Starting phenix.real_space_refine on Wed Feb 14 01:14:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffo_31570/02_2024/7ffo_31570_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffo_31570/02_2024/7ffo_31570.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffo_31570/02_2024/7ffo_31570.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffo_31570/02_2024/7ffo_31570.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffo_31570/02_2024/7ffo_31570_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ffo_31570/02_2024/7ffo_31570_neut.pdb" } resolution = 3.5 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 60 5.16 5 C 5237 2.51 5 N 1413 2.21 5 O 1545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8255 Number of models: 1 Model: "" Number of chains: 4 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: "N" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3229 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 30, 'TRANS': 381} Chain breaks: 1 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} Time building chain proxies: 4.93, per 1000 atoms: 0.60 Number of scatterers: 8255 At special positions: 0 Unit cell: (76.56, 149.16, 174.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 60 16.00 O 1545 8.00 N 1413 7.00 C 5237 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS L 7 " - pdb=" SG CYS L 16 " 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: 2.94 Conformation dependent library (CDL) restraints added in 1.6 seconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1986 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 30 sheets defined 17.4% alpha, 35.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'K' and resid 113 through 123 removed outlier: 3.801A 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: 3.786A pdb=" N THR L 30 " --> pdb=" O LYS L 26 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU L 31 " --> pdb=" O PRO L 27 " (cutoff:3.500A) removed outlier: 4.189A 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: 4.177A 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 'N' and resid 2 through 5 removed outlier: 3.729A pdb=" N LEU N 5 " --> pdb=" O THR N 2 " (cutoff:3.500A) No H-bonds generated for '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: 3.803A pdb=" N VAL N 355 " --> pdb=" O LEU N 351 " (cutoff:3.500A) removed outlier: 3.826A 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: 3.514A 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: 3.617A 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: 3.504A 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: 3.573A pdb=" N LEU O 286 " --> pdb=" O PRO O 283 " (cutoff:3.500A) removed outlier: 3.570A 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: 3.901A pdb=" N LEU O 413 " --> pdb=" O TRP O 409 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 440 removed outlier: 3.538A pdb=" N LYS O 440 " --> pdb=" O LEU O 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 135 through 139 removed outlier: 5.657A 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: 6.706A 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: 8.493A pdb=" N ALA K 206 " --> pdb=" O PRO K 217 " (cutoff:3.500A) removed outlier: 5.145A 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: 6.158A 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: 3.864A pdb=" N ALA K 239 " --> pdb=" O ILE K 230 " (cutoff:3.500A) removed outlier: 6.158A 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 '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=AA9, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.554A pdb=" N GLN N 48 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL N 36 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG N 46 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 9.536A pdb=" N SER N 50 " --> pdb=" O ASP N 69 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP N 69 " --> pdb=" O SER N 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 33 through 37 removed outlier: 6.554A pdb=" N GLN N 48 " --> pdb=" O GLU N 34 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N VAL N 36 " --> pdb=" O ARG N 46 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG N 46 " --> pdb=" O VAL N 36 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR N 98 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 10.196A pdb=" N SER N 51 " --> pdb=" O HIS N 96 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N HIS N 96 " --> pdb=" O SER N 51 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N TYR N 53 " --> pdb=" O ASP N 94 " (cutoff:3.500A) removed outlier: 10.082A pdb=" N ASP N 94 " --> pdb=" O TYR N 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'N' and resid 83 through 85 Processing sheet with id=AB3, first strand: chain 'N' and resid 147 through 154 Processing sheet with id=AB4, first strand: chain 'N' and resid 237 through 238 Processing sheet with id=AB5, first strand: chain 'N' and resid 173 through 174 removed outlier: 3.715A pdb=" N GLU N 173 " --> pdb=" O ARG N 230 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU N 197 " --> pdb=" O TYR N 229 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 179 through 181 removed outlier: 3.683A pdb=" N VAL N 186 " --> pdb=" O PHE N 217 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 275 through 279 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 307 through 311 Processing sheet with id=AC1, first strand: chain 'O' and resid 2 through 8 Processing sheet with id=AC2, first strand: chain 'O' and resid 15 through 19 removed outlier: 5.370A pdb=" N ILE O 31 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR O 136 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.359A 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: 3.606A pdb=" N THR O 41 " --> pdb=" O THR O 126 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N THR O 126 " --> pdb=" O THR O 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 46 through 48 removed outlier: 3.641A pdb=" N TYR O 46 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Processing sheet with id=AC4, 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=AC5, first strand: chain 'O' and resid 51 through 55 Processing sheet with id=AC6, first strand: chain 'O' and resid 87 through 88 removed outlier: 3.890A pdb=" N GLY O 91 " --> pdb=" O MET O 88 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 203 through 205 Processing sheet with id=AC8, first strand: chain 'O' and resid 220 through 221 Processing sheet with id=AC9, first strand: chain 'O' and resid 260 through 262 Processing sheet with id=AD1, first strand: chain 'O' and resid 296 through 306 removed outlier: 5.013A 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: 6.438A pdb=" N ILE O 315 " --> pdb=" O ASN O 304 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY O 350 " --> pdb=" O TYR O 320 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 326 through 328 Processing sheet with id=AD3, first strand: chain 'O' and resid 364 through 369 306 hydrogen bonds defined for protein. 789 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: 2.67 Time building geometry restraints manager: 3.21 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: 2608 1.34 - 1.46: 2052 1.46 - 1.59: 3729 1.59 - 1.71: 2 1.71 - 1.84: 80 Bond restraints: 8471 Sorted by residual: bond pdb=" CA ASP N 175 " pdb=" C ASP N 175 " ideal model delta sigma weight residual 1.526 1.614 -0.088 1.08e-02 8.57e+03 6.64e+01 bond pdb=" C ASP N 175 " pdb=" O ASP N 175 " ideal model delta sigma weight residual 1.235 1.311 -0.076 1.21e-02 6.83e+03 3.99e+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 2.88e+01 bond pdb=" CA VAL N 179 " pdb=" C VAL N 179 " ideal model delta sigma weight residual 1.525 1.589 -0.064 1.22e-02 6.72e+03 2.74e+01 bond pdb=" N ASP N 175 " pdb=" CA ASP N 175 " ideal model delta sigma weight residual 1.464 1.507 -0.043 1.25e-02 6.40e+03 1.18e+01 ... (remaining 8466 not shown) Histogram of bond angle deviations from ideal: 96.94 - 104.41: 192 104.41 - 111.87: 4061 111.87 - 119.34: 2829 119.34 - 126.81: 4304 126.81 - 134.27: 147 Bond angle restraints: 11533 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 107.44 123.30 -15.86 1.93e+00 2.68e-01 6.75e+01 angle pdb=" CA VAL N 179 " pdb=" C VAL N 179 " pdb=" N SER N 180 " ideal model delta sigma weight residual 115.77 123.03 -7.26 