Starting phenix.real_space_refine on Mon Mar 11 15:59:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/03_2024/7ffn_31569_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/03_2024/7ffn_31569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/03_2024/7ffn_31569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/03_2024/7ffn_31569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/03_2024/7ffn_31569_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/03_2024/7ffn_31569_neut.pdb" } resolution = 3.0 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 67 5.16 5 C 5434 2.51 5 N 1470 2.21 5 O 1617 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 57": "OD1" <-> "OD2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 18": "NH1" <-> "NH2" Residue "N ARG 21": "NH1" <-> "NH2" Residue "N ARG 103": "NH1" <-> "NH2" Residue "N ARG 120": "NH1" <-> "NH2" Residue "N ARG 281": "NH1" <-> "NH2" Residue "N ARG 362": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8589 Number of models: 1 Model: "" Number of chains: 6 Chain: "K" Number of atoms: 1281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1281 Classifications: {'peptide': 163} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 155} Chain: "L" Number of atoms: 375 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 375 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 5, 'TRANS': 44} Chain: "M" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 287 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 3, 'TRANS': 34} Chain: "N" Number of atoms: 3275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3275 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 30, 'TRANS': 388} Chain: "O" Number of atoms: 3370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3370 Classifications: {'peptide': 442} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 413} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.59 Number of scatterers: 8589 At special positions: 0 Unit cell: (150.48, 96.36, 176.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 67 16.00 O 1617 8.00 N 1470 7.00 C 5434 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " distance=2.03 Simple disulfide: pdb=" SG CYS M 29 " - pdb=" SG CYS M 42 " distance=2.03 Simple disulfide: pdb=" SG CYS M 37 " - pdb=" SG CYS M 55 " distance=1.09 Simple disulfide: pdb=" SG CYS M 49 " - pdb=" SG CYS M 64 " distance=2.03 Simple disulfide: pdb=" SG CYS N 19 " - pdb=" SG CYS N 123 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 27 " distance=2.03 Simple disulfide: pdb=" SG CYS N 90 " - pdb=" SG CYS N 104 " distance=2.02 Simple disulfide: pdb=" SG CYS N 151 " - pdb=" SG CYS N 266 " distance=2.03 Simple disulfide: pdb=" SG CYS N 200 " - pdb=" SG CYS N 226 " distance=2.02 Simple disulfide: pdb=" SG CYS N 202 " - pdb=" SG CYS N 220 " distance=2.02 Simple disulfide: pdb=" SG CYS O 62 " - pdb=" SG CYS O 94 " distance=2.04 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 259 " - pdb=" SG CYS O 271 " distance=2.03 Simple disulfide: pdb=" SG CYS O 301 " - pdb=" SG CYS O 376 " distance=2.03 Simple disulfide: pdb=" SG CYS O 306 " - pdb=" SG CYS O 380 " distance=2.03 Simple disulfide: pdb=" SG CYS O 328 " - pdb=" SG CYS O 370 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 2.0 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 31 sheets defined 17.4% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'K' and resid 113 through 123 removed outlier: 3.802A pdb=" N ARG K 117 " --> pdb=" O GLY K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 164 removed outlier: 3.874A pdb=" N ALA K 164 " --> pdb=" O ASP K 160 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 185 removed outlier: 3.590A pdb=" N ARG K 185 " --> pdb=" O GLN K 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 37 removed outlier: 3.785A pdb=" N THR L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU L 31 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N VAL L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASN L 37 " --> pdb=" O MET L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 52 removed outlier: 4.141A pdb=" N LYS L 52 " --> pdb=" O GLU L 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 46 through 48 No H-bonds generated for 'chain 'M' and resid 46 through 48' Processing helix chain 'M' and resid 55 through 59 removed outlier: 3.973A pdb=" N SER M 59 " --> pdb=" O PHE M 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 5 Processing helix chain 'N' and resid 6 through 11 Processing helix chain 'N' and resid 80 through 82 No H-bonds generated for 'chain 'N' and resid 80 through 82' Processing helix chain 'N' and resid 351 through 363 removed outlier: 3.805A pdb=" N VAL N 355 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ILE