Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 10:34:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/04_2023/7fin_31604_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/04_2023/7fin_31604.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/04_2023/7fin_31604_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/04_2023/7fin_31604_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/04_2023/7fin_31604_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/04_2023/7fin_31604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/04_2023/7fin_31604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/04_2023/7fin_31604_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/04_2023/7fin_31604_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.021 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 55 5.16 5 C 6081 2.51 5 N 1668 2.21 5 O 1720 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 131": "NH1" <-> "NH2" Residue "R ARG 136": "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 ARG 192": "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 ARG 331": "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 370": "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 317": "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 46": "NH1" <-> "NH2" Residue "B ARG 214": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 9524 Number of models: 1 Model: "" Number of chains: 8 Chain: "R" Number of atoms: 3123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3123 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 12, 'TRANS': 367} Chain breaks: 1 Chain: "P" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 240 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 196 Unusual residues: {'CLR': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GGL:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.45, per 1000 atoms: 0.57 Number of scatterers: 9524 At special positions: 0 Unit cell: (97.461, 97.461, 157.437, 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 55 16.00 O 1720 8.00 N 1668 7.00 C 6081 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=2.03 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=2.02 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: 3.95 Conformation dependent library (CDL) restraints added in 1.5 seconds 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 38.9% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'R' and resid 32 through 52 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 124 through 161 Processing helix chain 'R' and resid 168 through 193 Processing helix chain 'R' and resid 212 through 246 Processing helix chain 'R' and resid 256 through 280 Proline residue: R 267 - end of helix Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 293 through 328 removed outlier: 3.882A pdb=" N ILE R 298 " --> pdb=" O ALA R 294 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ILE R 299 " --> pdb=" O ILE R 295 " (cutoff:3.500A) Proline residue: R 302 - end of helix removed outlier: 3.618A pdb=" N THR R 306 " --> pdb=" O PRO R 302 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG R 328 " --> pdb=" O LYS R 324 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 350 removed outlier: 4.296A 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 353 through 356 No H-bonds generated for 'chain 'R' and resid 353 through 356' Processing helix chain 'R' and resid 362 through 366 Processing helix chain 'R' and resid 368 through 393 removed outlier: 3.633A pdb=" N LEU R 374 " --> pdb=" O PHE R 371 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE R 378 " --> pdb=" O GLY R 375 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE R 383 " --> pdb=" O LEU R 380 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN R 384 " --> pdb=" O SER R 381 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY R 385 " --> pdb=" O SER R 382 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 391 " --> pdb=" O VAL R 388 " (cutoff:3.500A) Processing helix chain 'R' and resid 397 through 414 Processing helix chain 'P' and resid 4 through 28 Processing helix chain 'A' and resid 10 through 39 removed outlier: 4.234A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.212A 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 277 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 303 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: 4.146A 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 4 through 24 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: 7.635A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.109A 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: 7.056A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.752A 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: 6.584A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.479A 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: 6.648A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.858A 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: 6.896A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.121A 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: 6.851A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.748A 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: 6.709A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.327A 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: 6.995A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.562A 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: 3.800A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 449 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: 2.54 Time building geometry restraints manager: 4.13 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: 3026 1.34 - 1.46: 1968 1.46 - 1.58: 4675 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9743 Sorted by residual: bond pdb=" CA ILE R 272 " pdb=" C ILE R 272 " ideal model delta sigma weight residual 1.520 1.538 -0.018 8.80e-03 1.29e+04 4.39e+00 bond pdb=" CD GGL P 501 " pdb=" OE1 GGL P 501 " ideal model delta sigma weight residual 1.259 1.220 0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" C ALA R 266 " pdb=" N PRO R 267 " ideal model delta sigma weight residual 1.335 1.361 -0.025 1.36e-02 5.41e+03 3.47e+00 bond pdb=" CB PRO R 267 " pdb=" CG PRO R 267 " ideal model delta sigma weight residual 1.492 1.407 0.085 5.00e-02 4.00e+02 2.90e+00 bond pdb=" C5 CLR R 606 " pdb=" C6 CLR R 606 " ideal model delta sigma weight residual 1.332 1.301 0.031 2.00e-02 2.50e+03 2.41e+00 ... (remaining 9738 not shown) Histogram of bond angle deviations from ideal: 100.02 - 106.82: 