Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 21 00:07:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/04_2023/7ffn_31569_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/04_2023/7ffn_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_31569/04_2023/7ffn_31569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/04_2023/7ffn_31569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/04_2023/7ffn_31569_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffn_31569/04_2023/7ffn_31569_neut.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 4.99, per 1000 atoms: 0.58 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: 3.08 Conformation dependent library (CDL) restraints added in 1.2 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: 0.61 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: 2.75 Time building geometry restraints manager: 3.39 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: 1.440 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: 4.480 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.280 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: 0.000 Load rotamer database and sin/cos tables:13.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.720 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 1.022 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 208 average time/residue: 1.1748 time to fit residues: 260.8421 Evaluate side-chains 106 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 105 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.0867 time to fit residues: 2.5540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 33 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** O 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 394 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 439 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2259 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= 0.185 Angle : 0.582 8.669 11992 Z= 0.304 Chirality : 0.044 0.164 1329 Planarity : 0.006 0.087 1549 Dihedral : 5.201 33.969 1202 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 3.40 % 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: -1.72 (0.24), residues: 1102 helix: 0.39 (0.45), residues: 129 sheet: -0.61 (0.27), residues: 347 loop : -1.84 (0.22), residues: 626 *********************** 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 164 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 1.028 Fit side-chains outliers start: 32 outliers final: 12 residues processed: 147 average time/residue: 1.1794 time to fit residues: 185.4166 Evaluate side-chains 115 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 4 residues processed: 8 average time/residue: 0.7297 time to fit residues: 7.8758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 67 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 88 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- 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 96 HIS N 152 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 GLN O 155 ASN O 392 GLN O 394 HIS O 439 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 8811 Z= 0.179 Angle : 0.565 11.379 11992 Z= 0.292 Chirality : 0.044 0.215 1329 Planarity : 0.005 0.078 1549 Dihedral : 4.868 34.073 1202 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 3.51 % 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: -1.23 (0.24), residues: 1102 helix: 0.89 (0.47), residues: 137 sheet: -0.31 (0.27), residues: 355 loop : -1.56 (0.23), residues: 610 *********************** 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 151 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 118 time to evaluate : 1.028 Fit side-chains outliers start: 33 outliers final: 14 residues processed: 139 average time/residue: 1.1297 time to fit residues: 168.4172 Evaluate side-chains 120 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 106 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 8 residues processed: 6 average time/residue: 0.4480 time to fit residues: 4.5193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 20.0000 chunk 51 optimal weight: 7.9990 chunk 10 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 159 GLN N 160 ASN O 386 HIS O 439 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 8811 Z= 0.382 Angle : 0.672 8.677 11992 Z= 0.345 Chirality : 0.048 0.261 1329 Planarity : 0.006 0.077 1549 Dihedral : 5.311 35.531 1202 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 5.21 % 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: -1.10 (0.25), residues: 1102 helix: 0.78 (0.46), residues: 148 sheet: -0.19 (0.28), residues: 348 loop : -1.47 (0.23), residues: 606 *********************** 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 165 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 116 time to evaluate : 1.087 Fit side-chains revert: symmetry clash outliers start: 49 outliers final: 24 residues processed: 148 average time/residue: 1.1317 time to fit residues: 179.7633 Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.099 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 9 average time/residue: 0.5403 time to fit residues: 7.0967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.4980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 8811 Z= 0.215 Angle : 0.603 10.009 11992 Z= 0.309 Chirality : 0.045 0.250 1329 Planarity : 0.005 0.071 1549 Dihedral : 5.089 34.691 1202 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 4.04 % 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: -0.88 (0.25), residues: 1102 helix: 0.96 (0.46), residues: 148 sheet: 0.02 (0.28), residues: 342 loop : -1.36 (0.24), residues: 612 *********************** 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 144 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 106 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 20 residues processed: 134 average time/residue: 1.0187 time to fit residues: 147.4173 Evaluate side-chains 116 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 16 residues processed: 4 average time/residue: 0.3590 time to fit residues: 3.1185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.0070 chunk 20 optimal weight: 20.0000 chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.0060 chunk 101 optimal weight: 4.9990 overall best weight: 1.