Starting phenix.real_space_refine on Sun Apr 7 04:00:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwp_10634/04_2024/6xwp_10634.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwp_10634/04_2024/6xwp_10634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwp_10634/04_2024/6xwp_10634.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwp_10634/04_2024/6xwp_10634.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwp_10634/04_2024/6xwp_10634.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xwp_10634/04_2024/6xwp_10634.pdb" } resolution = 3.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 48 5.16 5 C 6299 2.51 5 N 1544 2.21 5 O 1661 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 8": "NH1" <-> "NH2" Residue "A ARG 79": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 173": "NH1" <-> "NH2" Residue "A ARG 187": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 278": "NH1" <-> "NH2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 376": "OD1" <-> "OD2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 265": "NH1" <-> "NH2" Residue "B ASP 394": "OD1" <-> "OD2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ASP 409": "OD1" <-> "OD2" Residue "C ASP 11": "OD1" <-> "OD2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C ARG 401": "NH1" <-> "NH2" Residue "C ASP 501": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9552 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "B" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "C" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.56 Number of scatterers: 9552 At special positions: 0 Unit cell: (79.948, 102.212, 107.272, 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 48 16.00 O 1661 8.00 N 1544 7.00 C 6299 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.74 Conformation dependent library (CDL) restraints added in 2.0 seconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 0 sheets defined 81.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 13 through 35 removed outlier: 3.723A pdb=" N TRP A 20 " --> pdb=" O TRP A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 44 Processing helix chain 'A' and resid 46 through 74 removed outlier: 3.746A pdb=" N VAL A 53 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N MET A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix removed outlier: 3.802A pdb=" N SER A 67 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 110 Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 153 through 171 removed outlier: 4.009A pdb=" N PHE A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 222 Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 226 through 256 removed outlier: 3.765A pdb=" N LEU A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 3.928A pdb=" N LYS A 266 " --> pdb=" O LYS A 262 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ASP A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 298 through 313 removed outlier: 3.535A pdb=" N PHE A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N PHE A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 306 " --> pdb=" O PHE A 302 " (cutoff:3.500A) Proline residue: A 307 - end of helix removed outlier: 3.980A pdb=" N THR A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 removed outlier: 3.691A pdb=" N LEU A 326 " --> pdb=" O GLY A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 4.152A pdb=" N VAL A 343 " --> pdb=" O GLY A 339 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 removed outlier: 3.672A pdb=" N ILE A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 419 removed outlier: 3.703A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N MET A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N MET A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 13 through 35 removed outlier: 3.758A pdb=" N VAL B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.761A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 74 removed outlier: 3.736A pdb=" N SER B 67 