N 356 " --> pdb=" O PRO N 352 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR N 357 " --> pdb=" O HIS N 353 " (cutoff:3.500A) Processing helix chain 'N' and resid 363 through 402 removed outlier: 3.515A pdb=" N THR N 367 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE N 368 " --> pdb=" O PRO N 364 " (cutoff:3.500A) Proline residue: N 399 - end of helix removed outlier: 3.616A pdb=" N LEU N 402 " --> pdb=" O THR N 398 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 415 removed outlier: 4.118A pdb=" N VAL N 414 " --> pdb=" O PHE N 410 " (cutoff:3.500A) Processing helix chain 'O' and resid 238 through 246 Processing helix chain 'O' and resid 250 through 255 Processing helix chain 'O' and resid 256 through 259 removed outlier: 3.502A pdb=" N CYS O 259 " --> pdb=" O PRO O 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 256 through 259' Processing helix chain 'O' and resid 283 through 287 removed outlier: 3.572A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE O 287 " --> pdb=" O ASP O 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 283 through 287' Processing helix chain 'O' and resid 289 through 293 removed outlier: 3.582A pdb=" N GLU O 292 " --> pdb=" O ARG O 289 " (cutoff:3.500A) Processing helix chain 'O' and resid 403 through 415 removed outlier: 3.900A pdb=" N LEU O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 439 Processing sheet with id=AA1, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.658A pdb=" N ILE K 136 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU K 132 " --> pdb=" O ILE K 136 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY K 138 " --> pdb=" O ILE K 130 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 141 through 143 Processing sheet with id=AA3, first strand: chain 'K' and resid 168 through 170 Processing sheet with id=AA4, first strand: chain 'K' and resid 190 through 191 removed outlier: 6.705A pdb=" N LYS K 190 " --> pdb=" O VAL K 237 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'K' and resid 198 through 202 removed outlier: 8.494A pdb=" N ALA K 206 " --> pdb=" O PRO K 217 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N PHE K 214 " --> pdb=" O LEU K 253 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 229 through 230 removed outlier: 3.866A pdb=" N ALA K 239 " --> pdb=" O ILE K 230 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL K 241 " --> pdb=" O VAL K 256 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL K 256 " --> pdb=" O VAL K 241 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 6 through 8 Processing sheet with id=AA8, first strand: chain 'M' and resid 34 through 36 Processing sheet with id=AA9, first strand: chain 'N' and resid 17 through 19 removed outlier: 3.928A pdb=" N CYS N 27 " --> pdb=" O CYS N 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 35 through 37 removed outlier: 9.536A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 35 through 37 removed outlier: 5.834A pdb=" N TYR N 98 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 10.195A pdb=" N SER N 51 " --> pdb=" O HIS N 96 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N HIS N 96 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N TYR N 53 " --> pdb=" O ASP N 94 " (cutoff:3.500A) removed outlier: 10.084A pdb=" N ASP N 94 " --> pdb=" O TYR N 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AB4, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AB5, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AB6, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.714A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.684A pdb=" N VAL N 186 " --> pdb=" O PHE N 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AB9, first strand: chain 'N' and resid 275 through 279 Processing sheet with id=AC1, first strand: chain 'N' and resid 307 through 311 Processing sheet with id=AC2, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AC3, first strand: chain 'O' and resid 15 through 19 removed outlier: 5.369A pdb=" N ILE O 31 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N THR O 136 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASN O 134 " --> pdb=" O PRO O 33 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS O 35 " --> pdb=" O PHE O 132 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR O 41 " --> pdb=" O THR O 126 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N THR O 126 " --> pdb=" O THR O 41 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'O' and resid 46 through 48 removed outlier: 3.640A pdb=" N TYR O 46 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 51 through 55 removed outlier: 3.715A pdb=" N ALA O 59 " --> pdb=" O VAL O 103 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 51 