1.25e+00 6.40e-01 3.37e+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 122.47 129.62 -7.15 1.50e+00 4.44e-01 2.27e+01 angle pdb=" C CYS N 22 " pdb=" N ALA N 23 " pdb=" CA ALA N 23 " ideal model delta sigma weight residual 121.54 130.31 -8.77 1.91e+00 2.74e-01 2.11e+01 ... (remaining 11528 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 4899 17.61 - 35.22: 158 35.22 - 52.83: 29 52.83 - 70.44: 4 70.44 - 88.05: 5 Dihedral angle restraints: 5095 sinusoidal: 1995 harmonic: 3100 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 93.00 173.62 -80.62 1 1.00e+01 1.00e-02 8.03e+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 -135.76 -44.24 0 5.00e+00 4.00e-02 7.83e+01 dihedral pdb=" CA ASN O 264 " pdb=" C ASN O 264 " pdb=" N PRO O 265 " pdb=" CA PRO O 265 " ideal model delta harmonic sigma weight residual 180.00 137.36 42.64 0 5.00e+00 4.00e-02 7.27e+01 ... (remaining 5092 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1062 0.072 - 0.145: 199 0.145 - 0.217: 22 0.217 - 0.289: 1 0.289 - 0.362: 1 Chirality restraints: 1285 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 3.27e+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 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL O 80 " pdb=" CA VAL O 80 " pdb=" CG1 VAL O 80 " pdb=" CG2 VAL O 80 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.87e-01 ... (remaining 1282 not shown) Planarity restraints: 1483 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 7.80e+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 6.92e-02 7.65e+00 pdb=" N PRO N 89 " -0.120 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 1480 not shown) Histogram of nonbonded interaction distances: 1.29 - 2.01: 1 2.01 - 2.74: 608 2.74 - 3.46: 10400 3.46 - 4.18: 18567 4.18 - 4.90: 32583 Nonbonded interactions: 62159 Sorted by model distance: nonbonded pdb=" CE MET K 257 " pdb=" ND2 ASN O 442 " model vdw 1.293 3.540 nonbonded pdb=" CE MET K 257 " pdb=" CG ASN O 442 " model vdw 2.065 3.690 nonbonded pdb=" NZ LYS K 146 " pdb=" O ARG N 401 " model vdw 2.211 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 2.279 2.440 ... (remaining 62154 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 group one per residue 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: 0.820 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: 0.110 Set scattering table: 0.080 Process input model: 25.190 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 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 8471 Z= 0.507 Angle : 0.945 15.856 11533 Z= 0.516 Chirality : 0.057 0.362 1285 Planarity : 0.008 0.099 1483 Dihedral : 9.499 88.052 3070 Min Nonbonded Distance : 1.293 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.62 % Favored : 93.28 % Rotamer: Outliers : 0.33 % Allowed : 2.66 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % Twisted General : 0.20 % 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: -2.95 (0.22), residues: 1057 helix: -1.88 (0.34), residues: 134 sheet: -1.26 (0.26), residues: 340 loop : -2.46 (0.21), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 202 HIS 0.010 0.002 HIS N 28 PHE 0.023 0.003 PHE N 328 TYR 0.031 0.003 TYR O 122 ARG 0.009 0.001 ARG N 230 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 228 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 166 LYS cc_start: 0.5536 (tttt) cc_final: 0.5251 (ptmt) REVERT: K 231 LEU cc_start: 0.5389 (mt) cc_final: 0.5151 (mt) REVERT: K 238 VAL cc_start: 0.4926 (m) cc_final: 0.4245 (p) REVERT: N 152 GLN cc_start: 0.7738 (mt0) cc_final: 0.7409 (mt0) REVERT: N 365 MET cc_start: 0.7162 (ttt) cc_final: 0.6920 (pmm) REVERT: O 88 MET cc_start: 0.8872 (mmm) cc_final: 0.8396 (mmm) REVERT: O 143 VAL cc_start: 0.9188 (t) cc_final: 0.8892 (m) REVERT: O 147 TYR cc_start: 0.8366 (m-10) cc_final: 0.8093 (m-80) REVERT: O 266 ILE cc_start: 0.9007 (mt) cc_final: 0.8721 (mp) outliers start: 3 outliers final: 0 residues processed: 228 average time/residue: 0.2395 time to fit residues: 70.5899 Evaluate side-chains 124 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 54 optimal weight: 9.9990 chunk 42 optimal weight: 20.0000 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 