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU B 68 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 69 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL B 70 " --> pdb=" O ALA B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 109 removed outlier: 3.569A pdb=" N TYR B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 139 Processing helix chain 'B' and resid 143 through 151 removed outlier: 3.658A pdb=" N GLY B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 171 removed outlier: 3.839A pdb=" N VAL B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 211 removed outlier: 3.946A pdb=" N GLN B 205 " --> pdb=" O GLY B 201 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 211 through 223 Processing helix chain 'B' and resid 228 through 255 removed outlier: 4.297A pdb=" N TYR B 249 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 3.892A pdb=" N ARG B 265 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ASP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE B 272 " --> pdb=" O LYS B 268 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N THR B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 291 Processing helix chain 'B' and resid 301 through 313 Proline residue: B 307 - end of helix removed outlier: 4.665A pdb=" N THR B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 331 removed outlier: 3.742A pdb=" N LEU B 326 " --> pdb=" O GLY B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 353 removed outlier: 4.087A pdb=" N VAL B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 removed outlier: 4.327A pdb=" N ILE B 364 " --> pdb=" O GLY B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 389 removed outlier: 3.815A pdb=" N MET B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 420 removed outlier: 4.764A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 413 " --> pdb=" O ASP B 409 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'C' and resid 6 through 10 Processing helix chain 'C' and resid 17 through 36 Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 59 removed outlier: 3.912A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.530A pdb=" N ILE C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 110 Processing helix chain 'C' and resid 131 through 139 Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 152 through 171 removed outlier: 3.838A pdb=" N VAL C 156 " --> pdb=" O GLU C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 222 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 229 through 248 removed outlier: 3.785A pdb=" N VAL C 233 " --> pdb=" O PRO C 229 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 removed outlier: 4.302A pdb=" N LYS C 254 " --> pdb=" O PHE C 250 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 272 removed outlier: 5.455A pdb=" N ASP C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ALA C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 282 removed outlier: 3.503A pdb=" N GLY C 282 " --> pdb=" O SER C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 279 through 282' Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 298 through 309 removed outlier: 5.331A pdb=" N PHE C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU C 306 " --> pdb=" O PHE C 302 " (cutoff:3.500A) Proline residue: C 307 - end of helix Processing helix chain 'C' and resid 314 through 333 Processing helix chain 'C' and resid 337 through 354 removed outlier: 3.723A pdb=" N LEU C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 343 " --> pdb=" O GLY C 339 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY C 354 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 373 removed outlier: 3.887A pdb=" N VAL C 369 " --> pdb=" O MET C 365 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER C 372 " --> pdb=" O MET C 368 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL C 373 " --> pdb=" O VAL C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 420 removed outlier: 4.045A pdb=" N