.8599 (t80) REVERT: R 397 LYS cc_start: 0.8585 (mppt) cc_final: 0.8335 (mppt) REVERT: R 398 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8130 (tm-30) REVERT: P 9 ASP cc_start: 0.8992 (OUTLIER) cc_final: 0.8346 (m-30) REVERT: P 18 HIS cc_start: 0.8320 (t-170) cc_final: 0.7455 (t70) REVERT: P 21 ASP cc_start: 0.9221 (m-30) cc_final: 0.8972 (p0) REVERT: P 26 LEU cc_start: 0.9400 (mm) cc_final: 0.8713 (tm) REVERT: A 27 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8181 (mm-30) REVERT: A 33 ASP cc_start: 0.8525 (t70) cc_final: 0.8185 (m-30) REVERT: B 12 GLU cc_start: 0.9069 (tp30) cc_final: 0.8707 (tp30) REVERT: B 23 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9189 (tptp) REVERT: B 78 LYS cc_start: 0.8691 (tptt) cc_final: 0.8410 (tppt) REVERT: B 155 ASN cc_start: 0.8523 (m-40) cc_final: 0.8159 (t0) REVERT: B 172 GLU cc_start: 0.8669 (tp30) cc_final: 0.8379 (tp30) REVERT: G 29 LYS cc_start: 0.9080 (mmtt) cc_final: 0.8786 (mmtm) REVERT: G 52 THR cc_start: 0.8771 (m) cc_final: 0.8511 (p) REVERT: G 62 ARG cc_start: 0.7731 (pmt-80) cc_final: 0.7379 (pmt-80) REVERT: N 73 ASP cc_start: 0.8038 (t0) cc_final: 0.7461 (t0) REVERT: N 78 THR cc_start: 0.8611 (m) cc_final: 0.8301 (t) REVERT: N 86 LEU cc_start: 0.8973 (mm) cc_final: 0.8766 (mm) REVERT: N 91 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8490 (t) outliers start: 31 outliers final: 18 residues processed: 160 average time/residue: 1.1393 time to fit residues: 196.6032 Evaluate side-chains 157 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 245 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 0.1980 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.4682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9622 Z= 0.192 Angle : 0.561 10.647 13062 Z= 0.288 Chirality : 0.039 0.138 1454 Planarity : 0.004 0.045 1638 Dihedral : 4.422 50.287 1668 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.84 % Allowed : 19.55 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.28 (0.25), residues: 1136 helix: 2.38 (0.24), residues: 464 sheet: 0.01 (0.33), residues: 241 loop : -0.31 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.028 0.001 TYR P 10 ARG 0.008 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 153 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8937 (tm) REVERT: R 203 ASP cc_start: 0.8715 (m-30) cc_final: 0.8017 (t0) REVERT: R 344 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.8011 (mm) REVERT: R 376 PHE cc_start: 0.8842 (t80) cc_final: 0.8597 (t80) REVERT: R 397 LYS cc_start: 0.8589 (mppt) cc_final: 0.8315 (mppt) REVERT: R 398 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8102 (tm-30) REVERT: P 18 HIS cc_start: 0.8323 (t-170) cc_final: 0.7458 (t70) REVERT: P 21 ASP cc_start: 0.9231 (m-30) cc_final: 0.8984 (p0) REVERT: A 27 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8115 (mm-30) REVERT: A 33 ASP cc_start: 0.8503 (t70) cc_final: 0.8159 (m-30) REVERT: B 12 GLU cc_start: 0.9055 (tp30) cc_final: 0.8700 (tp30) REVERT: B 23 LYS cc_start: 0.9487 (mmmt) cc_final: 0.9222 (tptp) REVERT: B 78 LYS cc_start: 0.8686 (tptt) cc_final: 0.8403 (tppt) REVERT: B 155 ASN cc_start: 0.8515 (m-40) cc_final: 0.8165 (t0) REVERT: B 158 VAL cc_start: 0.8937 (t) cc_final: 0.8683 (p) REVERT: B 172 GLU cc_start: 0.8643 (tp30) cc_final: 0.8342 (tp30) REVERT: G 29 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8766 (mmtm) REVERT: G 52 THR cc_start: 0.8862 (m) cc_final: 0.8650 (p) REVERT: N 3 GLN cc_start: 0.7915 (pt0) cc_final: 0.7712 (tt0) REVERT: N 69 THR cc_start: 0.8980 (m) cc_final: 0.8483 (p) REVERT: N 73 ASP cc_start: 0.8032 (t0) cc_final: 0.7458 (t0) REVERT: N 78 THR cc_start: 0.8533 (m) cc_final: 0.8029 (p) REVERT: N 91 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8466 (t) outliers start: 28 outliers final: 19 residues processed: 158 average time/residue: 1.0709 time to fit residues: 182.7436 Evaluate side-chains 162 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 95 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9622 Z= 0.203 Angle : 0.565 9.922 13062 Z= 0.290 Chirality : 0.040 0.235 1454 Planarity : 0.003 0.041 1638 Dihedral : 4.378 50.772 1668 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.23 % Allowed : 20.47 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.25), residues: 1136 helix: 2.40 (0.24), residues: 464 sheet: 0.02 (0.33), residues: 241 loop : -0.32 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE A 212 TYR 0.022 0.001 TYR N 60 ARG 0.007 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: R 181 MET cc_start: 0.8506 (tpp) cc_final: 0.8240 (mmp) REVERT: R 203 ASP cc_start: 0.8697 (m-30) cc_final: 0.8170 (t70) REVERT: R 344 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.8013 (mm) REVERT: R 376 PHE cc_start: 0.8850 (t80) cc_final: 0.8618 (t80) REVERT: R 397 LYS cc_start: 0.8589 (mppt) cc_final: 