Starting phenix.real_space_refine on Fri Apr 5 21:42:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/04_2024/8tgj_41238_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/04_2024/8tgj_41238.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/04_2024/8tgj_41238_trim_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/04_2024/8tgj_41238_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/04_2024/8tgj_41238_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/04_2024/8tgj_41238.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/04_2024/8tgj_41238.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/04_2024/8tgj_41238_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgj_41238/04_2024/8tgj_41238_trim_updated.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 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= 0.001 sd= 0.018 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 57 5.16 5 C 3805 2.51 5 N 892 2.21 5 O 966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5720 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2837 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 23, 'TRANS': 357} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 2839 Classifications: {'peptide': 380} Link IDs: {'PTRANS': 21, 'TRANS': 358} Chain breaks: 2 Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.62, per 1000 atoms: 0.63 Number of scatterers: 5720 At special positions: 0 Unit cell: (74.26, 56.4, 115.62, 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 57 16.00 O 966 8.00 N 892 7.00 C 3805 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: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 25 through 40 Processing helix chain 'A' and resid 42 through 49 Proline residue: A 46 - end of helix Processing helix chain 'A' and resid 137 through 164 removed outlier: 3.877A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA A 147 " --> pdb=" O PHE A 143 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 159 - end of helix removed outlier: 4.312A pdb=" N ASN A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 186 Processing helix chain 'A' and resid 190 through 218 removed outlier: 3.943A pdb=" N VAL A 195 " --> pdb=" O THR A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 253 removed outlier: 4.602A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 256 through 277 removed outlier: 4.302A pdb=" N PHE A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.686A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' Processing helix chain 'A' and resid 300 through 330 removed outlier: 3.789A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 338 through 363 removed outlier: 3.956A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 4.109A pdb=" N GLY A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 389 through 421 removed outlier: 3.867A pdb=" N ILE A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Proline residue: A 395 - end of helix removed outlier: 3.515A pdb=" N SER A 408 " --> pdb=" O MET A 405 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N MET A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 3.785A pdb=" N ARG A 421 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 4.207A pdb=" N GLY A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE A 441 " --> pdb=" O PHE A 437 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 4.942A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 479 Proline residue: A 473 - end of helix removed outlier: 4.858A pdb=" N TYR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N TYR A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LEU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ARG A 479 " --> pdb=" O CYS A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 42 through 51 Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 136 through 163 removed outlier: 4.554A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.502A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix Processing helix chain 'B' and resid 167 through 186 Processing helix chain 'B' and resid 190 through 218 removed outlier: 3.738A pdb=" N PHE B 194 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 250 removed outlier: 3.901A pdb=" N LEU B 236 " --> pdb=" O ALA B 232 