MET C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ILE C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2088 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: 2.82 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2967 1.34 - 1.46: 1676 1.46 - 1.57: 4988 1.57 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 9727 Sorted by residual: bond pdb=" C SER A 76 " pdb=" N PRO A 77 " ideal model delta sigma weight residual 1.337 1.316 0.021 1.11e-02 8.12e+03 3.45e+00 bond pdb=" CB THR A 168 " pdb=" CG2 THR A 168 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.11e+00 bond pdb=" CB ILE A 162 " pdb=" CG2 ILE A 162 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB MET A 368 " pdb=" CG MET A 368 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.85e+00 bond pdb=" CB ILE B 162 " pdb=" CG2 ILE B 162 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.82e+00 ... (remaining 9722 not shown) Histogram of bond angle deviations from ideal: 96.62 - 104.12: 171 104.12 - 111.62: 4747 111.62 - 119.12: 3296 119.12 - 126.62: 4930 126.62 - 134.12: 94 Bond angle restraints: 13238 Sorted by residual: angle pdb=" N ILE A 396 " pdb=" CA ILE A 396 " pdb=" C ILE A 396 " ideal model delta sigma weight residual 112.96 107.98 4.98 1.00e+00 1.00e+00 2.48e+01 angle pdb=" N VAL C 373 " pdb=" CA VAL C 373 " pdb=" C VAL C 373 " ideal model delta sigma weight residual 111.91 107.51 4.40 8.90e-01 1.26e+00 2.44e+01 angle pdb=" C ILE A 301 " pdb=" N PHE A 302 " pdb=" CA PHE A 302 " ideal model delta sigma weight residual 122.38 114.84 7.54 1.81e+00 3.05e-01 1.74e+01 angle pdb=" N VAL B 64 " pdb=" CA VAL B 64 " pdb=" C VAL B 64 " ideal model delta sigma weight residual 113.39 108.10 5.29 1.47e+00 4.63e-01 1.29e+01 angle pdb=" N ALA C 207 " pdb=" CA ALA C 207 " pdb=" C ALA C 207 " ideal model delta sigma weight residual 109.81 116.51 -6.70 2.21e+00 2.05e-01 9.19e+00 ... (remaining 13233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 5184 17.15 - 34.29: 457 34.29 - 51.44: 85 51.44 - 68.59: 6 68.59 - 85.73: 2 Dihedral angle restraints: 5734 sinusoidal: 2127 harmonic: 3607 Sorted by residual: dihedral pdb=" CA PRO B 129 " pdb=" C PRO B 129 " pdb=" N PRO B 130 " pdb=" CA PRO B 130 " ideal model delta harmonic sigma weight residual -180.00 -156.66 -23.34 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA SER C 76 " pdb=" C SER C 76 " pdb=" N PRO C 77 " pdb=" CA PRO C 77 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA TRP C 16 " pdb=" C TRP C 16 " pdb=" N LYS C 17 " pdb=" CA LYS C 17 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5731 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 906 0.032 - 0.065: 531 0.065 - 0.097: 154 0.097 - 0.130: 52 0.130 - 0.162: 6 Chirality restraints: 1649 Sorted by residual: chirality pdb=" CA ILE A 75 " pdb=" N ILE A 75 " pdb=" C ILE A 75 " pdb=" CB ILE A 75 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.57e-01 chirality pdb=" CA ILE B 75 " pdb=" N ILE B 75 " pdb=" C ILE B 75 " pdb=" CB ILE B 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA PRO C 47 " pdb=" N PRO C 47 " pdb=" C PRO C 47 " pdb=" CB PRO C 47 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 1646 not shown) Planarity restraints: 1627 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 129 " 0.053 5.00e-02 4.00e+02 7.95e-02 1.01e+01 pdb=" N PRO B 130 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO B 130 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 130 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 228 " -0.036 5.00e-02 4.00e+02 5.47e-02 4.78e+00 pdb=" N PRO A 229 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 207 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO C 208 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.029 5.00e-02 4.00e+02 ... (remaining 1624 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 120 2.67 - 3.22: 10212 3.22 - 3.78: 15450 3.78 - 4.34: 20598 4.34 - 4.90: 34303 Nonbonded interactions: 80683 Sorted by model