through 55 Processing sheet with id=AC7, first strand: chain 'O' and resid 87 through 88 removed outlier: 3.889A pdb=" N GLY O 91 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AC9, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AD1, first strand: chain 'O' and resid 260 through 262 Processing sheet with id=AD2, first strand: chain 'O' and resid 296 through 306 removed outlier: 5.012A pdb=" N ALA O 298 " --> pdb=" O SER O 321 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER O 321 " --> pdb=" O ALA O 298 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY O 350 " --> pdb=" O TYR O 320 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AD4, first strand: chain 'O' and resid 364 through 369 316 hydrogen bonds defined for protein. 807 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: 2.68 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2743 1.34 - 1.46: 2134 1.46 - 1.59: 3844 1.59 - 1.71: 2 1.71 - 1.84: 88 Bond restraints: 8811 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.089 1.08e-02 8.57e+03 6.74e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.310 -0.076 1.21e-02 6.83e+03 3.90e+01 bond pdb=" N VAL N 179 " pdb=" CA VAL N 179 " ideal model delta sigma weight residual 1.457 1.528 -0.071 1.32e-02 5.74e+03 2.89e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.065 1.22e-02 6.72e+03 2.81e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.505 -0.041 1.25e-02 6.40e+03 1.09e+01 ... (remaining 8806 not shown) Histogram of bond angle deviations from ideal: 96.91 - 104.37: 199 104.37 - 111.84: 4160 111.84 - 119.31: 2988 119.31 - 126.77: 4494 126.77 - 134.24: 151 Bond angle restraints: 11992 Sorted by residual: angle pdb=" N ASP N 175 " pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 107.44 123.32 -15.88 1.93e+00 2.68e-01 6.77e+01 angle pdb=" CA VAL N 179 " pdb=" C VAL N 179 " pdb=" N SER N 180 " ideal model delta sigma weight residual 115.77 123.04 -7.27 1.25e+00 6.40e-01 3.39e+01 angle pdb=" N VAL N 179 " pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 109.80 117.18 -7.38 1.33e+00 5.65e-01 3.08e+01 angle pdb=" C VAL N 174 " pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 122.47 129.59 -7.12 1.50e+00 4.44e-01 2.25e+01 angle pdb=" C CYS N 22 " pdb=" N ALA N 23 " pdb=" CA ALA N 23 " ideal model delta sigma weight residual 121.54 130.32 -8.78 1.91e+00 2.74e-01 2.11e+01 ... (remaining 11987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 5089 17.61 - 35.22: 174 35.22 - 52.82: 37 52.82 - 70.43: 5 70.43 - 88.04: 6 Dihedral angle restraints: 5311 sinusoidal: 2086 harmonic: 3225 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 27 " pdb=" CB CYS N 27 " ideal model delta sinusoidal sigma weight residual 93.00 173.64 -80.64 1 1.00e+01 1.00e-02 8.04e+01 dihedral pdb=" CA ILE O 369 " pdb=" C ILE O 369 " pdb=" N CYS O 370 " pdb=" CA CYS O 370 " ideal model delta harmonic sigma weight residual 180.00 -135.79 -44.21 0 5.00e+00 4.00e-02 7.82e+01 dihedral pdb=" CB CYS M 37 " pdb=" SG CYS M 37 " pdb=" SG CYS M 55 " pdb=" CB CYS M 55 " ideal model delta sinusoidal sigma weight residual 93.00 14.07 78.93 1 1.00e+01 1.00e-02 7.76e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1081 0.072 - 0.144: 218 0.144 - 0.215: 27 0.215 - 0.287: 1 0.287 - 0.359: 2 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA ASP N 175 " pdb=" N ASP N 175 " pdb=" C ASP N 175 " pdb=" CB ASP N 175 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CA ASP M 57 " pdb=" N ASP M 57 " pdb=" C ASP M 57 " pdb=" CB ASP M 57 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA HIS N 156 " pdb=" N HIS N 156 " pdb=" C HIS N 156 " pdb=" CB HIS N 156 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 ... (remaining 1326 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN O 264 " 0.066 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO O 265 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO O 265 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO O 265 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 13 " -0.046 5.00e-02 4.00e+02 6.98e-02 7.79e+00 pdb=" N PRO N 14 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO N 14 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO N 14 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG N 88 " 0.046 5.00e-02 4.00e+02 6.89e-02 7.59e+00 pdb=" N PRO N 89 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO N 89 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO N 89 " 0.038 5.00e-02 4.00e+02 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 34 2.52 - 3.11: 5668 3.11 - 3.71: 12191 3.71 - 4.30: 17289 4.30 - 4.90: 29700 Nonbonded interactions: 64882 Sorted by model distance: nonbonded pdb=" OH TYR K 173 " pdb=" NE2 GLN O 439 " model vdw 1.924 2.520 