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 3.749A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 275 removed outlier: 4.669A pdb=" N PHE B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 296 No H-bonds generated for 'chain 'B' and resid 293 through 296' Processing helix chain 'B' and resid 300 through 330 removed outlier: 3.504A pdb=" N ALA B 305 " --> pdb=" O TYR B 301 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 338 through 341 No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 343 through 363 removed outlier: 3.750A pdb=" N TYR B 349 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASN B 361 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LYS B 362 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N MET B 363 " --> pdb=" O LEU B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 Proline residue: B 384 - end of helix Processing helix chain 'B' and resid 389 through 421 removed outlier: 4.023A pdb=" N ILE B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLY B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Proline residue: B 395 - end of helix removed outlier: 3.511A pdb=" N ASP B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET B 410 " --> pdb=" O ASP B 407 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N MET B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Proline residue: B 412 - end of helix removed outlier: 3.518A pdb=" N LEU B 420 " --> pdb=" O LEU B 417 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG B 421 " --> pdb=" O VAL B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 454 Proline residue: B 445 - end of helix removed outlier: 3.670A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 478 removed outlier: 3.652A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Proline residue: B 473 - end of helix removed outlier: 4.852A pdb=" N TYR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TYR B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1086 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: 1.62 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 849 1.31 - 1.43: 1551 1.43 - 1.56: 3360 1.56 - 1.69: 3 1.69 - 1.81: 100 Bond restraints: 5863 Sorted by residual: bond pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " ideal model delta sigma weight residual 1.572 1.432 0.140 2.00e-02 2.50e+03 4.94e+01 bond pdb=" C13 YHR B 601 " pdb=" C14 YHR B 601 " ideal model delta sigma weight residual 1.567 1.494 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C11 YHR B 601 " pdb=" C23 YHR B 601 " ideal model delta sigma weight residual 1.373 1.433 -0.060 2.00e-02 2.50e+03 8.87e+00 bond pdb=" C11 YHR B 601 " pdb=" C12 YHR B 601 " ideal model delta sigma weight residual 1.397 1.339 0.058 2.00e-02 2.50e+03 8.31e+00 bond pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sigma weight residual 1.531 1.477 0.054 2.00e-02 2.50e+03 7.18e+00 ... (remaining 5858 not shown) Histogram of bond angle deviations from ideal: 98.75 - 106.28: 216 106.28 - 113.81: 3329 113.81 - 121.34: 3304 121.34 - 128.87: 1102 128.87 - 136.39: 36 Bond angle restraints: 7987 Sorted by residual: angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 99.45 130.18 -30.73 3.00e+00 1.11e-01 1.05e+02 angle pdb=" C25 YHR B 601 " pdb=" C26 YHR B 601 " pdb=" O28 YHR B 601 " ideal model delta sigma weight residual 137.71 120.35 17.36 3.00e+00 1.11e-01 3.35e+01 angle pdb=" C27 YHR B 601 " pdb=" C26 YHR B 601 " pdb=" O28 YHR B 601 " ideal model delta sigma weight residual 101.89 118.30 -16.41 3.00e+00 1.11e-01 2.99e+01 angle pdb=" C12 YHR B 601 " pdb=" C13 YHR B 601 " pdb=" N8 YHR B 601 " ideal model delta sigma weight residual 117.31 101.80 15.51 3.00e+00 1.11e-01 2.67e+01 angle pdb=" C ARG B 479 " pdb=" N SER B 480 " pdb=" CA SER B 480 " ideal model delta sigma weight residual 122.83 128.17 -5.34 1.08e+00 8.57e-01 2.44e+01 ... (remaining 7982 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 2977 21.72 - 43.43: 360 43.43 - 65.15: 52 65.15 - 86.86: 4 86.86 - 108.58: 1 Dihedral angle restraints: 3394 sinusoidal: 1258 harmonic: 2136 Sorted by residual: dihedral pdb=" CA VAL B 358 " pdb=" C VAL B 358 " pdb=" N LEU B 359 " pdb=" CA LEU B 359 " ideal model delta harmonic sigma weight residual -180.00 -160.94 -19.06 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 