distance: nonbonded pdb=" OH TYR B 9 " pdb=" O GLN B 205 " model vdw 2.107 2.440 nonbonded pdb=" OD1 ASP C 424 " pdb=" OG SER C 426 " model vdw 2.163 2.440 nonbonded pdb=" NZ LYS B 17 " pdb=" OE1 GLN B 205 " model vdw 2.174 2.520 nonbonded pdb=" O ALA C 363 " pdb=" OH TYR C 387 " model vdw 2.195 2.440 nonbonded pdb=" OH TYR B 249 " pdb=" OD2 ASP B 315 " model vdw 2.204 2.440 ... (remaining 80678 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 5 through 430) selection = (chain 'C' and resid 5 through 430) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 4.140 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.560 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 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 0.058 9727 Z= 0.488 Angle : 0.716 7.542 13238 Z= 0.386 Chirality : 0.044 0.162 1649 Planarity : 0.006 0.079 1627 Dihedral : 12.987 85.734 3444 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.20), residues: 1272 helix: -1.65 (0.14), residues: 1003 sheet: None (None), residues: 0 loop : -3.00 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 16 HIS 0.003 0.001 HIS B 334 PHE 0.021 0.002 PHE B 302 TYR 0.014 0.002 TYR B 238 ARG 0.003 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.065 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8566 (tp) cc_final: 0.8325 (tt) REVERT: A 134 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8214 (tp40) REVERT: A 150 LYS cc_start: 0.8826 (mtmt) cc_final: 0.8499 (mttm) REVERT: A 244 GLN cc_start: 0.8944 (tp40) cc_final: 0.8356 (tp40) REVERT: A 341 GLN cc_start: 0.8969 (mt0) cc_final: 0.8765 (mt0) REVERT: A 368 MET cc_start: 0.8243 (ttp) cc_final: 0.7909 (ttm) REVERT: B 205 GLN cc_start: 0.8818 (mm-40) cc_final: 0.8153 (mm-40) REVERT: C 100 PHE cc_start: 0.8042 (t80) cc_final: 0.7110 (m-10) REVERT: C 219 MET cc_start: 0.8292 (mmm) cc_final: 0.7828 (mmm) REVERT: C 371 GLN cc_start: 0.7905 (mm110) cc_final: 0.7683 (mm-40) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2064 time to fit residues: 54.3151 Evaluate side-chains 149 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 32 optimal weight: 0.6980 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 0.0070 chunk 38 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 114 ASN B 128 GLN B 321 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 ASN C 371 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9727 Z= 0.180 Angle : 0.571 6.465 13238 Z= 0.293 Chirality : 0.039 0.137 1649 Planarity : 0.006 0.074 1627 Dihedral : 4.934 79.557 1364 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.79 % Allowed : 12.45 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.23), residues: 1272 helix: -0.17 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -2.17 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 20 HIS 0.002 0.001 HIS A 334 PHE 0.025 0.001 PHE B 242 TYR 0.013 0.001 TYR B 320 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 178 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 132 LEU cc_start: 0.8446 (tp) cc_final: 0.8245 (tt) REVERT: A 150 LYS cc_start: 0.8765 (mtmt) cc_final: 0.8493 (mttm) REVERT: A 219 MET cc_start: 0.8201 (mmm) cc_final: 0.7947 (mmm) REVERT: A 244 GLN cc_start: 0.8644 (tp40) cc_final: 0.8168 (tp40) REVERT: A 295 MET cc_start: 0.8118 (mpp) cc_final: 0.7581 (mpp) REVERT: A 368 MET cc_start: 0.8116 (ttp) cc_final: 0.7833 (ttm) REVERT: A 422 GLU cc_start: 0.7730 (mp0) cc_final: 0.6933 (mt-10) REVERT: B 8 ARG cc_start: 0.6422 (ppt170) cc_final: 0.6088 (ppt170) REVERT: B 100 PHE cc_start: 0.8320 (t80) cc_final: 0.7942 (t80) REVERT: B 196 MET cc_start: 0.9111 (mmt) cc_final: 0.8854 (mmt) REVERT: B 238 TYR cc_start: 0.8010 (m-80) cc_final: 0.7329 (m-80) REVERT: B 396 ILE cc_start: 0.7741 (mt) cc_final: 0.7271 (mm) REVERT: C 59 LEU cc_start: 0.8533 (mt) cc_final: 0.8212 (mt) REVERT: C 100 PHE cc_start: 0.7955 (t80) cc_final: 0.7056 (m-10) REVERT: C 196 MET cc_start: 0.8678 (mmt) cc_final: 0.8344 (mmt) REVERT: C 204 MET