156 HIS N 160 ASN N 353 HIS N 358 HIS O 264 ASN O 360 ASN O 394 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8471 Z= 0.245 Angle : 0.623 8.665 11533 Z= 0.325 Chirality : 0.046 0.162 1285 Planarity : 0.006 0.087 1483 Dihedral : 5.362 33.491 1156 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.22 % Allowed : 9.76 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.85 (0.24), residues: 1057 helix: 0.07 (0.44), residues: 138 sheet: -0.65 (0.27), residues: 332 loop : -1.95 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 202 HIS 0.010 0.001 HIS N 156 PHE 0.012 0.002 PHE N 328 TYR 0.019 0.002 TYR O 308 ARG 0.006 0.001 ARG K 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: K 166 LYS cc_start: 0.5781 (tttt) cc_final: 0.5548 (ptmt) REVERT: N 324 LYS cc_start: 0.8242 (mtmt) cc_final: 0.7944 (mtpp) REVERT: O 85 TYR cc_start: 0.8526 (t80) cc_final: 0.8313 (t80) REVERT: O 143 VAL cc_start: 0.9187 (t) cc_final: 0.8967 (m) REVERT: O 144 THR cc_start: 0.8967 (m) cc_final: 0.8678 (p) REVERT: O 266 ILE cc_start: 0.9110 (mt) cc_final: 0.8868 (mp) REVERT: O 377 LYS cc_start: 0.8487 (mtpt) cc_final: 0.7944 (mtpt) REVERT: O 421 ILE cc_start: 0.8621 (tp) cc_final: 0.8321 (mt) outliers start: 20 outliers final: 13 residues processed: 157 average time/residue: 0.1848 time to fit residues: 40.8862 Evaluate side-chains 138 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 160 ASP Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 110 ILE Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 348 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 85 optimal weight: 0.0170 chunk 95 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 overall best weight: 2.8024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8471 Z= 0.253 Angle : 0.602 8.242 11533 Z= 0.311 Chirality : 0.045 0.161 1285 Planarity : 0.005 0.080 1483 Dihedral : 5.136 35.576 1156 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.10 % Allowed : 11.64 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.31 (0.25), residues: 1057 helix: 0.86 (0.46), residues: 144 sheet: -0.61 (0.27), residues: 338 loop : -1.51 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 330 HIS 0.005 0.001 HIS N 168 PHE 0.019 0.002 PHE L 14 TYR 0.022 0.001 TYR O 308 ARG 0.009 0.001 ARG K 115 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 166 LYS cc_start: 0.5916 (tttt) cc_final: 0.5699 (ptmt) REVERT: K 225 ASP cc_start: 0.5543 (m-30) cc_final: 0.5251 (t0) REVERT: L 30 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8070 (m) REVERT: N 231 LEU cc_start: 0.7732 (mt) cc_final: 0.7476 (mt) REVERT: N 256 HIS cc_start: 0.6810 (p-80) cc_final: 0.6526 (p-80) REVERT: N 324 LYS cc_start: 0.8731 (mtmt) cc_final: 0.8338 (mtpp) REVERT: O 143 VAL cc_start: 0.9266 (t) cc_final: 0.8988 (m) REVERT: O 144 THR cc_start: 0.8958 (m) cc_final: 0.8624 (p) REVERT: O 266 ILE cc_start: 0.9109 (mt) cc_final: 0.8844 (mp) outliers start: 28 outliers final: 19 residues processed: 156 average time/residue: 0.2071 time to fit residues: 44.5514 Evaluate side-chains 139 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 119 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 153 VAL Chi-restraints excluded: chain K residue 188 THR Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 179 VAL Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 385 SER Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 102 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 0.0670 overall best weight: 0.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 140 HIS O 396 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8471 Z= 0.132 Angle : 0.555 7.847 11533 Z= 0.283 Chirality : 0.044 0.184 1285 Planarity : 0.005 0.077 1483 Dihedral : 4.796 34.494 1156 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.33 % Allowed : 12.97 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.96 (0.25), residues: 1057 helix: 1.32 (0.47), residues: 144 sheet: -0.36 (0.28), residues: 344 loop : -1.34 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 326 HIS 0.002 0.000 HIS N 308 PHE 0.010 0.001 PHE O 365 TYR 0.017 0.001 TYR O 308 ARG 0.006 0.000 ARG N 227 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 