Starting phenix.real_space_refine on Wed Feb 14 14:54:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/02_2024/7fin_31604_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/02_2024/7fin_31604.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/02_2024/7fin_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_31604/02_2024/7fin_31604_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/02_2024/7fin_31604_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/02_2024/7fin_31604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/02_2024/7fin_31604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/02_2024/7fin_31604_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fin_31604/02_2024/7fin_31604_updated.pdb" } resolution = 3.1 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= 0.021 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 5.28, per 1000 atoms: 0.55 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: 3.29 Conformation dependent library (CDL) restraints added in 1.7 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: 1.68 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: 2.74 Time building geometry restraints manager: 3.61 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: 5869 15.04 - 30.07: 191 30.07 - 45.11: 56 45.11 - 60.14: 4 60.14 - 75.18: 1 Dihedral angle restraints: 6121 sinusoidal: 2731 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 6118 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: 1.000 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: 4.100 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.030 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- 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 : 8.433 75.178 3915 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 % Allowed : 0.91 % Favored : 99.09 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 281 HIS 0.013 0.002 HIS A 220 PHE 0.024 0.002 PHE B 199 TYR 0.022 0.002 TYR R 141 ARG 0.007 0.000 ARG P 17 *********************** 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 : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 137 LEU cc_start: 0.7052 (mt) cc_final: 0.6625 (tp) REVERT: R 140 MET cc_start: 0.8733 (tmm) cc_final: 0.8475 (ttp) REVERT: R 153 LEU cc_start: 0.8755 (mt) cc_final: 0.8415 (mt) REVERT: R 304 LEU cc_start: 0.8424 (mt) cc_final: 0.8130 (pp) REVERT: R 389 SER cc_start: 0.9124 (t) cc_final: 0.8881 (p) REVERT: P 11 SER cc_start: 0.8043 (t) cc_final: 0.7736 (p) REVERT: A 220 HIS cc_start: 0.7503 (m-70) cc_final: 0.7064 (m-70) REVERT: A 296 LEU cc_start: 0.8048 (tp) cc_final: 0.7818 (tp) REVERT: A 378 ASP cc_start: 0.8444 (m-30) cc_final: 0.8122 (m-30) REVERT: B 35 ASN cc_start: 0.8200 (m-40) cc_final: 0.7755 (m110) REVERT: B 226 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7916 (mt-10) REVERT: N 60 TYR cc_start: 0.8935 (m-80) cc_final: 0.8577 (m-10) REVERT: N 73 ASP cc_start: 0.7648 (t0) cc_final: 0.7177 (t0) REVERT: N 90 ASP cc_start: 0.8383 (m-30) cc_final: 0.8119 (m-30) REVERT: N 113 THR cc_start: 0.9392 (m) cc_final: 0.9127 (p) REVERT: N 125 THR cc_start: 0.8473 (m) cc_final: 0.8083 (p) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2681 time to fit residues: 109.9053 Evaluate side-chains 170 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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: 0.9990 chunk 29 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 67 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 1 HIS P 3 GLN P 20 GLN A 19 GLN A 23 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 88 ASN B 91 HIS ** 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: 0.7758 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 9743 Z= 0.394 Angle : 0.678 9.156 13233 Z= 0.355 Chirality : 0.045 0.150 1471 Planarity : 0.005 0.043 1657 Dihedral : 6.601 56.114 1752 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.03 % Allowed : 9.58 % Favored : 86.