nonbonded pdb=" O ASN O 442 " pdb=" ND2 ASN O 442 " model vdw 2.111 2.520 nonbonded pdb=" OH TYR N 359 " pdb=" O ALA O 401 " model vdw 2.257 2.440 nonbonded pdb=" OE1 GLU O 120 " pdb=" OH TYR O 122 " model vdw 2.276 2.440 nonbonded pdb=" O GLY O 182 " pdb=" OG1 THR O 263 " model vdw 2.312 2.440 ... (remaining 64877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 4.050 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 27.530 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:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.098 8811 Z= 0.498 Angle : 0.945 15.884 11992 Z= 0.520 Chirality : 0.058 0.359 1329 Planarity : 0.008 0.099 1549 Dihedral : 9.733 88.037 3197 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.28 % Rotamer: Outliers : 0.53 % Allowed : 2.76 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % Twisted General : 0.19 % 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: -3.00 (0.21), residues: 1102 helix: -1.89 (0.34), residues: 134 sheet: -1.32 (0.26), residues: 347 loop : -2.48 (0.20), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP M 47 HIS 0.011 0.002 HIS N 28 PHE 0.023 0.003 PHE N 328 TYR 0.031 0.003 TYR O 308 ARG 0.010 0.001 ARG N 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 206 time to evaluate : 0.919 Fit side-chains REVERT: K 166 LYS cc_start: 0.6128 (tttt) cc_final: 0.5681 (pttt) REVERT: K 232 ASP cc_start: 0.1805 (p0) cc_final: 0.1476 (p0) REVERT: N 9 TYR cc_start: 0.8310 (m-80) cc_final: 0.8040 (m-80) REVERT: N 365 MET cc_start: 0.7551 (ttt) cc_final: 0.7237 (pmt) REVERT: N 398 THR cc_start: 0.8150 (m) cc_final: 0.7610 (t) REVERT: O 13 ILE cc_start: 0.9253 (mt) cc_final: 0.9043 (mm) REVERT: O 115 LEU cc_start: 0.8498 (tm) cc_final: 0.8134 (tp) REVERT: O 281 ASP cc_start: 0.7805 (t0) cc_final: 0.7575 (t0) REVERT: O 409 TRP cc_start: 0.8455 (m100) cc_final: 0.8235 (m100) REVERT: O 442 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5851 (t0) outliers start: 5 outliers final: 1 residues processed: 208 average time/residue: 1.1027 time to fit residues: 244.9384 Evaluate side-chains 110 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 257 MET Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 20.0000 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN K 211 ASN M 27 ASN M 30 ASN N 7 ASN N 52 GLN N 96 HIS N 159 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 225 GLN N 353 HIS O 66 GLN O 125 HIS O 157 ASN O 264 ASN ** O 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 386 HIS O 392 GLN O 394 HIS O 439 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8811 Z= 0.214 Angle : 0.596 8.513 11992 Z= 0.312 Chirality : 0.044 0.158 1329 Planarity : 0.006 0.089 1549 Dihedral : 5.472 52.138 1207 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.61 % Allowed : 11.05 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.70 (0.24), residues: 1102 helix: 0.36 (0.45), residues: 131 sheet: -0.57 (0.27), residues: 345 loop : -1.83 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 202 HIS 0.004 0.001 HIS N 41 PHE 0.013 0.002 PHE N 328 TYR 0.020 0.002 TYR O 308 ARG 0.006 0.001 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 139 time to evaluate : 1.029 Fit side-chains REVERT: K 166 LYS cc_start: 0.5929 (tttt) cc_final: 0.5519 (pttt) REVERT: K 173 TYR cc_start: 0.2284 (m-80) cc_final: 0.1943 (m-80) REVERT: N 9 TYR cc_start: 0.8224 (m-80) cc_final: 0.7926 (m-80) REVERT: N 66 MET cc_start: 0.9245 (ttt) cc_final: 0.8992 (ttt) REVERT: N 76 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7968 (pt0) REVERT: N 88 ARG cc_start: 0.8121 (mtm110) cc_final: 0.6511 (mtt180) REVERT: N 113 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7473 (mt-10) REVERT: N 173 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7239 (mm-30) REVERT: N 365 MET cc_start: 0.7698 (ttt) cc_final: 0.7375 (pmt) REVERT: O 24 TYR cc_start: 0.8089 (m-80) cc_final: 0.7696 (m-80) REVERT: O 95 PHE cc_start: 0.7698 (OUTLIER) cc_final: 0.7012 (p90) REVERT: O 115 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8253 (tp) REVERT: O 144 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8661 (p) REVERT: O 246 ASP cc_start: 0.7988 (m-30) cc_final: 0.7720 (m-30) REVERT: O 281 ASP cc_start: 0.8113 (t0) cc_final: 0.7813 (t70) REVERT: O 409 TRP cc_start: 0.8490 (m100) cc_final: 0.8050 (m100) REVERT: O 442 ASN cc_start: 0.6865 (OUTLIER) cc_final: 0.6637 (t0) outliers start: 34 outliers final: 12 residues processed: 157 average time/residue: 1.1378 time to fit residues: 190.9424 Evaluate side-chains 127 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 197 LEU Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 99 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN K 211 ASN N 152 GLN N 159 