225 ASP cc_start: 0.5452 (m-30) cc_final: 0.5139 (t0) REVERT: N 7 ASN cc_start: 0.4437 (OUTLIER) cc_final: 0.4148 (t0) REVERT: N 256 HIS cc_start: 0.6703 (p-80) cc_final: 0.6489 (p-80) REVERT: N 324 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8400 (mtpp) REVERT: N 342 GLU cc_start: 0.7460 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: N 391 ARG cc_start: 0.8238 (mtp180) cc_final: 0.8019 (mtm180) REVERT: O 143 VAL cc_start: 0.9234 (t) cc_final: 0.8955 (m) REVERT: O 144 THR cc_start: 0.8899 (m) cc_final: 0.8656 (p) REVERT: O 266 ILE cc_start: 0.9060 (mt) cc_final: 0.8806 (mp) outliers start: 21 outliers final: 16 residues processed: 134 average time/residue: 0.1905 time to fit residues: 35.6837 Evaluate side-chains 127 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 198 VAL Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 342 GLU Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 70 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 34 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 7 ASN N 52 GLN O 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 8471 Z= 0.122 Angle : 0.564 12.689 11533 Z= 0.286 Chirality : 0.043 0.186 1285 Planarity : 0.005 0.087 1483 Dihedral : 4.707 33.953 1156 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.66 % Allowed : 13.53 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.78 (0.26), residues: 1057 helix: 1.61 (0.47), residues: 143 sheet: -0.24 (0.28), residues: 338 loop : -1.26 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 326 HIS 0.002 0.000 HIS K 152 PHE 0.009 0.001 PHE O 365 TYR 0.016 0.001 TYR O 308 ARG 0.004 0.000 ARG O 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 225 ASP cc_start: 0.5443 (m-30) cc_final: 0.5120 (t0) REVERT: N 161 ARG cc_start: 0.6949 (mpt-90) cc_final: 0.6744 (mmt90) REVERT: N 256 HIS cc_start: 0.6627 (p-80) cc_final: 0.6411 (p-80) REVERT: N 324 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8465 (mtpp) REVERT: O 88 MET cc_start: 0.8720 (mmm) cc_final: 0.8264 (mtp) REVERT: O 143 VAL cc_start: 0.9232 (t) cc_final: 0.8938 (m) REVERT: O 144 THR cc_start: 0.8864 (m) cc_final: 0.8622 (p) REVERT: O 266 ILE cc_start: 0.9034 (mt) cc_final: 0.8772 (mp) outliers start: 24 outliers final: 20 residues processed: 137 average time/residue: 0.1923 time to fit residues: 38.1323 Evaluate side-chains 132 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 141 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 108 ASP Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 0.0980 chunk 20 optimal weight: 20.0000 chunk 60 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 8471 Z= 0.155 Angle : 0.548 7.919 11533 Z= 0.279 Chirality : 0.044 0.191 1285 Planarity : 0.005 0.088 1483 Dihedral : 4.649 37.006 1156 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.22 % Allowed : 12.86 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.60 (0.26), residues: 1057 helix: 1.74 (0.47), residues: 143 sheet: -0.09 (0.28), residues: 341 loop : -1.16 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 407 HIS 0.002 0.001 HIS N 41 PHE 0.010 0.001 PHE N 328 TYR 0.018 0.001 TYR O 308 ARG 0.005 0.000 ARG O 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 225 ASP cc_start: 0.5054 (m-30) cc_final: 0.4722 (t0) REVERT: N 94 ASP cc_start: 0.7018 (OUTLIER) cc_final: 0.6749 (m-30) REVERT: N 256 HIS cc_start: 0.6618 (p-80) cc_final: 0.6288 (p-80) REVERT: N 324 LYS cc_start: 0.8885 (mtmt) cc_final: 0.8469 (mtpp) REVERT: O 88 MET cc_start: 0.8720 (mmm) cc_final: 0.8353 (mtp) REVERT: O 266 ILE cc_start: 0.9036 (mt) cc_final: 0.8770 (mp) outliers start: 29 outliers final: 23 residues processed: 132 average time/residue: 0.1699 time to fit residues: 32.3078 Evaluate side-chains 136 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 141 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 94 ASP Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 167 MET Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 205 THR Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain N residue 398 THR Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 370 CYS Chi-restraints excluded: chain O residue 