cc_start: 0.7908 (mmt) cc_final: 0.7669 (mmt) REVERT: C 219 MET cc_start: 0.8137 (mmm) cc_final: 0.7671 (mmp) REVERT: C 221 GLU cc_start: 0.7406 (tp30) cc_final: 0.7131 (tp30) REVERT: C 244 GLN cc_start: 0.8113 (tm-30) cc_final: 0.7831 (tm-30) REVERT: C 371 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7633 (mm-40) REVERT: C 403 MET cc_start: 0.8077 (tmm) cc_final: 0.7840 (tmm) outliers start: 18 outliers final: 8 residues processed: 187 average time/residue: 0.2066 time to fit residues: 54.9806 Evaluate side-chains 175 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.7980 chunk 35 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 0.2980 chunk 123 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 205 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9727 Z= 0.193 Angle : 0.565 7.476 13238 Z= 0.285 Chirality : 0.039 0.159 1649 Planarity : 0.005 0.073 1627 Dihedral : 4.801 80.920 1364 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.89 % Allowed : 15.84 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1272 helix: 0.43 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : -1.88 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 20 HIS 0.002 0.000 HIS A 334 PHE 0.022 0.001 PHE A 302 TYR 0.009 0.001 TYR B 238 ARG 0.004 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 178 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 110 ASN cc_start: 0.8666 (t0) cc_final: 0.7959 (t0) REVERT: A 132 LEU cc_start: 0.8488 (tp) cc_final: 0.8285 (tt) REVERT: A 150 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8500 (mttm) REVERT: A 244 GLN cc_start: 0.8570 (tp40) cc_final: 0.8053 (tp40) REVERT: A 295 MET cc_start: 0.8047 (mpp) cc_final: 0.7687 (mpp) REVERT: A 368 MET cc_start: 0.8043 (ttp) cc_final: 0.7822 (ttm) REVERT: B 8 ARG cc_start: 0.6512 (ppt170) cc_final: 0.6225 (ppt170) REVERT: B 100 PHE cc_start: 0.8237 (t80) cc_final: 0.7875 (t80) REVERT: B 196 MET cc_start: 0.9100 (mmt) cc_final: 0.8876 (mmt) REVERT: C 11 ASP cc_start: 0.7913 (m-30) cc_final: 0.7608 (m-30) REVERT: C 100 PHE cc_start: 0.8035 (t80) cc_final: 0.7103 (m-10) REVERT: C 196 MET cc_start: 0.8700 (mmt) cc_final: 0.8419 (mmt) REVERT: C 219 MET cc_start: 0.8170 (mmm) cc_final: 0.7772 (mmp) REVERT: C 371 GLN cc_start: 0.7891 (mm-40) cc_final: 0.7682 (mm-40) REVERT: C 403 MET cc_start: 0.8154 (tmm) cc_final: 0.7882 (tmm) outliers start: 19 outliers final: 12 residues processed: 186 average time/residue: 0.2007 time to fit residues: 53.9534 Evaluate side-chains 171 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 159 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 12 optimal weight: 0.3980 chunk 54 optimal weight: 0.2980 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 121 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN C 116 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9727 Z= 0.221 Angle : 0.562 7.210 13238 Z= 0.286 Chirality : 0.039 0.175 1649 Planarity : 0.005 0.075 1627 Dihedral : 4.795 83.440 1364 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.29 % Allowed : 16.33 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1272 helix: 0.72 (0.17), residues: 1026 sheet: None (None), residues: 0 loop : -1.72 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 PHE 0.020 0.001 PHE A 302 TYR 0.010 0.001 TYR B 238 ARG 0.005 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 169 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8834 (tp) REVERT: A 110 ASN cc_start: 0.8638 (t0) cc_final: 0.8014 (t0) REVERT: A 132 LEU cc_start: 0.8522 (tp) cc_final: 0.8313 (tt) REVERT: A 150 LYS cc_start: 0.8784 (mtmt) cc_final: 0.8522 (mttm) REVERT: A 244 GLN cc_start: 0.8535 (tp40) cc_final: 0.8054 (tp40) REVERT: A 364 ILE cc_start: 0.8969 (mm) cc_final: 0.8756 (mp) REVERT: A 368 MET cc_start: 0.8028 (ttp) cc_final: 0.7793 (ttm) REVERT: B 100 PHE cc_start: 0.8194 (t80) cc_final: 0.7966 (t80) REVERT: C 11 ASP cc_start: 0.7901 (m-30) cc_final: 0.7622 (m-30) REVERT: C 92 