53.17 -55.41 108.58 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" CA PHE B 356 " pdb=" C PHE B 356 " pdb=" N GLY B 357 " pdb=" CA GLY B 357 " ideal model delta harmonic sigma weight residual 180.00 163.28 16.72 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 721 0.045 - 0.089: 179 0.089 - 0.134: 51 0.134 - 0.178: 7 0.178 - 0.223: 3 Chirality restraints: 961 Sorted by residual: chirality pdb=" CA LEU A 24 " pdb=" N LEU A 24 " pdb=" C LEU A 24 " pdb=" CB LEU A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA MET B 331 " pdb=" N MET B 331 " pdb=" C MET B 331 " pdb=" CB MET B 331 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" C16 YHR B 601 " pdb=" C15 YHR B 601 " pdb=" C17 YHR B 601 " pdb=" C3 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.75 2.57 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 958 not shown) Planarity restraints: 972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 472 " -0.079 5.00e-02 4.00e+02 1.18e-01 2.21e+01 pdb=" N PRO B 473 " 0.203 5.00e-02 4.00e+02 pdb=" CA PRO B 473 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 473 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 471 " 0.013 2.00e-02 2.50e+03 1.76e-02 6.18e+00 pdb=" CG TYR A 471 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 471 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 471 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 471 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 471 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 471 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 471 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY B 158 " 0.039 5.00e-02 4.00e+02 5.94e-02 5.65e+00 pdb=" N PRO B 159 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " 0.033 5.00e-02 4.00e+02 ... (remaining 969 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1676 2.81 - 3.34: 5897 3.34 - 3.86: 9596 3.86 - 4.38: 10445 4.38 - 4.90: 18832 Nonbonded interactions: 46446 Sorted by model distance: nonbonded pdb=" OE1 GLU B 135 " pdb=" NH1 ARG B 138 " model vdw 2.292 2.520 nonbonded pdb=" O PHE A 143 " pdb=" NH2 ARG A 197 " model vdw 2.339 2.520 nonbonded pdb=" O VAL A 375 " pdb=" OG SER A 379 " model vdw 2.343 2.440 nonbonded pdb=" O SER A 284 " pdb=" OG SER A 284 " model vdw 2.373 2.440 nonbonded pdb=" OD1 ASN A 154 " pdb=" OG SER A 205 " model vdw 2.422 2.440 ... (remaining 46441 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' and (resid 19 through 278 or resid 289 through 482)) selection = (chain 'B' and ((resid 19 and (name CA or name C or name O or name CB or name OG \ )) or resid 20 through 50 or resid 136 through 482)) } 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: 1.350 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: 6.750 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.170 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 5863 Z= 0.287 Angle : 0.899 30.726 7987 Z= 0.422 Chirality : 0.044 0.223 961 Planarity : 0.008 0.118 972 Dihedral : 17.568 108.577 2038 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.66 % Allowed : 34.59 % Favored : 64.75 % 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: 0.58 (0.30), residues: 751 helix: 0.87 (0.21), residues: 593 sheet: None (None), residues: 0 loop : -1.26 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 336 HIS 0.003 0.001 HIS A 223 PHE 0.036 0.001 PHE B 28 TYR 0.043 0.002 TYR A 471 ARG 0.003 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 159 time to evaluate : 0.652 Fit side-chains REVERT: A 190 TYR cc_start: 0.6527 (t80) cc_final: 0.5808 (t80) REVERT: A 194 PHE cc_start: 0.8027 (t80) cc_final: 0.7420 (m-80) REVERT: A 268 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7767 (mp) REVERT: B 439 MET cc_start: 0.7454 (tpp) cc_final: 0.7215 (mmm) outliers start: 4 outliers final: 1 residues processed: 161 average time/residue: 0.1291 time to fit residues: 29.0749 Evaluate side-chains 163 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 161 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain B residue 36 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.8980 chunk 57 optimal weight: 0.0980 chunk 31 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 overall best weight: 0.