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 GLN O 155 ASN O 360 ASN O 439 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 8811 Z= 0.294 Angle : 0.628 12.874 11992 Z= 0.324 Chirality : 0.046 0.247 1329 Planarity : 0.006 0.081 1549 Dihedral : 5.168 35.537 1204 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 4.78 % Allowed : 14.03 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -1.22 (0.24), residues: 1102 helix: 0.86 (0.47), residues: 138 sheet: -0.28 (0.27), residues: 351 loop : -1.57 (0.23), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 202 HIS 0.005 0.001 HIS N 41 PHE 0.015 0.002 PHE N 328 TYR 0.023 0.002 TYR O 308 ARG 0.008 0.001 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 122 time to evaluate : 1.144 Fit side-chains REVERT: K 270 GLU cc_start: 0.6707 (tt0) cc_final: 0.6385 (pm20) REVERT: N 66 MET cc_start: 0.9294 (ttt) cc_final: 0.9081 (ttt) REVERT: N 88 ARG cc_start: 0.8449 (mtm110) cc_final: 0.6856 (mtt180) REVERT: N 173 GLU cc_start: 0.7536 (mt-10) cc_final: 0.7178 (mm-30) REVERT: N 256 HIS cc_start: 0.7759 (p90) cc_final: 0.7506 (p90) REVERT: N 365 MET cc_start: 0.7564 (ttt) cc_final: 0.7311 (pmt) REVERT: O 24 TYR cc_start: 0.8331 (m-80) cc_final: 0.8008 (m-80) REVERT: O 95 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7085 (p90) REVERT: O 175 ARG cc_start: 0.7511 (ttp-110) cc_final: 0.7285 (ttp-110) REVERT: O 246 ASP cc_start: 0.7961 (m-30) cc_final: 0.7708 (m-30) REVERT: O 281 ASP cc_start: 0.8336 (t0) cc_final: 0.8132 (t70) REVERT: O 409 TRP cc_start: 0.8591 (m100) cc_final: 0.8160 (m100) REVERT: O 442 ASN cc_start: 0.6577 (OUTLIER) cc_final: 0.6364 (t0) outliers start: 45 outliers final: 21 residues processed: 151 average time/residue: 1.0761 time to fit residues: 174.8277 Evaluate side-chains 130 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 307 THR Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 304 ASN Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Chi-restraints excluded: chain O residue 442 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 51 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN K 211 ASN N 160 ASN N 358 HIS O 439 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 8811 Z= 0.513 Angle : 0.748 11.474 11992 Z= 0.386 Chirality : 0.052 0.269 1329 Planarity : 0.007 0.073 1549 Dihedral : 5.728 35.011 1204 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.28 % Rotamer: Outliers : 5.95 % Allowed : 13.71 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.10 % 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: -1.17 (0.24), residues: 1102 helix: 0.73 (0.46), residues: 144 sheet: -0.11 (0.28), residues: 334 loop : -1.56 (0.23), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 202 HIS 0.009 0.002 HIS N 41 PHE 0.023 0.002 PHE N 278 TYR 0.022 0.003 TYR O 51 ARG 0.008 0.001 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 115 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: N 88 ARG cc_start: 0.8470 (mtm110) cc_final: 0.6999 (mtt180) REVERT: N 113 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: N 173 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6879 (mm-30) REVERT: N 207 ILE cc_start: 0.8070 (mt) cc_final: 0.7861 (tp) REVERT: N 239 ASN cc_start: 0.7892 (t0) cc_final: 0.7386 (t0) REVERT: N 313 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7352 (mp0) REVERT: N 365 MET cc_start: 0.7837 (ttt) cc_final: 0.7321 (pmt) REVERT: O 18 ILE cc_start: 0.8436 (pt) cc_final: 0.8087 (pp) REVERT: O 79 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8788 (ttmt) REVERT: O 95 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7067 (p90) REVERT: O 140 HIS cc_start: 0.7801 (m-70) cc_final: 0.7477 (m-70) REVERT: O 175 ARG cc_start: 0.7706 (ttp-110) cc_final: 0.7298 (ttp-110) REVERT: O 246 ASP cc_start: 0.7867 (m-30) cc_final: 0.7607 (m-30) REVERT: O 263 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7881 (m) REVERT: O 281 ASP cc_start: 0.8544 (t0) cc_final: 0.8225 (t0) REVERT: O 305 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8094 (tp30) outliers start: 56 outliers final: 29 residues processed: 153 average time/residue: 0.9881 time to fit residues: 163.1741 Evaluate side-chains 141 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 242 LEU Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 277 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 79 LYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 144 THR Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 305 GLU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 439 GLN O 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8811 Z= 0.288 Angle : 0.642 9.313 11992 Z= 0.328 Chirality : 0.046 0.259 1329 Planarity : 0.005 0.071 1549 Dihedral : 5.306 34.882 1202 