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8242 (mm) REVERT: C 100 PHE cc_start: 0.7993 (t80) cc_final: 0.7126 (m-10) REVERT: C 196 MET cc_start: 0.8706 (mmt) cc_final: 0.8471 (mmt) REVERT: C 219 MET cc_start: 0.8252 (mmm) cc_final: 0.7864 (mmp) REVERT: C 403 MET cc_start: 0.8156 (tmm) cc_final: 0.7824 (tmm) outliers start: 23 outliers final: 17 residues processed: 181 average time/residue: 0.2050 time to fit residues: 52.9149 Evaluate side-chains 176 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 157 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 chunk 0 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 128 GLN C 116 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9727 Z= 0.203 Angle : 0.564 8.345 13238 Z= 0.285 Chirality : 0.039 0.147 1649 Planarity : 0.005 0.073 1627 Dihedral : 4.759 84.565 1364 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.49 % Allowed : 17.93 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.24), residues: 1272 helix: 0.93 (0.17), residues: 1025 sheet: None (None), residues: 0 loop : -1.64 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 PHE 0.019 0.001 PHE A 302 TYR 0.010 0.001 TYR B 238 ARG 0.007 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8829 (tp) REVERT: A 110 ASN cc_start: 0.8644 (t0) cc_final: 0.8055 (t0) REVERT: A 150 LYS cc_start: 0.8762 (mtmt) cc_final: 0.8498 (mttm) REVERT: A 244 GLN cc_start: 0.8436 (tp40) cc_final: 0.8120 (tp40) REVERT: B 196 MET cc_start: 0.9110 (mmt) cc_final: 0.8817 (mmt) REVERT: B 288 MET cc_start: 0.8801 (mtp) cc_final: 0.8597 (mtp) REVERT: B 295 MET cc_start: 0.8949 (mtm) cc_final: 0.8456 (mtt) REVERT: C 100 PHE cc_start: 0.7971 (t80) cc_final: 0.7105 (m-10) REVERT: C 196 MET cc_start: 0.8709 (mmt) cc_final: 0.8483 (mmt) REVERT: C 219 MET cc_start: 0.8264 (mmm) cc_final: 0.7860 (mmp) REVERT: C 222 GLN cc_start: 0.7179 (mp10) cc_final: 0.6845 (mp10) REVERT: C 403 MET cc_start: 0.8198 (tmm) cc_final: 0.7904 (tmm) outliers start: 25 outliers final: 15 residues processed: 181 average time/residue: 0.2124 time to fit residues: 55.6126 Evaluate side-chains 172 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 156 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 0.0670 chunk 121 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 0.2980 chunk 64 optimal weight: 0.0010 chunk 117 optimal weight: 8.9990 overall best weight: 0.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9727 Z= 0.161 Angle : 0.563 9.764 13238 Z= 0.282 Chirality : 0.039 0.135 1649 Planarity : 0.005 0.074 1627 Dihedral : 4.670 84.293 1364 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.69 % Allowed : 19.72 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1272 helix: 1.19 (0.17), residues: 1023 sheet: None (None), residues: 0 loop : -1.46 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 PHE 0.034 0.001 PHE B 100 TYR 0.007 0.001 TYR B 238 ARG 0.009 0.000 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.055 Fit side-chains REVERT: A 51 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8808 (tp) REVERT: A 110 ASN cc_start: 0.8642 (t0) cc_final: 0.7993 (t0) REVERT: A 134 GLN cc_start: 0.8544 (tp-100) cc_final: 0.8267 (tp40) REVERT: A 150 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8501 (mttm) REVERT: A 265 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7600 (mmm-85) REVERT: B 100 PHE cc_start: 0.8010 (t80) cc_final: 0.7714 (t80) REVERT: C 100 PHE cc_start: 0.7912 (t80) cc_final: 0.7100 (m-10) REVERT: C 219 MET cc_start: 0.8297 (mmm) cc_final: 0.7908 (mmp) REVERT: C 403 MET cc_start: 0.8171 (tmm) cc_final: 0.7870 (tmm) outliers start: 17 outliers final: 11 residues processed: 179 average time/residue: 0.2002 time to fit residues: 51.3748 Evaluate side-chains 169 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 157 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9727 Z= 0.213 Angle : 0.579 8.319 13238 Z= 0.290 Chirality : 0.040 0.256 1649 Planarity : 0.005 0.074 1627 Dihedral : 4.681 83.154 