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1149 helix: 1.60 (0.23), residues: 453 sheet: -0.45 (0.33), residues: 219 loop : -0.88 (0.25), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 281 HIS 0.009 0.002 HIS A 220 PHE 0.022 0.002 PHE R 270 TYR 0.030 0.003 TYR R 141 ARG 0.007 0.001 ARG B 197 *********************** 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 208 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.7783 (t80) cc_final: 0.7551 (t80) REVERT: R 137 LEU cc_start: 0.7380 (mt) cc_final: 0.7044 (tp) REVERT: R 138 GLN cc_start: 0.7927 (tt0) cc_final: 0.7607 (tm-30) REVERT: R 140 MET cc_start: 0.8779 (tmm) cc_final: 0.8501 (ttp) REVERT: R 153 LEU cc_start: 0.8796 (mt) cc_final: 0.8488 (mt) REVERT: R 261 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7694 (tp) REVERT: R 389 SER cc_start: 0.9264 (t) cc_final: 0.8776 (p) REVERT: P 25 TRP cc_start: 0.6389 (t60) cc_final: 0.5976 (t60) REVERT: A 311 TYR cc_start: 0.8060 (m-10) cc_final: 0.7435 (m-80) REVERT: B 27 ASP cc_start: 0.8531 (t70) cc_final: 0.8041 (m-30) REVERT: B 35 ASN cc_start: 0.8333 (m-40) cc_final: 0.8026 (m110) REVERT: B 134 ARG cc_start: 0.7176 (ptt180) cc_final: 0.6755 (mmp80) REVERT: B 226 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7988 (mt-10) REVERT: B 298 ASP cc_start: 0.8354 (t0) cc_final: 0.8127 (t0) REVERT: B 301 LYS cc_start: 0.8945 (mmmm) cc_final: 0.8570 (mmtm) REVERT: G 11 GLN cc_start: 0.9243 (pp30) cc_final: 0.8906 (pp30) REVERT: N 73 ASP cc_start: 0.7838 (t0) cc_final: 0.7226 (t0) REVERT: N 90 ASP cc_start: 0.8706 (m-30) cc_final: 0.8341 (m-30) REVERT: N 125 THR cc_start: 0.8431 (m) cc_final: 0.7844 (p) outliers start: 40 outliers final: 29 residues processed: 200 average time/residue: 0.2547 time to fit residues: 67.7308 Evaluate side-chains 173 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 262 LEU Chi-restraints excluded: chain R residue 276 ILE Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain P residue 9 ASP Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 91 THR 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: 115 random chunks: chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 ** 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** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9743 Z= 0.173 Angle : 0.538 7.416 13233 Z= 0.278 Chirality : 0.040 0.208 1471 Planarity : 0.004 0.038 1657 Dihedral : 6.336 58.730 1752 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.02 % Allowed : 12.70 % Favored : 84.27 % 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: 0.80 (0.24), residues: 1149 helix: 2.09 (0.24), residues: 460 sheet: -0.23 (0.33), residues: 230 loop : -0.64 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE R 270 TYR 0.022 0.001 TYR R 141 ARG 0.006 0.000 ARG B 19 *********************** 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 187 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.191 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: R 42 TYR cc_start: 0.7913 (t80) cc_final: 0.7639 (t80) REVERT: R 138 GLN cc_start: 0.7873 (tt0) cc_final: 0.7608 (tm-30) REVERT: R 261 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7611 (tp) REVERT: R 389 SER cc_start: 0.9277 (t) cc_final: 0.8773 (p) REVERT: R 403 ILE cc_start: 0.8858 (mm) cc_final: 0.8440 (pt) REVERT: A 311 TYR cc_start: 0.7996 (m-10) cc_final: 0.7634 (m-80) REVERT: A 378 ASP cc_start: 0.8428 (m-30) cc_final: 0.8051 (m-30) REVERT: B 8 ARG cc_start: 0.8822 (mtp180) cc_final: 0.8189 (mtp85) REVERT: B 9 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8425 (mm110) REVERT: B 13 GLN cc_start: 0.8529 (pp30) cc_final: 0.8322 (pp30) REVERT: B 15 LYS cc_start: 0.9408 (mtmt) cc_final: 0.8782 (tmtt) REVERT: B 27 ASP cc_start: 0.8660 (t70) cc_final: 0.8419 (m-30) REVERT: B 35 ASN cc_start: 0.8226 (m-40) cc_final: 0.7886 (m110) REVERT: B 226 GLU cc_start: 0.8166 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 298 ASP cc_start: 0.8261 (t0) cc_final: 0.7993 (t0) REVERT: B 301 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8496 (mmtm) REVERT: G 18 GLN cc_start: 0.7860 (tp40) cc_final: 0.7576 (tp40) REVERT: G 29 LYS cc_start: 0.7958 (mmtt) cc_final: 0.7684 (ptpp) REVERT: N 1 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7848 (tp40) REVERT: N 73 ASP cc_start: 0.7780 (t0) cc_final: 0.7173 (t0) REVERT: N 90 ASP cc_start: 0.8689 (m-30) cc_final: 0.8271 (m-30) outliers start: 30 outliers final: 22 residues processed: 180 average time/residue: 0.2560 time to fit residues: 61.4613 Evaluate side-chains 164 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain P residue 14 LEU Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.0970 chunk 104 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 0.0020 chunk 29 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- 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 G 18 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.4082 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= 0.216 Angle : 0.543 9.239 13233 Z= 0.281 Chirality : 0.040 0.184 1471 Planarity : 0.004 0.037 1657 Dihedral : 6.306 58.911 1752 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.53 % Allowed : 12.40 % Favored : 84.07 % 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: 1.03 (0.25), residues: 1149 helix: 2.44 (0.24), residues: 455 sheet: -0.37 (0.32), residues: 238 loop : -0.50 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS A 387 PHE 0.018 0.001 PHE R 270 TYR 0.022 0.001 TYR R 141 ARG 0.006 0.000 ARG G 62 *********************** 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 187 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 152 time to evaluate : 1.144 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: R 42 TYR cc_start: 0.7963 (t80) cc_final: 0.7685 (t80) REVERT: R 140 MET cc_start: 0.9153 (ttp) cc_final: 0.8834 (ttp) REVERT: R 261 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7651 (tp) REVERT: R 389 SER cc_start: 0.9318 (t) cc_final: 0.8818 (p) REVERT: A 15 GLU cc_start: 0.8277 (pp20) cc_final: 0.8017 (pp20) REVERT: A 311 TYR cc_start: 0.8165 (m-10) cc_final: 0.7595 (m-80) REVERT: A 378 ASP cc_start: 0.8424 (m-30) cc_final: 0.8062 (m-30) REVERT: B 8 ARG cc_start: 0.8813 (mtp180) cc_final: 0.8207 (mtp85) REVERT: B 15 LYS cc_start: 0.9405 (mtmt) cc_final: 0.8793 (tmtt) REVERT: B 27 ASP cc_start: 0.8685 (t70) cc_final: 0.8422 (m-30) REVERT: B 35 ASN cc_start: 0.8261 (m-40) cc_final: 0.7689 (m110) REVERT: B 44 GLN cc_start: 0.8318 (mp10) cc_final: 0.8109 (mt0) REVERT: B 226 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7920 (mt-10) REVERT: B 298 ASP cc_start: 0.8268 (t0) cc_final: 0.7988 (t0) REVERT: B 301 LYS cc_start: 0.8914 (mmmm) cc_final: 0.8459 (mmtm) REVERT: G 18 GLN cc_start: 0.7908 (tp-100) cc_final: 0.7592 (tp40) REVERT: G 20 LYS cc_start: 0.8458 (mtmt) cc_final: 0.8202 (ptpt) REVERT: G 29 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7710 (ptpp) REVERT: G 36 ASP cc_start: 0.8112 (m-30) cc_final: 0.7866 (m-30) REVERT: G 58 GLU cc_start: 0.8014 (pm20) cc_final: 0.7763 (pm20) REVERT: N 1 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7792 (tp40) REVERT: N 73 ASP cc_start: 0.7714 (t0) cc_final: 0.7145 (t0) REVERT: N 90 ASP cc_start: 0.8745 (m-30) cc_final: 0.8304 (m-30) outliers start: 35 outliers final: 25 residues processed: 178 average time/residue: 0.2423 time to fit residues: 58.0503 Evaluate side-chains 168 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 141 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 0.0570 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- 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 1 HIS ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9743 Z= 0.390 Angle : 0.656 10.149 13233 Z= 0.338 Chirality : 0.044 0.202 1471 Planarity : 0.004 0.042 1657 Dihedral : 6.599 58.654 1752 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.03 % Allowed : 12.40 % Favored : 83.57 % 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: 0.92 (0.25), residues: 1149 helix: 2.35 (0.24), residues: 457 sheet: -0.41 (0.33), residues: 230 loop : -0.59 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 209 HIS 0.007 0.001 HIS P 1 PHE 0.019 0.002 PHE R 270 TYR 0.023 0.002 TYR R 141 ARG 0.018 0.001 ARG R 38 *********************** 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 184 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 144 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 TYR cc_start: 0.8076 (t80) cc_final: 0.7632 (t80) REVERT: R 146 SER cc_start: 0.8796 (m) cc_final: 0.8587 (p) REVERT: R 153 LEU cc_start: 0.9061 (mt) cc_final: 0.8664 (mt) REVERT: R 380 LEU cc_start: 0.9058 (tp) cc_final: 0.8829 (tp) REVERT: R 389 SER cc_start: 0.9278 (t) cc_final: 0.9008 (p) REVERT: A 221 MET cc_start: 0.8694 (ttm) cc_final: 0.8464 (ttp) REVERT: A 311 TYR cc_start: 0.8253 (m-10) cc_final: 0.7686 (m-80) REVERT: B 8 ARG cc_start: 0.8825 (mtp180) cc_final: 0.8229 (mtp85) REVERT: B 15 LYS cc_start: 0.9413 (mtmt) cc_final: 0.8805 (tmtt) REVERT: B 27 ASP cc_start: 0.8760 (t70) cc_final: 0.8366 (m-30) REVERT: B 59 TYR cc_start: 0.9142 (OUTLIER) cc_final: 0.8330 (m-80) REVERT: B 226 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 298 ASP cc_start: 0.8298 (t0) cc_final: 0.8071 (t0) REVERT: B 301 LYS cc_start: 0.9064 (mmmm) cc_final: 0.8480 (mmtm) REVERT: G 20 LYS cc_start: 0.8493 (mtmt) cc_final: 0.8247 (ptpt) REVERT: N 73 ASP cc_start: 0.7830 (t0) cc_final: 0.7186 (t0) REVERT: N 113 THR cc_start: 0.9362 (m) cc_final: 0.9104 (p) outliers start: 40 outliers final: 33 residues processed: 173 average time/residue: 0.2709 time to fit residues: 63.6098 Evaluate side-chains 172 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 138 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 174 ILE Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 271 VAL Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 327 THR Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 111 optimal weight: 0.0050 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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** ** R 310 ASN ** 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: 0.7754 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 0.042 9743 Z= 0.181 Angle : 0.559 9.161 13233 Z= 0.285 Chirality : 0.040 0.183 1471 Planarity : 0.004 0.039 1657 Dihedral : 6.351 59.620 1752 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.33 % Allowed : 13.61 % Favored : 83.06 % 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: 1.13 (0.25), residues: 1149 helix: 2.56 (0.24), residues: 457 sheet: -0.26 (0.33), residues: 224 loop : -0.55 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.017 0.001 PHE R 270 TYR 0.018 0.001 TYR R 141 ARG 0.008 0.000 ARG R 38 *********************** 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 177 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 144 time to evaluate : 1.052 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: R 42 TYR cc_start: 0.8230 (t80) cc_final: 0.7816 (t80) REVERT: R 85 PRO cc_start: 0.6714 (Cg_endo) cc_final: 0.6402 (Cg_exo) REVERT: R 146 SER cc_start: 0.8801 (m) cc_final: 0.8585 (p) REVERT: R 153 LEU cc_start: 0.9046 (mt) cc_final: 0.8623 (mt) REVERT: R 380 LEU cc_start: 0.8995 (tp) cc_final: 0.8657 (tp) REVERT: R 389 SER cc_start: 0.9295 (t) cc_final: 0.9028 (p) REVERT: A 15 GLU cc_start: 0.8224 (pp20) cc_final: 0.7961 (pp20) REVERT: A 221 MET cc_start: 0.8537 (ttm) cc_final: 0.8305 (ttp) REVERT: A 311 TYR cc_start: 0.8229 (m-10) cc_final: 0.7628 (m-80) REVERT: A 378 ASP cc_start: 0.8343 (m-30) cc_final: 0.7905 (m-30) REVERT: B 8 ARG cc_start: 0.8822 (mtp180) cc_final: 0.8206 (mtp85) REVERT: B 15 LYS cc_start: 0.9402 (mtmt) cc_final: 0.8821 (tmtt) REVERT: B 27 ASP cc_start: 0.8640 (t70) cc_final: 0.8338 (m-30) REVERT: B 45 MET cc_start: 0.8720 (mtp) cc_final: 0.8397 (mtm) REVERT: B 226 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7762 (mt-10) REVERT: B 298 ASP cc_start: 0.8250 (t0) cc_final: 0.7965 (t70) REVERT: B 301 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8393 (tppt) REVERT: G 13 ARG cc_start: 0.8752 (ttp80) cc_final: 0.8549 (tmm160) REVERT: G 14 LYS cc_start: 0.9016 (ptpp) cc_final: 0.8222 (ptpp) REVERT: G 20 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8181 (ptpt) REVERT: G 41 CYS cc_start: 0.8224 (m) cc_final: 0.8023 (m) REVERT: N 73 ASP cc_start: 0.7679 (t0) cc_final: 0.7191 (t0) REVERT: N 113 THR cc_start: 0.9365 (m) cc_final: 0.9108 (p) outliers start: 33 outliers final: 25 residues processed: 168 average time/residue: 0.2565 time to fit residues: 57.6989 Evaluate side-chains 161 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 387 LEU Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 110 optimal weight: 0.1980 chunk 69 optimal weight: 0.2980 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9743 Z= 0.163 Angle : 0.555 10.888 13233 Z= 0.279 Chirality : 0.040 0.323 1471 Planarity : 0.004 0.042 1657 Dihedral : 6.076 57.132 1752 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.72 % Allowed : 14.82 % Favored : 82.46 % 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: 1.21 (0.25), residues: 1149 helix: 2.62 (0.24), residues: 456 sheet: -0.22 (0.33), residues: 236 loop : -0.49 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.003 0.001 HIS A 357 PHE 0.019 0.001 PHE R 270 TYR 0.019 0.001 TYR R 141 ARG 0.008 0.000 ARG R 38 *********************** 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 173 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 1.179 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: R 37 GLN cc_start: 0.9165 (tm-30) cc_final: 0.8856 (tm-30) REVERT: R 42 TYR cc_start: 0.8294 (t80) cc_final: 0.7932 (t80) REVERT: R 85 PRO cc_start: 0.6576 (Cg_endo) cc_final: 0.6252 (Cg_exo) REVERT: R 138 GLN cc_start: 0.7992 (tt0) cc_final: 0.7426 (tm-30) REVERT: R 146 SER cc_start: 0.8797 (m) cc_final: 0.8579 (p) REVERT: R 153 LEU cc_start: 0.9036 (mt) cc_final: 0.8666 (mt) REVERT: R 261 LEU cc_start: 0.8003 (OUTLIER) cc_final: 0.7658 (tp) REVERT: R 380 LEU cc_start: 0.8985 (tp) cc_final: 0.8681 (tp) REVERT: R 389 SER cc_start: 0.9247 (t) cc_final: 0.8987 (p) REVERT: A 15 GLU cc_start: 0.8229 (pp20) cc_final: 0.8026 (pp20) REVERT: A 311 TYR cc_start: 0.8206 (m-10) cc_final: 0.7595 (m-80) REVERT: A 378 ASP cc_start: 0.8336 (m-30) cc_final: 0.7973 (m-30) REVERT: B 8 ARG cc_start: 0.8839 (mtp180) cc_final: 0.8230 (mtp85) REVERT: B 12 GLU cc_start: 0.8761 (tp30) cc_final: 0.8211 (tp30) REVERT: B 15 LYS cc_start: 0.9399 (mtmt) cc_final: 0.8831 (tmtt) REVERT: B 27 ASP cc_start: 0.8510 (t70) cc_final: 0.8306 (m-30) REVERT: B 188 MET cc_start: 0.8372 (mmm) cc_final: 0.8130 (mmm) REVERT: B 226 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7773 (mt-10) REVERT: B 298 ASP cc_start: 0.8230 (t0) cc_final: 0.7889 (t70) REVERT: B 301 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8422 (mmtm) REVERT: G 14 LYS cc_start: 0.9033 (ptpp) cc_final: 0.8784 (mtmm) REVERT: G 20 LYS cc_start: 0.8431 (mtmt) cc_final: 0.8195 (ptpt) REVERT: N 73 ASP cc_start: 0.7670 (t0) cc_final: 0.7205 (t0) outliers start: 27 outliers final: 24 residues processed: 162 average time/residue: 0.2453 time to fit residues: 53.8603 Evaluate side-chains 165 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 140 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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** ** 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: 0.7786 moved from start: 0.4919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9743 Z= 0.295 Angle : 0.592 8.551 13233 Z= 0.303 Chirality : 0.042 0.349 1471 Planarity : 0.004 0.043 1657 Dihedral : 6.146 56.941 1752 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.63 % Allowed : 14.21 % Favored : 82.16 % 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: 1149 helix: 2.59 (0.24), residues: 457 sheet: -0.33 (0.32), residues: 236 loop : -0.45 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS A 357 PHE 0.017 0.002 PHE R 270 TYR 0.021 0.002 TYR R 141 ARG 0.007 0.000 ARG R 38 *********************** 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 179 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 143 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 37 GLN cc_start: 0.9161 (tm-30) cc_final: 0.8850 (tm-30) REVERT: R 42 TYR cc_start: 0.8313 (t80) cc_final: 0.8083 (t80) REVERT: R 85 PRO cc_start: 0.6590 (Cg_endo) cc_final: 0.6259 (Cg_exo) REVERT: R 146 SER cc_start: 0.8803 (m) cc_final: 0.8595 (p) REVERT: R 153 LEU cc_start: 0.9065 (mt) cc_final: 0.8687 (mt) REVERT: R 261 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7727 (tp) REVERT: R 380 LEU cc_start: 0.9044 (tp) cc_final: 0.8727 (tp) REVERT: R 389 SER cc_start: 0.9282 (t) cc_final: 0.9026 (p) REVERT: A 15 GLU cc_start: 0.8335 (pp20) cc_final: 0.8074 (pp20) REVERT: A 311 TYR cc_start: 0.8263 (m-10) cc_final: 0.7642 (m-80) REVERT: A 378 ASP cc_start: 0.8394 (m-30) cc_final: 0.8080 (m-30) REVERT: B 8 ARG cc_start: 0.8865 (mtp180) cc_final: 0.8275 (mtp85) REVERT: B 12 GLU cc_start: 0.8805 (tp30) cc_final: 0.8269 (tp30) REVERT: B 15 LYS cc_start: 0.9392 (mtmt) cc_final: 0.8788 (tmtt) REVERT: B 38 ASP cc_start: 0.8562 (OUTLIER) cc_final: 0.8261 (t0) REVERT: B 45 MET cc_start: 0.8769 (mtp) cc_final: 0.8450 (mtm) REVERT: B 188 MET cc_start: 0.8545 (mmm) cc_final: 0.8251 (mmm) REVERT: B 226 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 234 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8940 (m-80) REVERT: B 298 ASP cc_start: 0.8244 (t0) cc_final: 0.7960 (t0) REVERT: B 301 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8473 (mmtm) REVERT: G 20 LYS cc_start: 0.8467 (mtmt) cc_final: 0.8204 (ptpt) REVERT: N 73 ASP cc_start: 0.7696 (t0) cc_final: 0.7250 (t0) outliers start: 36 outliers final: 29 residues processed: 166 average time/residue: 0.2585 time to fit residues: 57.4883 Evaluate side-chains 171 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 139 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain N residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 310 ASN A 278 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9743 Z= 0.234 Angle : 0.602 10.555 13233 Z= 0.305 Chirality : 0.041 0.330 1471 Planarity : 0.004 0.042 1657 Dihedral : 6.141 55.968 1752 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.12 % Allowed : 14.92 % Favored : 81.96 % 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: 1.23 (0.25), residues: 1149 helix: 2.60 (0.24), residues: 452 sheet: -0.13 (0.33), residues: 234 loop : -0.45 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE R 270 TYR 0.020 0.001 TYR R 141 ARG 0.006 0.000 ARG G 13 *********************** 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 172 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.146 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: R 138 GLN cc_start: 0.8026 (tt0) cc_final: 0.7434 (tm-30) REVERT: R 146 SER cc_start: 0.8806 (m) cc_final: 0.8600 (p) REVERT: R 153 LEU cc_start: 0.9063 (mt) cc_final: 0.8689 (mt) REVERT: R 261 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7723 (tp) REVERT: R 380 LEU cc_start: 0.9021 (tp) cc_final: 0.8691 (tp) REVERT: R 389 SER cc_start: 0.9285 (t) cc_final: 0.9022 (p) REVERT: A 15 GLU cc_start: 0.8244 (pp20) cc_final: 0.8043 (pp20) REVERT: A 311 TYR cc_start: 0.8242 (m-10) cc_final: 0.7555 (m-80) REVERT: A 378 ASP cc_start: 0.8329 (m-30) cc_final: 0.7918 (m-30) REVERT: B 8 ARG cc_start: 0.8868 (mtp180) cc_final: 0.8260 (mtp85) REVERT: B 12 GLU cc_start: 0.8804 (tp30) cc_final: 0.8255 (tp30) REVERT: B 15 LYS cc_start: 0.9373 (mtmt) cc_final: 0.8765 (tmtt) REVERT: B 45 MET cc_start: 0.8730 (mtp) cc_final: 0.8422 (mtm) REVERT: B 188 MET cc_start: 0.8509 (mmm) cc_final: 0.8237 (mmm) REVERT: B 226 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7836 (mt-10) REVERT: B 234 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8933 (m-80) REVERT: B 298 ASP cc_start: 0.8216 (t0) cc_final: 0.7901 (t70) REVERT: B 301 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8450 (mmtm) REVERT: G 20 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8221 (ptpt) REVERT: N 73 ASP cc_start: 0.7713 (t0) cc_final: 0.7275 (t0) outliers start: 31 outliers final: 26 residues processed: 161 average time/residue: 0.2603 time to fit residues: 56.1336 Evaluate side-chains 163 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 310 ASN Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 58 ILE Chi-restraints excluded: chain N residue 83 MET 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: 115 random chunks: chunk 66 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 0.0170 chunk 72 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- 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 ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9743 Z= 0.222 Angle : 0.600 9.378 13233 Z= 0.305 Chirality : 0.042 0.339 1471 Planarity : 0.004 0.043 1657 Dihedral : 6.092 55.387 1752 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.82 % Allowed : 15.73 % Favored : 81.45 % 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: 1.14 (0.25), residues: 1149 helix: 2.44 (0.24), residues: 461 sheet: -0.14 (0.33), residues: 234 loop : -0.50 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.005 0.001 HIS A 357 PHE 0.018 0.001 PHE R 270 TYR 0.019 0.001 TYR R 141 ARG 0.008 0.000 ARG A 228 ********************** 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 164 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 136 time to evaluate : 1.110 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: R 37 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8878 (tm-30) REVERT: R 146 SER cc_start: 0.8806 (m) cc_final: 0.8600 (p) REVERT: R 153 LEU cc_start: 0.9067 (mt) cc_final: 0.8692 (mt) REVERT: R 261 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7739 (tp) REVERT: R 389 SER cc_start: 0.9284 (t) cc_final: 0.9020 (p) REVERT: A 15 GLU cc_start: 0.8248 (pp20) cc_final: 0.8047 (pp20) REVERT: A 311 TYR cc_start: 0.8258 (m-10) cc_final: 0.7572 (m-80) REVERT: A 378 ASP cc_start: 0.8381 (m-30) cc_final: 0.8001 (m-30) REVERT: B 8 ARG cc_start: 0.8841 (mtp180) cc_final: 0.8251 (mtp85) REVERT: B 12 GLU cc_start: 0.8797 (tp30) cc_final: 0.8325 (tp30) REVERT: B 15 LYS cc_start: 0.9371 (mtmt) cc_final: 0.8757 (tmtt) REVERT: B 45 MET cc_start: 0.8725 (mtp) cc_final: 0.8415 (mtm) REVERT: B 188 MET cc_start: 0.8502 (mmm) cc_final: 0.8239 (mmm) REVERT: B 226 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7788 (mt-10) REVERT: B 234 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8937 (m-80) REVERT: B 298 ASP cc_start: 0.8218 (t0) cc_final: 0.7900 (t70) REVERT: B 301 LYS cc_start: 0.8954 (mmmm) cc_final: 0.8448 (mmtm) REVERT: G 14 LYS cc_start: 0.9136 (mtmm) cc_final: 0.8893 (mtmm) REVERT: G 20 LYS cc_start: 0.8492 (mtmt) cc_final: 0.8233 (ptpt) REVERT: N 73 ASP cc_start: 0.7691 (t0) cc_final: 0.7251 (t0) outliers start: 28 outliers final: 24 residues processed: 155 average time/residue: 0.2719 time to fit residues: 56.3622 Evaluate side-chains 162 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 157 LEU Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 290 ASN Chi-restraints excluded: chain R residue 315 ILE Chi-restraints excluded: chain R residue 347 VAL Chi-restraints excluded: chain R residue 393 CYS Chi-restraints excluded: chain R residue 403 ILE Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 58 ILE 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: 115 random chunks: chunk 27 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 13 optimal weight: 0.2980 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 93 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 80 optimal weight: 0.0050 chunk 5 optimal weight: 5.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** G 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.125878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.085375 restraints weight = 18371.888| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 3.27 r_work: 0.3097 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9743 Z= 0.166 Angle : 0.580 9.895 13233 Z= 0.291 Chirality : 0.041 0.328 1471 Planarity : 0.004 0.043 1657 Dihedral : 5.917 53.894 1752 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.32 % Allowed : 16.33 % Favored : 81.35 % 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: 1.21 (0.25), residues: 1149 helix: 2.55 (0.25), residues: 457 sheet: -0.10 (0.33), residues: 236 loop : -0.49 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 169 HIS 0.004 0.001 HIS A 357 PHE 0.019 0.001 PHE R 270 TYR 0.018 0.001 TYR R 141 ARG 0.008 0.000 ARG A 228 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2498.39 seconds wall clock time: 45 minutes 57.55 seconds (2757.55 seconds total)