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.46 % Allowed : 15.62 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.25), residues: 1102 helix: 0.92 (0.47), residues: 144 sheet: 0.05 (0.28), residues: 337 loop : -1.43 (0.23), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 89 HIS 0.006 0.001 HIS O 386 PHE 0.015 0.001 PHE N 328 TYR 0.023 0.002 TYR O 308 ARG 0.004 0.000 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: K 270 GLU cc_start: 0.6015 (mm-30) cc_final: 0.5719 (pt0) REVERT: N 66 MET cc_start: 0.9318 (ttt) cc_final: 0.9048 (ttt) REVERT: N 88 ARG cc_start: 0.8407 (mtm110) cc_final: 0.6915 (mtt180) REVERT: N 160 ASN cc_start: 0.6797 (t0) cc_final: 0.6543 (t0) REVERT: N 207 ILE cc_start: 0.8088 (mt) cc_final: 0.7837 (tp) REVERT: N 239 ASN cc_start: 0.7825 (t0) cc_final: 0.7397 (t0) REVERT: N 365 MET cc_start: 0.7834 (ttt) cc_final: 0.7318 (pmt) REVERT: O 18 ILE cc_start: 0.8403 (pt) cc_final: 0.8059 (pp) REVERT: O 95 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7002 (p90) REVERT: O 175 ARG cc_start: 0.7677 (ttp-110) cc_final: 0.7307 (ttp-110) REVERT: O 246 ASP cc_start: 0.7820 (m-30) cc_final: 0.7567 (m-30) REVERT: O 281 ASP cc_start: 0.8555 (t0) cc_final: 0.8326 (t70) REVERT: O 341 GLU cc_start: 0.7532 (OUTLIER) cc_final: 0.7237 (mm-30) outliers start: 42 outliers final: 26 residues processed: 140 average time/residue: 1.0578 time to fit residues: 159.4376 Evaluate side-chains 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 105 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 341 GLU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 34 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 8811 Z= 0.310 Angle : 0.636 9.362 11992 Z= 0.326 Chirality : 0.047 0.199 1329 Planarity : 0.005 0.072 1549 Dihedral : 5.257 35.347 1202 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.99 % Allowed : 15.62 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.10 % 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: -0.81 (0.25), residues: 1102 helix: 0.99 (0.46), residues: 145 sheet: 0.13 (0.28), residues: 347 loop : -1.35 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 89 HIS 0.006 0.001 HIS N 41 PHE 0.020 0.002 PHE K 128 TYR 0.024 0.002 TYR O 434 ARG 0.005 0.000 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 110 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: K 270 GLU cc_start: 0.5733 (mm-30) cc_final: 0.5405 (pt0) REVERT: N 66 MET cc_start: 0.9364 (ttt) cc_final: 0.9149 (ttt) REVERT: N 88 ARG cc_start: 0.8422 (mtm110) cc_final: 0.6922 (mtt180) REVERT: N 160 ASN cc_start: 0.6874 (t0) cc_final: 0.6606 (t0) REVERT: N 207 ILE cc_start: 0.8118 (mt) cc_final: 0.7836 (tp) REVERT: N 239 ASN cc_start: 0.7983 (t0) cc_final: 0.7503 (t0) REVERT: N 365 MET cc_start: 0.7862 (ttt) cc_final: 0.7331 (pmt) REVERT: O 18 ILE cc_start: 0.8416 (pt) cc_final: 0.8083 (pp) REVERT: O 95 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.6999 (p90) REVERT: O 175 ARG cc_start: 0.7704 (ttp-110) cc_final: 0.7336 (ttp-110) REVERT: O 246 ASP cc_start: 0.7781 (m-30) cc_final: 0.7535 (m-30) REVERT: O 281 ASP cc_start: 0.8522 (t0) cc_final: 0.8285 (t70) REVERT: O 341 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7316 (mm-30) outliers start: 47 outliers final: 33 residues processed: 141 average time/residue: 1.0066 time to fit residues: 152.8666 Evaluate side-chains 142 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 304 ASN Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 341 GLU Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 425 LEU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.0010 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 8811 Z= 0.349 Angle : 0.653 9.049 11992 Z= 0.335 Chirality : 0.047 0.219 1329 Planarity : 0.006 0.072 1549 Dihedral : 5.332 36.123 1202 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 5.53 % Allowed : 15.41 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.10 % 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: -0.78 (0.25), residues: 1102 helix: 1.01 (0.46), residues: 145 sheet: 0.15 (0.28), residues: 347 loop : -1.33 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 330 HIS 0.006 0.001 HIS N 41 PHE 0.023 0.002 PHE K 128 TYR 0.021 0.002 TYR O 308 ARG 0.005 0.000 ARG N 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 109 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: K 270 GLU cc_start: 0.5719 (mm-30) cc_final: 0.5427 (pt0) REVERT: N 88 ARG cc_start: 0.8439 (mtm110) cc_final: 0.6925 (mtt180) REVERT: N 160 ASN cc_start: 0.6940 (t0) cc_final: 0.6682 (t0) REVERT: N 207 ILE cc_start: 0.8134 (mt) cc_final: 0.7841 (tp) REVERT: N 239 ASN cc_start: 0.8011 (t0) cc_final: 0.7507 (t0) REVERT: N 365 MET cc_start: 0.7801 (ttt) cc_final: 0.7327 (pmt) REVERT: O 18 ILE cc_start: 0.8430 (pt) cc_final: 0.8092 (pp) REVERT: O 95 PHE cc_start: 0.7842 (OUTLIER) cc_final: 0.7011 (p90) REVERT: O 175 ARG cc_start: 0.7690 (ttp-110) cc_final: 0.7321 (ttp-110) REVERT: O 246 ASP cc_start: 0.7788 (m-30) cc_final: 0.7538 (m-30) REVERT: O 281 ASP cc_start: 0.8755 (t0) cc_final: 0.8438 (t0) outliers start: 52 outliers final: 38 residues processed: 146 average time/residue: 1.0637 time to fit residues: 166.9203 Evaluate side-chains 145 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 106 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 126 LYS Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 166 LYS Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 LEU Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 257 VAL Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain N residue 371 LEU Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 143 VAL Chi-restraints excluded: chain O residue 151 GLU Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 263 THR Chi-restraints excluded: chain O residue 304 ASN Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 348 GLU Chi-restraints excluded: chain O residue 425 LEU Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 0.0870 chunk 82 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 2.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8811 Z= 0.229 Angle : 0.609 9.741 11992 Z= 0.313 Chirality : 0.045 0.197 1329 Planarity : 0.005 0.073 1549 Dihedral : 5.165 36.203 1202 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.83 % Allowed : 17.22 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -0.65 (0.25), residues: 1102 helix: 1.14 (0.47), residues: 145 sheet: 0.22 (0.28), residues: 347 loop : -1.25 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 89 HIS 0.005 0.001 HIS O 386 PHE 0.024 0.001 PHE K 128 TYR 0.023 0.001 TYR O 434 ARG 0.002 0.000 ARG K 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 110 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: K 270 GLU cc_start: 0.5509 (mm-30) cc_final: 0.5188 (pt0) REVERT: N 88 ARG cc_start: 0.8397 (mtm110) cc_final: 0.6911 (mtt180) REVERT: N 120 ARG cc_start: 0.7812 (ttm170) cc_final: 0.7567 (ttm-80) REVERT: N 160 ASN cc_start: 0.6851 (t0) cc_final: 0.6622 (t0) REVERT: N 239 ASN cc_start: 0.7963 (t0) cc_final: 0.7492 (t0) REVERT: N 313 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: N 365 MET cc_start: 0.7731 (ttt) cc_final: 0.7238 (pmt) REVERT: O 18 ILE cc_start: 0.8385 (pt) cc_final: 0.8051 (pp) REVERT: O 24 TYR cc_start: 0.8458 (m-80) cc_final: 0.8159 (m-80) REVERT: O 95 PHE cc_start: 0.7815 (OUTLIER) cc_final: 0.7015 (p90) REVERT: O 175 ARG cc_start: 0.7659 (ttp-110) cc_final: 0.7299 (ttp-110) REVERT: O 246 ASP cc_start: 0.7677 (m-30) cc_final: 0.7425 (m-30) REVERT: O 281 ASP cc_start: 0.8500 (t0) cc_final: 0.8278 (t70) outliers start: 36 outliers final: 28 residues processed: 134 average time/residue: 1.0598 time to fit residues: 153.4929 Evaluate side-chains 137 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 107 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 251 THR Chi-restraints excluded: chain K residue 254 SER Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 368 ILE Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 151 GLU Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 304 ASN Chi-restraints excluded: chain O residue 327 LYS Chi-restraints excluded: chain O residue 426 VAL Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 88 optimal weight: 0.0770 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 overall best weight: 1.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8811 Z= 0.169 Angle : 0.569 8.683 11992 Z= 0.292 Chirality : 0.044 0.171 1329 Planarity : 0.005 0.075 1549 Dihedral : 4.924 36.301 1202 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.29 % Allowed : 18.07 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -0.51 (0.25), residues: 1102 helix: 1.42 (0.48), residues: 139 sheet: 0.28 (0.28), residues: 344 loop : -1.14 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 89 HIS 0.003 0.001 HIS O 386 PHE 0.021 0.001 PHE K 128 TYR 0.019 0.001 TYR O 308 ARG 0.002 0.000 ARG K 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 109 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: K 270 GLU cc_start: 0.5505 (mm-30) cc_final: 0.4952 (pm20) REVERT: N 88 ARG cc_start: 0.8428 (mtm110) cc_final: 0.6971 (mtt180) REVERT: N 120 ARG cc_start: 0.7766 (ttm170) cc_final: 0.7504 (ttm-80) REVERT: N 313 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: N 365 MET cc_start: 0.7594 (ttt) cc_final: 0.7316 (pmt) REVERT: O 18 ILE cc_start: 0.8301 (pt) cc_final: 0.7983 (pp) REVERT: O 24 TYR cc_start: 0.8410 (m-80) cc_final: 0.8064 (m-80) REVERT: O 95 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.6908 (p90) REVERT: O 175 ARG cc_start: 0.7641 (ttp-110) cc_final: 0.7283 (ttp-110) REVERT: O 281 ASP cc_start: 0.8502 (t0) cc_final: 0.8275 (t70) REVERT: O 377 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8627 (mtpt) outliers start: 31 outliers final: 22 residues processed: 129 average time/residue: 1.0330 time to fit residues: 143.4532 Evaluate side-chains 131 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 107 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 77 ILE Chi-restraints excluded: chain N residue 113 GLU Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 313 GLU Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 304 ASN Chi-restraints excluded: chain O residue 433 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 10.0000 chunk 99 optimal weight: 0.0270 chunk 86 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 overall best weight: 2.9444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8811 Z= 0.262 Angle : 0.608 8.844 11992 Z= 0.311 Chirality : 0.046 0.177 1329 Planarity : 0.005 0.073 1549 Dihedral : 5.048 36.849 1202 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.66 % Allowed : 19.66 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.25), residues: 1102 helix: 1.42 (0.48), residues: 139 sheet: 0.28 (0.29), residues: 325 loop : -1.15 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 409 HIS 0.004 0.001 HIS N 41 PHE 0.025 0.001 PHE K 128 TYR 0.023 0.002 TYR O 434 ARG 0.003 0.000 ARG N 298 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 110 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: K 261 LYS cc_start: 0.6686 (mmtt) cc_final: 0.6317 (mttt) REVERT: K 270 GLU cc_start: 0.5524 (mm-30) cc_final: 0.5132 (pm20) REVERT: N 88 ARG cc_start: 0.8386 (mtm110) cc_final: 0.7089 (mtt180) REVERT: N 120 ARG cc_start: 0.7792 (ttm170) cc_final: 0.7519 (ttm-80) REVERT: N 239 ASN cc_start: 0.7966 (t0) cc_final: 0.7457 (t0) REVERT: N 365 MET cc_start: 0.7721 (ttt) cc_final: 0.7301 (pmt) REVERT: O 18 ILE cc_start: 0.8362 (pt) cc_final: 0.8026 (pp) REVERT: O 24 TYR cc_start: 0.8447 (m-80) cc_final: 0.8100 (m-80) REVERT: O 95 PHE cc_start: 0.7820 (OUTLIER) cc_final: 0.7021 (p90) REVERT: O 175 ARG cc_start: 0.7651 (ttp-110) cc_final: 0.7295 (ttp-110) REVERT: O 246 ASP cc_start: 0.7668 (m-30) cc_final: 0.7455 (m-30) REVERT: O 281 ASP cc_start: 0.8501 (t0) cc_final: 0.8271 (t70) REVERT: O 439 GLN cc_start: 0.5888 (OUTLIER) cc_final: 0.5335 (mm110) outliers start: 25 outliers final: 20 residues processed: 127 average time/residue: 1.0758 time to fit residues: 146.8321 Evaluate side-chains 132 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 110 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 143 VAL Chi-restraints excluded: chain K residue 183 ASN Chi-restraints excluded: chain K residue 268 THR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 134 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain N residue 282 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 320 THR Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 63 CYS Chi-restraints excluded: chain O residue 80 VAL Chi-restraints excluded: chain O residue 84 VAL Chi-restraints excluded: chain O residue 95 PHE Chi-restraints excluded: chain O residue 104 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 133 LEU Chi-restraints excluded: chain O residue 167 SER Chi-restraints excluded: chain O residue 304 ASN Chi-restraints excluded: chain O residue 433 MET Chi-restraints excluded: chain O residue 439 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 256 HIS ** 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 = 0.3632 r_free = 0.3632 target = 0.142963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.108996 restraints weight = 10895.500| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.64 r_work: 0.2867 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 8811 Z= 0.371 Angle : 0.932 59.198 11992 Z= 0.520 Chirality : 0.048 0.265 1329 Planarity : 0.005 0.073 1549 Dihedral : 5.059 36.952 1202 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 2.66 % Allowed : 19.77 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.37 % 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: -0.55 (0.25), residues: 1102 helix: 1.38 (0.48), residues: 139 sheet: 0.28 (0.29), residues: 325 loop : -1.15 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 409 HIS 0.005 0.001 HIS N 256 PHE 0.021 0.002 PHE K 128 TYR 0.021 0.002 TYR O 308 ARG 0.005 0.000 ARG N 298 =============================================================================== Job complete usr+sys time: 3483.85 seconds wall clock time: 62 minutes 37.19 seconds (3757.19 seconds total)