Starting phenix.real_space_refine on Wed Feb 14 00:45:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7axz_11933/02_2024/7axz_11933.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7axz_11933/02_2024/7axz_11933.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7axz_11933/02_2024/7axz_11933.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7axz_11933/02_2024/7axz_11933.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7axz_11933/02_2024/7axz_11933.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7axz_11933/02_2024/7axz_11933.pdb" } resolution = 3.2 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= 0.004 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 41 5.16 5 C 5266 2.51 5 N 1389 2.21 5 O 1529 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 36": "OD1" <-> "OD2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 140": "OD1" <-> "OD2" Residue "A TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A ASP 192": "OD1" <-> "OD2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A ASP 341": "OD1" <-> "OD2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 391": "OE1" <-> "OE2" Residue "A PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 530": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B ASP 65": "OD1" <-> "OD2" Residue "B ASP 87": "OD1" <-> "OD2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 158": "OD1" <-> "OD2" Residue "B GLU 206": "OE1" <-> "OE2" Residue "B TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B GLU 304": "OE1" <-> "OE2" Residue "B TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 541": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8225 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 4033 Classifications: {'peptide': 499} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 28, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4192 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 25, 'TRANS': 498} Chain breaks: 3 Time building chain proxies: 4.63, per 1000 atoms: 0.56 Number of scatterers: 8225 At special positions: 0 Unit cell: (97.464, 86.984, 119.472, 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 41 16.00 O 1529 8.00 N 1389 7.00 C 5266 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: 3.21 Conformation dependent library (CDL) restraints added in 1.6 seconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1954 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 34.2% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 58 through 77 Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 124 through 135 removed outlier: 3.532A pdb=" N MET A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 157 removed outlier: 4.238A pdb=" N VAL A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 196 removed outlier: 3.620A pdb=" N ALA A 183 " --> pdb=" O ASP A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 removed outlier: 3.563A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 314 No H-bonds generated for 'chain 'A' and resid 312 through 314' Processing helix chain 'A' and resid 330 through 334 Processing helix chain 'A' and resid 352 through 356 Processing helix chain 'A' and resid 377 through 391 removed outlier: 3.625A pdb=" N LEU A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 468 Processing helix chain 'A' and resid 480 through 494 removed outlier: 3.680A pdb=" N GLN A 484 " --> pdb=" O ASN A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 519 Processing helix chain 'A' and resid 520 through 530 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 29 through 47 Processing helix chain 'B' and resid 69 through 73 Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.631A pdb=" N LEU B 91 " --> pdb=" O ASP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.540A pdb=" N LYS B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N LYS B 156 " --> pdb=" O HIS B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.539A pdb=" N LEU B 221 " --> pdb=" O GLU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 Processing helix chain 'B' and resid 370 through 388 Processing helix chain 'B' and resid 447 through 462 removed outlier: 3.707A pdb=" N LEU B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 500 removed outlier: 3.963A pdb=" N GLN B 488 " --> pdb=" O ASN B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 516 Processing helix chain 'B' and resid 519 through 537 removed outlier: 3.776A pdb=" N THR B 523 " --> pdb=" O PRO B 519 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE B 528 " --> pdb=" O THR B 524 " (cutoff:3.500A) Proline residue: B 529 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 102 through 106 removed outlier: 6.364A pdb=" N VAL A 85 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP A 36 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ALA A 84 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 38 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N PHE A 40 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N TYR A 88 