397 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 86 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 47 optimal weight: 0.0020 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 0.2980 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8471 Z= 0.125 Angle : 0.525 7.958 11533 Z= 0.267 Chirality : 0.043 0.187 1285 Planarity : 0.005 0.086 1483 Dihedral : 4.494 38.208 1156 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.88 % Allowed : 13.53 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.52 (0.26), residues: 1057 helix: 1.78 (0.47), residues: 144 sheet: 0.02 (0.28), residues: 341 loop : -1.15 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP O 407 HIS 0.001 0.000 HIS N 308 PHE 0.008 0.001 PHE O 365 TYR 0.020 0.001 TYR K 177 ARG 0.005 0.000 ARG N 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 173 TYR cc_start: 0.4613 (m-80) cc_final: 0.4219 (m-80) REVERT: K 225 ASP cc_start: 0.5186 (m-30) cc_final: 0.4881 (t0) REVERT: N 108 ASP cc_start: 0.8007 (p0) cc_final: 0.7673 (p0) REVERT: N 256 HIS cc_start: 0.6547 (p-80) cc_final: 0.6313 (p-80) REVERT: N 324 LYS cc_start: 0.8926 (mtmt) cc_final: 0.8493 (mtpp) REVERT: O 88 MET cc_start: 0.8754 (mmm) cc_final: 0.8407 (mtp) REVERT: O 305 GLU cc_start: 0.7799 (tt0) cc_final: 0.7486 (tt0) outliers start: 26 outliers final: 20 residues processed: 137 average time/residue: 0.1671 time to fit residues: 33.4104 Evaluate side-chains 129 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 109 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 141 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 245 VAL Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 370 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 0.4980 overall best weight: 3.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8471 Z= 0.275 Angle : 0.605 11.687 11533 Z= 0.308 Chirality : 0.046 0.175 1285 Planarity : 0.005 0.095 1483 Dihedral : 4.809 35.405 1156 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.77 % Allowed : 14.19 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -0.61 (0.26), residues: 1057 helix: 1.66 (0.48), residues: 144 sheet: -0.05 (0.29), residues: 342 loop : -1.19 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 330 HIS 0.005 0.001 HIS O 362 PHE 0.013 0.001 PHE N 328 TYR 0.024 0.002 TYR O 308 ARG 0.005 0.001 ARG N 362 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 225 ASP cc_start: 0.4854 (m-30) cc_final: 0.4424 (t0) REVERT: N 256 HIS cc_start: 0.6905 (p-80) cc_final: 0.6614 (p-80) REVERT: N 324 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8516 (mtpp) REVERT: O 55 MET cc_start: 0.8162 (mtm) cc_final: 0.7958 (mtm) outliers start: 25 outliers final: 21 residues processed: 132 average time/residue: 0.1590 time to fit residues: 30.9844 Evaluate side-chains 126 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 141 CYS Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain K residue 265 VAL Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 174 ASP Chi-restraints excluded: chain O residue 208 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 370 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 74 optimal weight: 0.0050 chunk 29 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 90 optimal weight: 0.0070 chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 overall best weight: 0.5612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8471 Z= 0.123 Angle : 0.537 11.217 11533 Z= 0.273 Chirality : 0.043 0.218 1285 Planarity : 0.005 0.084 1483 Dihedral : 4.552 36.372 1156 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.00 % Allowed : 15.52 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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 (0.26), residues: 1057 helix: 1.88 (0.48), residues: 142 sheet: 0.01 (0.29), residues: 335 loop : -1.12 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 326 HIS 0.001 0.000 HIS N 305 PHE 0.009 0.001 PHE K 189 TYR 0.022 0.001 TYR K 177 ARG 0.003 0.000 ARG N 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 225 ASP cc_start: 0.4884 (m-30) cc_final: 0.4467 (t0) REVERT: N 239 ASN cc_start: 0.8436 (t0) cc_final: 0.7849 (t0) REVERT: N 256 