1364 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.89 % Allowed : 19.82 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1272 helix: 1.26 (0.17), residues: 1023 sheet: None (None), residues: 0 loop : -1.41 (0.40), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.001 0.000 HIS C 34 PHE 0.029 0.001 PHE A 242 TYR 0.009 0.001 TYR B 238 ARG 0.009 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 159 time to evaluate : 1.055 Fit side-chains REVERT: A 51 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8815 (tp) REVERT: A 110 ASN cc_start: 0.8667 (t0) cc_final: 0.8100 (t0) REVERT: A 134 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8246 (tp40) REVERT: A 150 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8543 (mttm) REVERT: A 244 GLN cc_start: 0.8526 (tp40) cc_final: 0.8202 (tp40) REVERT: B 100 PHE cc_start: 0.8072 (t80) cc_final: 0.7820 (t80) REVERT: C 100 PHE cc_start: 0.7884 (t80) cc_final: 0.7110 (m-10) REVERT: C 219 MET cc_start: 0.8334 (mmm) cc_final: 0.7978 (mmp) outliers start: 19 outliers final: 16 residues processed: 171 average time/residue: 0.1918 time to fit residues: 48.0842 Evaluate side-chains 170 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 11 optimal weight: 0.0670 chunk 95 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 106 optimal weight: 7.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9727 Z= 0.195 Angle : 0.583 11.027 13238 Z= 0.287 Chirality : 0.039 0.191 1649 Planarity : 0.005 0.075 1627 Dihedral : 4.588 78.171 1364 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.39 % Allowed : 20.12 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1272 helix: 1.34 (0.17), residues: 1025 sheet: None (None), residues: 0 loop : -1.28 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 20 HIS 0.001 0.000 HIS C 34 PHE 0.027 0.001 PHE A 242 TYR 0.009 0.001 TYR B 238 ARG 0.006 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.035 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8799 (tp) REVERT: A 110 ASN cc_start: 0.8640 (t0) cc_final: 0.8097 (t0) REVERT: A 134 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8203 (tp40) REVERT: A 150 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8519 (mttm) REVERT: A 244 GLN cc_start: 0.8423 (tp40) cc_final: 0.8140 (tp-100) REVERT: A 265 ARG cc_start: 0.7868 (ttm170) cc_final: 0.7595 (mmm-85) REVERT: B 100 PHE cc_start: 0.8025 (t80) cc_final: 0.7747 (t80) REVERT: B 221 GLU cc_start: 0.7989 (tp30) cc_final: 0.7696 (tp30) REVERT: C 28 PHE cc_start: 0.8476 (t80) cc_final: 0.8242 (t80) REVERT: C 59 LEU cc_start: 0.8139 (mt) cc_final: 0.7375 (pp) REVERT: C 100 PHE cc_start: 0.7901 (t80) cc_final: 0.7102 (m-10) REVERT: C 204 MET cc_start: 0.7782 (mmt) cc_final: 0.7357 (mmt) REVERT: C 219 MET cc_start: 0.8326 (mmm) cc_final: 0.7927 (mmp) outliers start: 24 outliers final: 16 residues processed: 177 average time/residue: 0.2065 time to fit residues: 53.8252 Evaluate side-chains 175 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 233 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9727 Z= 0.209 Angle : 0.605 9.936 13238 Z= 0.296 Chirality : 0.040 0.188 1649 Planarity : 0.005 0.075 1627 Dihedral : 4.560 75.570 1364 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.89 % Allowed : 20.62 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1272 helix: 1.37 (0.17), residues: 1021 sheet: None (None), residues: 0 loop : -1.29 (0.40), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.001 0.000 HIS C 34 PHE 0.029 0.001 PHE A 242 TYR 0.009 0.001 TYR B 238 ARG 0.006 0.000 ARG C 401 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 160 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8782 (tp) REVERT: A 110 ASN cc_start: 0.8658 (t0) cc_final: 0.8159 (t0) REVERT: A 134 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8182 (tp40) REVERT: A 150 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8525 (mttm) REVERT: A 244 GLN cc_start: 0.8518 (tp40) cc_final: 0.8184 (tp-100) REVERT: A 265 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7629 (mmm-85) REVERT: B 128 GLN cc_start: 0.6043 (OUTLIER) cc_final: 0.4677 (tm130) REVERT: B 221 GLU cc_start: 0.8069 (tp30) cc_final: 0.7828 (tp30) REVERT: C 28 PHE cc_start: 0.8479 (t80) cc_final: 0.8209 (t80) REVERT: C 100 PHE cc_start: 0.7910 (t80) cc_final: 0.7115 (m-10) REVERT: C 204 MET cc_start: 0.7769 (mmt) cc_final: 0.7362 (mmt) REVERT: C 219 MET cc_start: 0.8347 (mmm) cc_final: 0.7936 (mmp) outliers start: 19 outliers final: 16 residues processed: 170 average time/residue: 0.1917 time to fit residues: 47.4509 Evaluate side-chains 177 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 358 VAL Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.0270 chunk 106 optimal weight: 5.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 116 ASN ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9727 Z= 0.191 Angle : 0.608 10.163 13238 Z= 0.298 Chirality : 0.040 0.177 1649 Planarity : 0.005 0.075 1627 Dihedral : 4.543 74.090 1364 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.09 % Allowed : 20.92 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.24), residues: 1272 helix: 1.42 (0.17), residues: 1021 sheet: None (None), residues: 0 loop : -1.24 (0.41), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 20 HIS 0.001 0.000 HIS C 34 PHE 0.048 0.001 PHE B 100 TYR 0.009 0.001 TYR B 238 ARG 0.006 0.000 ARG C 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 165 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8790 (tp) REVERT: A 110 ASN cc_start: 0.8662 (t0) cc_final: 0.8159 (t0) REVERT: A 134 GLN cc_start: 0.8556 (tp-100) cc_final: 0.8207 (tp40) REVERT: A 150 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8547 (mttm) REVERT: A 244 GLN cc_start: 0.8412 (tp40) cc_final: 0.8169 (tp-100) REVERT: A 265 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7620 (mmm-85) REVERT: B 100 PHE cc_start: 0.8176 (t80) cc_final: 0.7941 (t80) REVERT: B 128 GLN cc_start: 0.6010 (OUTLIER) cc_final: 0.4653 (tm130) REVERT: C 28 PHE cc_start: 0.8454 (t80) cc_final: 0.8208 (t80) REVERT: C 100 PHE cc_start: 0.7884 (t80) cc_final: 0.7133 (m-10) REVERT: C 204 MET cc_start: 0.7735 (mmt) cc_final: 0.7327 (mmt) REVERT: C 219 MET cc_start: 0.8317 (mmm) cc_final: 0.7901 (mmp) outliers start: 21 outliers final: 17 residues processed: 177 average time/residue: 0.1963 time to fit residues: 51.3936 Evaluate side-chains 174 residues out of total 1004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 155 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 68 LEU Chi-restraints excluded: chain B residue 128 GLN Chi-restraints excluded: chain B residue 196 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 116 ASN Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 389 MET Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 396 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.5980 chunk 41 optimal weight: 0.0050 chunk 102 optimal weight: 0.9990 chunk 12 optimal weight: 0.0470 chunk 18 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 overall best weight: 0.4492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.112671 restraints weight = 13116.237| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.67 r_work: 0.3176 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9727 Z= 0.176 Angle : 0.603 9.810 13238 Z= 0.295 Chirality : 0.039 0.153 1649 Planarity : 0.005 0.074 1627 Dihedral : 4.460 68.624 1364 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.89 % Allowed : 21.61 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.24), residues: 1272 helix: 1.48 (0.17), residues: 1023 sheet: None (None), residues: 0 loop : -1.25 (0.41), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 20 HIS 0.001 0.000 HIS A 334 PHE 0.048 0.001 PHE B 100 TYR 0.014 0.001 TYR A 197 ARG 0.006 0.000 ARG A 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.56 seconds wall clock time: 40 minutes 40.22 seconds (2440.22 seconds total)