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** B 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN B 337 GLN B 396 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5863 Z= 0.220 Angle : 0.656 9.119 7987 Z= 0.318 Chirality : 0.043 0.188 961 Planarity : 0.006 0.057 972 Dihedral : 6.436 88.595 820 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.74 % Allowed : 28.36 % Favored : 65.90 % 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: 1.00 (0.31), residues: 751 helix: 1.14 (0.21), residues: 594 sheet: None (None), residues: 0 loop : -0.98 (0.49), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.002 0.001 HIS B 416 PHE 0.015 0.001 PHE A 253 TYR 0.017 0.001 TYR A 471 ARG 0.002 0.000 ARG B 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 168 time to evaluate : 0.621 Fit side-chains revert: symmetry clash REVERT: A 467 ILE cc_start: 0.7812 (tt) cc_final: 0.7530 (tp) REVERT: A 471 TYR cc_start: 0.7845 (t80) cc_final: 0.6997 (t80) REVERT: B 170 MET cc_start: 0.6975 (tpp) cc_final: 0.6686 (tpp) REVERT: B 314 MET cc_start: 0.7393 (OUTLIER) cc_final: 0.7184 (ttm) REVERT: B 373 MET cc_start: 0.7494 (mtp) cc_final: 0.7227 (mmm) REVERT: B 439 MET cc_start: 0.7469 (tpp) cc_final: 0.7206 (mmm) REVERT: B 461 MET cc_start: 0.6893 (mmm) cc_final: 0.6478 (mmt) outliers start: 35 outliers final: 19 residues processed: 183 average time/residue: 0.1384 time to fit residues: 34.6370 Evaluate side-chains 182 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 162 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.2980 chunk 57 optimal weight: 0.0370 chunk 46 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.1382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5863 Z= 0.226 Angle : 0.629 8.286 7987 Z= 0.307 Chirality : 0.042 0.133 961 Planarity : 0.005 0.060 972 Dihedral : 5.659 77.910 815 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.41 % Allowed : 30.82 % Favored : 63.77 % 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: 0.86 (0.31), residues: 751 helix: 1.10 (0.22), residues: 593 sheet: None (None), residues: 0 loop : -1.31 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.001 HIS B 416 PHE 0.019 0.001 PHE A 253 TYR 0.013 0.001 TYR A 471 ARG 0.002 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7359 (tt0) cc_final: 0.7121 (tt0) REVERT: A 463 ILE cc_start: 0.7527 (mt) cc_final: 0.7077 (mp) REVERT: A 467 ILE cc_start: 0.7881 (tt) cc_final: 0.7579 (tp) REVERT: A 471 TYR cc_start: 0.7880 (t80) cc_final: 0.7209 (t80) REVERT: B 439 MET cc_start: 0.7409 (tpp) cc_final: 0.7124 (mmm) REVERT: B 461 MET cc_start: 0.6905 (mmm) cc_final: 0.6517 (mmt) outliers start: 33 outliers final: 23 residues processed: 180 average time/residue: 0.1446 time to fit residues: 35.4464 Evaluate side-chains 182 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 159 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 35 optimal weight: 0.0980 chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.0980 chunk 73 optimal weight: 0.4980 chunk 36 optimal weight: 0.2980 chunk 65 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5863 Z= 0.195 Angle : 0.617 8.443 7987 Z= 0.298 Chirality : 0.041 0.127 961 Planarity : 0.005 0.059 972 Dihedral : 5.533 74.569 815 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.57 % Allowed : 30.98 % Favored : 63.44 % 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 (0.31), residues: 751 helix: 1.17 (0.22), residues: 597 sheet: None (None), residues: 0 loop : -1.35 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 336 HIS 0.001 0.000 HIS A 422 PHE 0.021 0.001 PHE A 253 TYR 0.011 0.001 TYR A 430 ARG 0.002 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7338 (tt0) cc_final: 0.7133 (tt0) REVERT: A 249 VAL cc_start: 0.7885 (m) cc_final: 0.7434 (p) REVERT: A 250 MET cc_start: 0.7697 (OUTLIER) cc_final: 0.6615 (mpp) REVERT: A 463 ILE cc_start: 0.7524 (mt) cc_final: 0.7053 (mp) REVERT: A 467 ILE cc_start: 0.7876 (tt) cc_final: 0.7555 (tp) REVERT: A 471 TYR cc_start: 0.7954 (t80) cc_final: 0.7314 (t80) REVERT: B 149 MET cc_start: 0.7659 (tpp) cc_final: 0.7360 (tpp) REVERT: B 314 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7204 (ttm) REVERT: B 331 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7337 (mtm) REVERT: B 373 MET cc_start: 0.7568 (mtp) cc_final: 0.7356 (mmm) REVERT: B 439 MET cc_start: 0.7382 (tpp) cc_final: 0.7091 (mmm) REVERT: B 452 VAL cc_start: 0.7374 (m) cc_final: 0.7018 (p) REVERT: B 461 MET cc_start: 0.6851 (mmm) cc_final: 0.6609 (mmt) outliers start: 34 outliers final: 22 residues processed: 183 average time/residue: 0.1444 time to fit residues: 35.6275 Evaluate side-chains 190 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 150 GLN Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 432 ILE Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.8980 chunk 41 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 62 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.0170 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.0570 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 HIS B 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5863 Z= 0.227 Angle : 0.627 8.009 7987 Z= 0.304 Chirality : 0.043 0.174 961 Planarity : 0.005 0.061 972 Dihedral : 5.534 71.393 815 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 6.39 % Allowed : 30.16 % Favored : 63.44 % 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: 0.94 (0.31), residues: 751 helix: 1.19 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.38 (0.45), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 326 HIS 0.001 0.001 HIS B 387 PHE 0.018 0.001 PHE A 253 TYR 0.014 0.001 TYR A 430 ARG 0.002 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 166 time to evaluate : 0.577 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7376 (tt0) cc_final: 0.7095 (tt0) REVERT: A 249 VAL cc_start: 0.7882 (m) cc_final: 0.7335 (p) REVERT: A 250 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6702 (mpp) REVERT: A 348 SER cc_start: 0.8197 (OUTLIER) cc_final: 0.7691 (t) REVERT: A 463 ILE cc_start: 0.7531 (mt) cc_final: 0.7033 (mp) REVERT: A 467 ILE cc_start: 0.7873 (tt) cc_final: 0.7574 (tp) REVERT: A 471 TYR cc_start: 0.8084 (t80) cc_final: 0.7255 (t80) REVERT: A 474 LEU cc_start: 0.7842 (mt) cc_final: 0.7497 (mp) REVERT: B 314 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7220 (ttm) REVERT: B 331 MET cc_start: 0.7595 (OUTLIER) cc_final: 0.7169 (mtm) REVERT: B 439 MET cc_start: 0.7372 (tpp) cc_final: 0.7067 (mmm) REVERT: B 452 VAL cc_start: 0.7372 (m) cc_final: 0.7045 (p) REVERT: B 461 MET cc_start: 0.6859 (mmm) cc_final: 0.6617 (mmt) outliers start: 39 outliers final: 24 residues processed: 183 average time/residue: 0.1365 time to fit residues: 34.1302 Evaluate side-chains 191 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 387 HIS Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 73 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5863 Z= 0.250 Angle : 0.653 7.975 7987 Z= 0.316 Chirality : 0.043 0.137 961 Planarity : 0.005 0.062 972 Dihedral : 5.551 69.661 815 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.57 % Allowed : 31.64 % Favored : 62.79 % 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: 0.95 (0.31), residues: 751 helix: 1.18 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.31 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 326 HIS 0.001 0.000 HIS A 422 PHE 0.025 0.001 PHE A 253 TYR 0.014 0.001 TYR A 430 ARG 0.003 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 168 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7388 (tt0) cc_final: 0.7114 (tt0) REVERT: A 249 VAL cc_start: 0.7826 (m) cc_final: 0.7399 (p) REVERT: A 250 MET cc_start: 0.7742 (OUTLIER) cc_final: 0.6675 (mpp) REVERT: A 348 SER cc_start: 0.8263 (OUTLIER) cc_final: 0.7744 (t) REVERT: A 463 ILE cc_start: 0.7538 (mt) cc_final: 0.7084 (mm) REVERT: A 471 TYR cc_start: 0.8095 (t80) cc_final: 0.7179 (t80) REVERT: A 474 LEU cc_start: 0.7844 (mt) cc_final: 0.7489 (mp) REVERT: B 331 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7178 (mtm) REVERT: B 439 MET cc_start: 0.7377 (tpp) cc_final: 0.7078 (mmm) REVERT: B 452 VAL cc_start: 0.7392 (m) cc_final: 0.7074 (p) REVERT: B 461 MET cc_start: 0.6895 (mmm) cc_final: 0.6655 (mmt) outliers start: 34 outliers final: 22 residues processed: 183 average time/residue: 0.1427 time to fit residues: 35.6982 Evaluate side-chains 189 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 229 MET Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 421 ARG Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.9990 