0.8316 (mppt) REVERT: P 18 HIS cc_start: 0.8328 (t-170) cc_final: 0.7447 (t70) REVERT: P 21 ASP cc_start: 0.9231 (m-30) cc_final: 0.8998 (p0) REVERT: A 27 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 33 ASP cc_start: 0.8519 (t70) cc_final: 0.8178 (m-30) REVERT: B 12 GLU cc_start: 0.9076 (tp30) cc_final: 0.8722 (tp30) REVERT: B 23 LYS cc_start: 0.9482 (mmmt) cc_final: 0.9218 (tptp) REVERT: B 78 LYS cc_start: 0.8682 (tptt) cc_final: 0.8394 (tppt) REVERT: B 155 ASN cc_start: 0.8515 (m-40) cc_final: 0.8169 (t0) REVERT: B 158 VAL cc_start: 0.8938 (t) cc_final: 0.8697 (p) REVERT: B 172 GLU cc_start: 0.8674 (tp30) cc_final: 0.8371 (tp30) REVERT: G 13 ARG cc_start: 0.9019 (tmm160) cc_final: 0.8627 (tmm160) REVERT: G 14 LYS cc_start: 0.9574 (tppp) cc_final: 0.9299 (tppt) REVERT: G 29 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8767 (mmtm) REVERT: N 73 ASP cc_start: 0.8037 (t0) cc_final: 0.7463 (t0) REVERT: N 78 THR cc_start: 0.8540 (m) cc_final: 0.8225 (t) REVERT: N 91 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8484 (t) outliers start: 22 outliers final: 17 residues processed: 151 average time/residue: 1.1167 time to fit residues: 181.3441 Evaluate side-chains 151 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain R residue 344 LEU Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 54 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9622 Z= 0.201 Angle : 0.572 10.391 13062 Z= 0.295 Chirality : 0.040 0.206 1454 Planarity : 0.003 0.038 1638 Dihedral : 4.333 51.296 1668 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.43 % Allowed : 20.97 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.35 (0.26), residues: 1136 helix: 2.54 (0.24), residues: 453 sheet: 0.05 (0.33), residues: 241 loop : -0.31 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE R 394 TYR 0.022 0.001 TYR N 60 ARG 0.008 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 136 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: R 203 ASP cc_start: 0.8704 (m-30) cc_final: 0.8173 (t70) REVERT: R 397 LYS cc_start: 0.8576 (mppt) cc_final: 0.7692 (mppt) REVERT: P 18 HIS cc_start: 0.8330 (t-170) cc_final: 0.7429 (t70) REVERT: P 21 ASP cc_start: 0.9243 (m-30) cc_final: 0.8980 (p0) REVERT: P 22 PHE cc_start: 0.9129 (t80) cc_final: 0.8857 (t80) REVERT: P 26 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8595 (tm) REVERT: A 27 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 33 ASP cc_start: 0.8523 (t70) cc_final: 0.8181 (m-30) REVERT: A 392 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7648 (mm-30) REVERT: B 12 GLU cc_start: 0.9048 (tp30) cc_final: 0.8682 (tp30) REVERT: B 19 ARG cc_start: 0.8556 (tmm-80) cc_final: 0.8194 (tmm-80) REVERT: B 23 LYS cc_start: 0.9482 (mmmt) cc_final: 0.9222 (tptp) REVERT: B 78 LYS cc_start: 0.8682 (tptt) cc_final: 0.8394 (tppt) REVERT: B 155 ASN cc_start: 0.8513 (m-40) cc_final: 0.8172 (t0) REVERT: B 158 VAL cc_start: 0.8920 (t) cc_final: 0.8693 (p) REVERT: B 172 GLU cc_start: 0.8677 (tp30) cc_final: 0.8370 (tp30) REVERT: G 13 ARG cc_start: 0.8971 (tmm160) cc_final: 0.8358 (tmm160) REVERT: G 14 LYS cc_start: 0.9559 (tppp) cc_final: 0.9318 (tppt) REVERT: G 29 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8765 (mmtm) REVERT: N 73 ASP cc_start: 0.8045 (t0) cc_final: 0.7464 (t0) REVERT: N 78 THR cc_start: 0.8583 (m) cc_final: 0.8240 (t) REVERT: N 91 THR cc_start: 0.8744 (OUTLIER) cc_final: 0.8453 (t) outliers start: 24 outliers final: 17 residues processed: 152 average time/residue: 1.1535 time to fit residues: 188.3586 Evaluate side-chains 151 residues out of total 987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 143 VAL Chi-restraints excluded: chain R residue 305 MET Chi-restraints excluded: chain R residue 382 SER Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain P residue 26 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 84 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 0.0020 chunk 64 optimal weight: 9.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.078832 restraints weight = 17180.006| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.16 r_work: 0.2978 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9622 Z= 0.197 Angle : 0.570 10.350 13062 Z= 0.294 Chirality : 0.040 0.205 1454 Planarity : 0.003 0.039 1638 Dihedral : 4.297 51.861 1668 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.62 % Allowed : 21.78 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % 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: 1.41 (0.26), residues: 1136 helix: 2.67 (0.24), residues: 447 sheet: 0.01 (0.34), residues: 241 loop : -0.29 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.023 0.001 TYR N 60 ARG 0.009 0.000 ARG N 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3961.64 seconds wall clock time: 70 minutes 22.48 seconds (4222.48 seconds total)