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 8811 Z= 0.194 Angle : 0.582 9.407 11992 Z= 0.297 Chirality : 0.044 0.197 1329 Planarity : 0.005 0.068 1549 Dihedral : 4.897 33.851 1202 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 4.46 % 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: -0.66 (0.25), residues: 1102 helix: 1.14 (0.47), residues: 145 sheet: 0.19 (0.28), residues: 346 loop : -1.23 (0.24), residues: 611 *********************** 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 149 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 107 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 24 residues processed: 135 average time/residue: 1.0200 time to fit residues: 148.7166 Evaluate side-chains 124 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 0.943 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 5 average time/residue: 0.5636 time to fit residues: 4.5000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 77 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 8811 Z= 0.197 Angle : 0.580 9.032 11992 Z= 0.296 Chirality : 0.044 0.207 1329 Planarity : 0.005 0.068 1549 Dihedral : 4.848 34.174 1202 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 3.51 % 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: -0.58 (0.25), residues: 1102 helix: 1.21 (0.47), residues: 145 sheet: 0.26 (0.28), residues: 346 loop : -1.19 (0.24), residues: 611 *********************** 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 143 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 110 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 24 residues processed: 135 average time/residue: 1.0380 time to fit residues: 151.3637 Evaluate side-chains 125 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 0.993 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 4 average time/residue: 0.3435 time to fit residues: 3.0174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 439 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 8811 Z= 0.238 Angle : 0.609 8.839 11992 Z= 0.310 Chirality : 0.045 0.174 1329 Planarity : 0.005 0.068 1549 Dihedral : 4.955 35.254 1202 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 2.98 % 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: -0.58 (0.25), residues: 1102 helix: 1.21 (0.47), residues: 145 sheet: 0.23 (0.28), residues: 347 loop : -1.18 (0.24), residues: 610 *********************** 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 134 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 106 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 22 residues processed: 128 average time/residue: 1.1176 time to fit residues: 153.8745 Evaluate side-chains 123 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 101 time to evaluate : 1.008 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 2 average time/residue: 0.5708 time to fit residues: 2.6717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 76 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 88 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN ** N 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 130 GLN O 439 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 8811 Z= 0.409 Angle : 0.692 10.196 11992 Z= 0.355 Chirality : 0.049 0.191 1329 Planarity : 0.006 0.068 1549 Dihedral : 5.362 36.096 1202 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.44 % Favored : 93.47 % Rotamer Outliers : 3.08 % 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: -0.69 (0.25), residues: 1102 helix: 1.23 (0.47), residues: 139 sheet: 0.22 (0.28), residues: 342 loop : -1.28 (0.23), residues: 621 *********************** 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 137 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 108 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 23 residues processed: 132 average time/residue: 1.0933 time to fit residues: 155.4319 Evaluate side-chains 127 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 104 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 21 residues processed: 2 average time/residue: 0.5864 time to fit residues: 2.7719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 108 optimal weight: 10.0000 chunk 99 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 197 GLN O 43 ASN O 439 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4487 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= 0.188 Angle : 0.597 9.567 11992 Z= 0.306 Chirality : 0.045 0.178 1329 Planarity : 0.005 0.072 1549 Dihedral : 4.999 36.032 1202 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % 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: -0.50 (0.25), residues: 1102 helix: 1.35 (0.48), residues: 140 sheet: 0.26 (0.28), residues: 357 loop : -1.14 (0.24), residues: 605 ********************** 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 133 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 109 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 131 average time/residue: 1.0615 time to fit residues: 149.9532 Evaluate side-chains 123 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 19 residues processed: 0 time to fit residues: 1.2859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 88 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 62 optimal weight: 7.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.144551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.110109 restraints weight = 10944.084| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.61 r_work: 0.2878 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 8811 Z= 0.285 Angle : 0.636 10.023 11992 Z= 0.326 Chirality : 0.046 0.183 1329 Planarity : 0.005 0.071 1549 Dihedral : 5.061 36.618 1202 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.74 % 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: -0.56 (0.25), residues: 1102 helix: 1.27 (0.47), residues: 140 sheet: 0.31 (0.29), residues: 338 loop : -1.18 (0.24), residues: 624 =============================================================================== Job complete usr+sys time: 3448.77 seconds wall clock time: 61 minutes 51.28 seconds (3711.28 seconds total)