HIS cc_start: 0.6608 (p-80) cc_final: 0.6349 (p-80) REVERT: N 324 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8516 (mtpp) REVERT: N 354 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6869 (mt-10) REVERT: O 305 GLU cc_start: 0.7669 (tt0) cc_final: 0.7353 (tt0) outliers start: 18 outliers final: 17 residues processed: 123 average time/residue: 0.1598 time to fit residues: 29.4468 Evaluate side-chains 122 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 144 GLU Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 370 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 8 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8471 Z= 0.210 Angle : 0.573 11.079 11533 Z= 0.291 Chirality : 0.044 0.198 1285 Planarity : 0.005 0.091 1483 Dihedral : 4.637 35.452 1156 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.11 % Allowed : 15.63 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.26), residues: 1057 helix: 1.90 (0.48), residues: 142 sheet: 0.02 (0.29), residues: 344 loop : -1.21 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 330 HIS 0.003 0.001 HIS O 362 PHE 0.011 0.001 PHE N 328 TYR 0.025 0.001 TYR K 177 ARG 0.003 0.000 ARG N 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 223 LYS cc_start: 0.6514 (tttt) cc_final: 0.6305 (ttpp) REVERT: K 225 ASP cc_start: 0.4856 (m-30) cc_final: 0.4470 (t0) REVERT: N 239 ASN cc_start: 0.8442 (t0) cc_final: 0.7866 (t0) REVERT: N 256 HIS cc_start: 0.6722 (p-80) cc_final: 0.6455 (p-80) REVERT: N 324 LYS cc_start: 0.8962 (mtmt) cc_final: 0.8546 (mtpp) REVERT: O 88 MET cc_start: 0.8174 (mtp) cc_final: 0.7880 (mtt) REVERT: O 305 GLU cc_start: 0.7690 (tt0) cc_final: 0.7390 (tt0) outliers start: 19 outliers final: 17 residues processed: 127 average time/residue: 0.1642 time to fit residues: 30.7782 Evaluate side-chains 124 residues out of total 902 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 107 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 137 ASN Chi-restraints excluded: chain K residue 142 VAL Chi-restraints excluded: chain N residue 6 PHE Chi-restraints excluded: chain N residue 29 SER Chi-restraints excluded: chain N residue 36 VAL Chi-restraints excluded: chain N residue 119 VAL Chi-restraints excluded: chain N residue 180 SER Chi-restraints excluded: chain N residue 231 LEU Chi-restraints excluded: chain N residue 291 ASN Chi-restraints excluded: chain O residue 30 SER Chi-restraints excluded: chain O residue 42 VAL Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 137 VAL Chi-restraints excluded: chain O residue 213 LEU Chi-restraints excluded: chain O residue 219 LEU Chi-restraints excluded: chain O residue 346 LEU Chi-restraints excluded: chain O residue 370 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 9.9990 chunk 77 optimal weight: 0.0060 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 84 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 chunk 86 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 4 optimal weight: 40.0000 overall best weight: 2.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.137923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.109120 restraints weight = 11471.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.107775 restraints weight = 19293.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.108874 restraints weight = 19011.284| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8471 Z= 0.188 Angle : 0.562 10.924 11533 Z= 0.285 Chirality : 0.044 0.202 1285 Planarity : 0.005 0.089 1483 Dihedral : 4.622 35.587 1156 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.33 % Allowed : 15.52 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.86 % 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 (0.26), residues: 1057 helix: 1.61 (0.47), residues: 149 sheet: 0.12 (0.29), residues: 338 loop : -1.17 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP N 330 HIS 0.003 0.001 HIS N 305 PHE 0.010 0.001 PHE K 189 TYR 0.022 0.001 TYR K 177 ARG 0.004 0.000 ARG K 117 =============================================================================== Job complete usr+sys time: 1832.65 seconds wall clock time: 34 minutes 5.57 seconds (2045.57 seconds total)