chunk 41 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 0.0970 chunk 73 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5863 Z= 0.241 Angle : 0.660 8.043 7987 Z= 0.317 Chirality : 0.043 0.251 961 Planarity : 0.005 0.063 972 Dihedral : 5.566 68.399 815 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 6.56 % Allowed : 31.64 % Favored : 61.80 % 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: 0.93 (0.31), residues: 751 helix: 1.16 (0.22), residues: 591 sheet: None (None), residues: 0 loop : -1.28 (0.46), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 366 HIS 0.001 0.000 HIS A 167 PHE 0.022 0.001 PHE A 253 TYR 0.013 0.001 TYR A 430 ARG 0.003 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 160 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.7354 (tt0) cc_final: 0.7097 (tt0) REVERT: A 249 VAL cc_start: 0.7792 (m) cc_final: 0.7327 (p) REVERT: A 250 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.6684 (mpp) REVERT: A 348 SER cc_start: 0.8240 (OUTLIER) cc_final: 0.7722 (t) REVERT: A 439 MET cc_start: 0.6349 (OUTLIER) cc_final: 0.6027 (ttp) REVERT: A 471 TYR cc_start: 0.8078 (t80) cc_final: 0.7273 (t80) REVERT: A 474 LEU cc_start: 0.7845 (mt) cc_final: 0.7493 (mp) REVERT: B 331 MET cc_start: 0.7544 (OUTLIER) cc_final: 0.7157 (mtm) REVERT: B 439 MET cc_start: 0.7351 (tpp) cc_final: 0.7060 (mmm) REVERT: B 452 VAL cc_start: 0.7384 (m) cc_final: 0.7079 (p) REVERT: B 461 MET cc_start: 0.6908 (mmm) cc_final: 0.6667 (mmt) outliers start: 40 outliers final: 23 residues processed: 177 average time/residue: 0.1405 time to fit residues: 34.0119 Evaluate side-chains 185 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 380 LEU Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 44 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 chunk 57 optimal weight: 0.0040 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.3980 chunk 41 optimal weight: 0.0670 overall best weight: 0.3130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5863 Z= 0.205 Angle : 0.656 8.283 7987 Z= 0.311 Chirality : 0.042 0.198 961 Planarity : 0.005 0.062 972 Dihedral : 5.494 67.690 815 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.92 % Allowed : 33.44 % Favored : 61.64 % 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: 0.97 (0.31), residues: 751 helix: 1.16 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -1.20 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 336 HIS 0.001 0.000 HIS A 223 PHE 0.023 0.001 PHE A 253 TYR 0.012 0.001 TYR A 430 ARG 0.005 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 167 time to evaluate : 0.618 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8425 (tp) cc_final: 0.8165 (tt) REVERT: A 249 VAL cc_start: 0.7711 (m) cc_final: 0.7310 (p) REVERT: A 250 MET cc_start: 0.7706 (OUTLIER) cc_final: 0.6647 (mpp) REVERT: A 348 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7712 (t) REVERT: A 471 TYR cc_start: 0.8070 (t80) cc_final: 0.7400 (t80) REVERT: A 474 LEU cc_start: 0.7845 (mt) cc_final: 0.7496 (mp) REVERT: B 331 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7089 (mtm) REVERT: B 439 MET cc_start: 0.7345 (tpp) cc_final: 0.7083 (tpp) REVERT: B 452 VAL cc_start: 0.7346 (m) cc_final: 0.7083 (p) REVERT: B 479 ARG cc_start: 0.5082 (OUTLIER) cc_final: 0.4862 (ptt-90) outliers start: 30 outliers final: 20 residues processed: 178 average time/residue: 0.1459 time to fit residues: 36.1727 Evaluate side-chains 188 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 164 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 44 optimal weight: 0.0980 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 0.0570 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5863 Z= 0.202 Angle : 0.657 8.566 7987 Z= 0.311 Chirality : 0.042 0.183 961 Planarity : 0.005 0.062 972 Dihedral : 5.519 66.876 815 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.26 % Allowed : 34.10 % Favored : 61.64 % 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: 1.04 (0.32), residues: 751 helix: 1.21 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -1.17 (0.47), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 336 HIS 0.001 0.000 HIS A 387 PHE 0.021 0.001 PHE A 253 TYR 0.012 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8427 (tp) cc_final: 0.8150 (tt) REVERT: A 249 VAL cc_start: 0.7675 (m) cc_final: 0.7260 (p) REVERT: A 250 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.6630 (mpp) REVERT: A 348 SER cc_start: 0.8225 (OUTLIER) cc_final: 0.7707 (t) REVERT: A 471 TYR cc_start: 0.8118 (t80) cc_final: 0.7414 (t80) REVERT: A 474 LEU cc_start: 0.7862 (mt) cc_final: 0.7523 (mp) REVERT: B 331 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.6986 (mtm) REVERT: B 439 MET cc_start: 0.7343 (tpp) cc_final: 0.7075 (tpp) REVERT: B 452 VAL cc_start: 0.7339 (m) cc_final: 0.7082 (p) REVERT: B 479 ARG cc_start: 0.5016 (OUTLIER) cc_final: 0.4728 (ptt-90) outliers start: 26 outliers final: 19 residues processed: 183 average time/residue: 0.1413 time to fit residues: 35.3863 Evaluate side-chains 193 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 170 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.3980 chunk 60 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN B 468 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5863 Z= 0.273 Angle : 0.689 9.378 7987 Z= 0.331 Chirality : 0.044 0.183 961 Planarity : 0.006 0.063 972 Dihedral : 5.552 66.533 815 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 4.10 % Allowed : 33.44 % Favored : 62.46 % 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: 0.91 (0.31), residues: 751 helix: 1.12 (0.22), residues: 593 sheet: None (None), residues: 0 loop : -1.20 (0.46), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 366 HIS 0.002 0.000 HIS A 422 PHE 0.023 0.001 PHE A 253 TYR 0.013 0.001 TYR A 476 ARG 0.003 0.001 ARG B 421 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1502 Ramachandran restraints generated. 751 Oldfield, 0 Emsley, 751 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8482 (tp) cc_final: 0.8224 (tt) REVERT: A 206 PHE cc_start: 0.7707 (m-80) cc_final: 0.7477 (m-80) REVERT: A 348 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.7737 (t) REVERT: A 373 MET cc_start: 0.7620 (mmm) cc_final: 0.7340 (tpp) REVERT: A 463 ILE cc_start: 0.7429 (mt) cc_final: 0.7174 (mt) REVERT: A 474 LEU cc_start: 0.7942 (mt) cc_final: 0.7573 (mp) REVERT: B 452 VAL cc_start: 0.7399 (m) cc_final: 0.7109 (p) REVERT: B 461 MET cc_start: 0.6932 (mmm) cc_final: 0.6705 (mmt) REVERT: B 479 ARG cc_start: 0.5036 (OUTLIER) cc_final: 0.4819 (ptt-90) outliers start: 25 outliers final: 21 residues processed: 177 average time/residue: 0.1322 time to fit residues: 32.7348 Evaluate side-chains 188 residues out of total 611 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 PHE Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 246 PHE Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 437 PHE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 156 PHE Chi-restraints excluded: chain B residue 195 VAL Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 262 ILE Chi-restraints excluded: chain B residue 270 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 393 ILE Chi-restraints excluded: chain B residue 479 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 chunk 62 optimal weight: 0.0980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 53 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 337 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.140292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.126685 restraints weight = 8968.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.130566 restraints weight = 4554.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133076 restraints weight = 2652.689| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5863 Z= 0.211 Angle : 0.670 9.918 7987 Z= 0.318 Chirality : 0.043 0.180 961 Planarity : 0.005 0.062 972 Dihedral : 5.530 65.946 815 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.61 % Allowed : 33.28 % Favored : 63.11 % 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: 0.97 (0.31), residues: 751 helix: 1.16 (0.22), residues: 594 sheet: None (None), residues: 0 loop : -1.18 (0.46), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 326 HIS 0.001 0.000 HIS A 387 PHE 0.022 0.001 PHE A 253 TYR 0.011 0.001 TYR A 430 ARG 0.003 0.000 ARG B 479 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1619.05 seconds wall clock time: 29 minutes 59.14 seconds (1799.14 seconds total)