256 106.82 - 113.62: 5398 113.62 - 120.42: 3789 120.42 - 127.22: 3682 127.22 - 134.02: 108 Bond angle restraints: 13233 Sorted by residual: angle pdb=" C LEU R 269 " pdb=" N PHE R 270 " pdb=" CA PHE R 270 " ideal model delta sigma weight residual 122.26 115.97 6.29 1.59e+00 3.96e-01 1.56e+01 angle pdb=" CA TYR R 141 " pdb=" CB TYR R 141 " pdb=" CG TYR R 141 " ideal model delta sigma weight residual 113.90 121.01 -7.11 1.80e+00 3.09e-01 1.56e+01 angle pdb=" N ALA R 358 " pdb=" CA ALA R 358 " pdb=" C ALA R 358 " ideal model delta sigma weight residual 109.81 117.13 -7.32 2.21e+00 2.05e-01 1.10e+01 angle pdb=" C ASP R 66 " pdb=" N MET R 67 " pdb=" CA MET R 67 " ideal model delta sigma weight residual 121.54 127.84 -6.30 1.91e+00 2.74e-01 1.09e+01 angle pdb=" N AIB P 2 " pdb=" CA AIB P 2 " pdb=" C AIB P 2 " ideal model delta sigma weight residual 111.00 119.70 -8.70 2.80e+00 1.28e-01 9.67e+00 ... (remaining 13228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 5517 15.04 - 30.07: 166 30.07 - 45.11: 43 45.11 - 60.14: 0 60.14 - 75.18: 1 Dihedral angle restraints: 5727 sinusoidal: 2337 harmonic: 3390 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 93.00 137.60 -44.60 1 1.00e+01 1.00e-02 2.76e+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 180.00 158.84 21.16 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 161.84 18.16 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 5724 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1323 0.089 - 0.178: 126 0.178 - 0.267: 8 0.267 - 0.355: 7 0.355 - 0.444: 7 Chirality restraints: 1471 Sorted by residual: chirality pdb=" C14 CLR R 604 " pdb=" C13 CLR R 604 " pdb=" C15 CLR R 604 " pdb=" C8 CLR R 604 " both_signs ideal model delta sigma weight residual False -2.32 -2.76 0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.43 2.00e-01 2.50e+01 4.61e+00 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 0.42 2.00e-01 2.50e+01 4.31e+00 ... (remaining 1468 not shown) Planarity restraints: 1657 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 194 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO R 195 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO R 195 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 195 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO G 49 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " 0.032 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO A 332 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " 0.027 5.00e-02 4.00e+02 ... (remaining 1654 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1664 2.78 - 3.31: 8531 3.31 - 3.84: 15139 3.84 - 4.37: 17271 4.37 - 4.90: 30613 Nonbonded interactions: 73218 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 2.299 2.440 nonbonded pdb=" O ASN A 239 " pdb=" OG1 THR A 285 " model vdw 2.325 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.336 2.440 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.336 2.440 ... (remaining 73213 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: 1.110 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: 4.470 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.610 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 0.085 9743 Z= 0.252 Angle : 0.807 8.705 13233 Z= 0.432 Chirality : 0.063 0.444 1471 Planarity : 0.006 0.053 1657 Dihedral : 8.003 75.178 3521 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.21), residues: 1149 helix: -0.09 (0.19), residues: 453 sheet: -0.51 (0.32), residues: 221 loop : -1.38 (0.24), residues: 475 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 1.255 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 outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2716 time to fit residues: 111.4668 Evaluate side-chains 162 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.147 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 0.2980 chunk 67 optimal weight: 10.0000 chunk 104 optimal weight: 30.0000 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 173 HIS ** R 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 1 HIS P 3 GLN P 20 GLN A 19 GLN A 23 ASN A 267 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 88 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 9743 Z= 0.472 Angle : 0.744 9.725 13233 Z= 0.389 Chirality : 0.047 0.159 1471 Planarity : 0.005 0.048 1657 Dihedral : 5.464 59.229 1358 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer Outliers : 4.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1149 helix: 1.45 (0.23), residues: 457 sheet: -0.58 (0.33), residues: 221 loop : -0.85 (0.26), residues: 471 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 159 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 33 residues processed: 194 average time/residue: 0.2636 time to fit residues: 68.3821 Evaluate side-chains 167 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 1.285 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.0887 time to fit residues: 6.8656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.6980 chunk 32 optimal weight: 0.0980 chunk 86 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 7.9990 chunk 113 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN R 255 HIS R 310 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 41 HIS ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 9743 Z= 0.173 Angle : 0.548 8.150 13233 Z= 0.284 Chirality : 0.040 0.154 1471 Planarity : 0.004 0.037 1657 Dihedral : 5.011 55.567 1358 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.01 % 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: 0.75 (0.24), residues: 1149 helix: 2.13 (0.24), residues: 452 sheet: -0.48 (0.32), residues: 230 loop : -0.57 (0.27), residues: 467 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 157 average time/residue: 0.2654 time to fit residues: 56.1728 Evaluate side-chains 128 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0850 time to fit residues: 2.0857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.0030 chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 104 optimal weight: 20.0000 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 310 ASN P 3 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 9743 Z= 0.167 Angle : 0.543 8.973 13233 Z= 0.281 Chirality : 0.040 0.251 1471 Planarity : 0.004 0.038 1657 Dihedral : 4.902 51.147 1358 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.92 % 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: 0.93 (0.25), residues: 1149 helix: 2.32 (0.24), residues: 449 sheet: -0.40 (0.33), residues: 232 loop : -0.49 (0.27), residues: 468 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 11 residues processed: 150 average time/residue: 0.2646 time to fit residues: 53.3788 Evaluate side-chains 139 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.201 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1288 time to fit residues: 3.9582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 56 optimal weight: 0.0010 chunk 99 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9743 Z= 0.165 Angle : 0.544 9.497 13233 Z= 0.276 Chirality : 0.039 0.183 1471 Planarity : 0.003 0.038 1657 Dihedral : 4.722 46.792 1358 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 1.01 % 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: 1.08 (0.25), residues: 1149 helix: 2.48 (0.25), residues: 449 sheet: -0.31 (0.33), residues: 238 loop : -0.45 (0.28), residues: 462 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 145 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 150 average time/residue: 0.2642 time to fit residues: 53.4782 Evaluate side-chains 135 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 131 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1024 time to fit residues: 2.2986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 chunk 65 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN R 408 HIS P 3 GLN A 220 HIS ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 9743 Z= 0.265 Angle : 0.593 11.352 13233 Z= 0.303 Chirality : 0.041 0.366 1471 Planarity : 0.004 0.038 1657 Dihedral : 4.824 44.912 1358 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer Outliers : 1.51 % 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: 1.01 (0.25), residues: 1149 helix: 2.46 (0.25), residues: 452 sheet: -0.30 (0.33), residues: 236 loop : -0.59 (0.27), residues: 461 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 139 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 147 average time/residue: 0.2811 time to fit residues: 55.2109 Evaluate side-chains 142 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.202 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0963 time to fit residues: 3.2602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 81 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 102 GLN ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 9743 Z= 0.190 Angle : 0.569 10.748 13233 Z= 0.289 Chirality : 0.040 0.300 1471 Planarity : 0.004 0.038 1657 Dihedral : 4.719 43.435 1358 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer Outliers : 1.01 % 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: 1.10 (0.25), residues: 1149 helix: 2.57 (0.25), residues: 452 sheet: -0.35 (0.32), residues: 240 loop : -0.53 (0.28), residues: 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 147 average time/residue: 0.2699 time to fit residues: 53.1790 Evaluate side-chains 134 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.130 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0894 time to fit residues: 2.5605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.0970 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 0.0170 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 0.002 0.043 9743 Z= 0.161 Angle : 0.575 13.592 13233 Z= 0.290 Chirality : 0.039 0.170 1471 Planarity : 0.004 0.042 1657 Dihedral : 4.602 42.092 1358 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 1.21 % 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: 1.08 (0.25), residues: 1149 helix: 2.38 (0.24), residues: 463 sheet: -0.16 (0.33), residues: 238 loop : -0.52 (0.28), residues: 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 144 average time/residue: 0.2680 time to fit residues: 51.6551 Evaluate side-chains 131 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 1.161 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1015 time to fit residues: 2.4695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.0070 chunk 93 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 102 optimal weight: 0.0670 chunk 67 optimal weight: 0.0000 chunk 109 optimal weight: 2.9990 overall best weight: 0.2940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9743 Z= 0.160 Angle : 0.586 13.168 13233 Z= 0.294 Chirality : 0.039 0.286 1471 Planarity : 0.004 0.041 1657 Dihedral : 4.532 41.257 1358 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 0.50 % 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: 1.05 (0.25), residues: 1149 helix: 2.29 (0.25), residues: 463 sheet: -0.06 (0.33), residues: 233 loop : -0.54 (0.28), residues: 453 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 134 average time/residue: 0.2689 time to fit residues: 48.3356 Evaluate side-chains 127 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 1.150 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0888 time to fit residues: 2.0282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 91 optimal weight: 0.0980 chunk 9 optimal weight: 0.0370 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 9743 Z= 0.168 Angle : 0.599 13.101 13233 Z= 0.300 Chirality : 0.040 0.341 1471 Planarity : 0.004 0.041 1657 Dihedral : 4.498 40.860 1358 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer Outliers : 0.20 % 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: 1.06 (0.25), residues: 1149 helix: 2.25 (0.25), residues: 462 sheet: -0.07 (0.33), residues: 238 loop : -0.46 (0.29), residues: 449 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 125 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.2822 time to fit residues: 47.5606 Evaluate side-chains 124 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0946 time to fit residues: 1.6529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN ** P 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 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 = 0.3894 r_free = 0.3894 target = 0.125838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.084581 restraints weight = 18303.452| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.28 r_work: 0.3090 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 9743 Z= 0.246 Angle : 0.622 13.414 13233 Z= 0.315 Chirality : 0.040 0.177 1471 Planarity : 0.004 0.040 1657 Dihedral : 4.642 40.792 1358 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer Outliers : 0.50 % 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: 1.09 (0.25), residues: 1149 helix: 2.37 (0.25), residues: 456 sheet: -0.13 (0.33), residues: 243 loop : -0.48 (0.28), residues: 450 =============================================================================== Job complete usr+sys time: 2360.28 seconds wall clock time: 43 minutes 39.16 seconds (2619.16 seconds total)