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N VAL A 42 " --> pdb=" O TYR A 88 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 41 " --> pdb=" O MET A 167 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS A 164 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASP A 201 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE A 166 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 257 through 262 removed outlier: 4.731A pdb=" N PHE A 410 " --> pdb=" O LEU A 437 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 397 " --> pdb=" O MET A 348 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 345 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N LYS A 260 " --> pdb=" O LEU A 345 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N LEU A 347 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LYS A 262 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N GLY A 349 " --> pdb=" O LYS A 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 288 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 325 through 329 Processing sheet with id=AA5, first strand: chain 'A' and resid 375 through 376 Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 84 removed outlier: 6.459A pdb=" N LEU B 56 " --> pdb=" O HIS B 80 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N HIS B 82 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ILE B 54 " --> pdb=" O HIS B 82 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ALA B 8 " --> pdb=" O GLU B 53 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ALA B 55 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 10 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL B 57 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU B 12 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE B 59 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N MET B 14 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 135 removed outlier: 6.232A pdb=" N ILE B 134 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N PHE B 163 " --> pdb=" O TYR B 225 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 247 through 253 removed outlier: 5.461A pdb=" N ALA B 366 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N GLU B 417 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 8.718A pdb=" N MET B 389 " --> pdb=" O PRO B 410 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 313 through 316 Processing sheet with id=AB1, first strand: chain 'B' and resid 464 through 466 314 hydrogen bonds defined for protein. 855 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: 2.41 Time building geometry restraints manager: 3.48 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: 2676 1.34 - 1.46: 1370 1.46 - 1.57: 4273 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 8388 Sorted by residual: bond pdb=" CA THR A 472 " pdb=" CB THR A 472 " ideal model delta sigma weight residual 1.526 1.467 0.060 1.76e-02 3.23e+03 1.14e+01 bond pdb=" C ASP A 342 " pdb=" N PRO A 343 " ideal model delta sigma weight residual 1.334 1.305 0.029 1.11e-02 8.12e+03 6.68e+00 bond pdb=" CA TYR A 409 " pdb=" C TYR A 409 " ideal model delta sigma weight residual 1.526 1.499 0.027 1.36e-02 5.41e+03 3.84e+00 bond pdb=" C ARG B 271 " pdb=" N VAL B 272 " ideal model delta sigma weight residual 1.334 1.310 0.024 1.24e-02 6.50e+03 3.60e+00 bond pdb=" CB PRO A 438 " pdb=" CG PRO A 438 " ideal model delta sigma weight residual 1.492 1.398 0.094 5.00e-02 4.00e+02 3.56e+00 ... (remaining 8383 not shown) Histogram of bond angle deviations from ideal: 95.59 - 103.27: 88 103.27 - 110.95: 3035 110.95 - 118.62: 3632 118.62 - 126.30: 4462 126.30 - 133.98: 89 Bond angle restraints: 11306 Sorted by residual: angle pdb=" N LEU A 337 " pdb=" CA LEU A 337 " pdb=" C LEU A 337 " ideal model delta sigma weight residual 112.72 105.91 6.81 1.36e+00 5.41e-01 2.51e+01 angle pdb=" N ARG A 339 " pdb=" CA ARG A 339 " pdb=" CB ARG A 339 " ideal model delta sigma weight residual 109.51 116.70 -7.19 1.58e+00 4.01e-01 2.07e+01 angle pdb=" CG ARG A 339 " pdb=" CD ARG A 339 " pdb=" NE ARG A 339 " ideal model delta sigma weight residual 112.00 119.45 -7.45 2.20e+00 2.07e-01 1.15e+01 angle pdb=" CA LYS A 338 " pdb=" C LYS A 338 " pdb=" N ARG A 339 " ideal model delta sigma weight residual 116.84 122.56 -5.72 1.71e+00 3.42e-01 1.12e+01 angle pdb=" C GLN B 510 " pdb=" N HIS B 511 " pdb=" CA HIS B 511 " ideal model delta sigma weight residual 120.72 115.21 5.51 1.67e+00 3.59e-01 1.09e+01 ... (remaining 11301 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4612 17.91 - 35.81: 468 35.81 - 53.72: 79 53.72 - 71.62: 11 71.62 - 89.53: 11 Dihedral angle restraints: 5181 sinusoidal: 2183 harmonic: 2998 Sorted by residual: dihedral pdb=" CA MET B 389 " pdb=" C MET B 389 " pdb=" N VAL B 390 " pdb=" CA VAL B 390 " ideal model delta harmonic sigma weight residual -180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 dihedral pdb=" CA ASP A 341 " pdb=" C ASP A 341 " pdb=" N ASP A 342 " pdb=" CA ASP A 342 " ideal model delta harmonic sigma weight residual 180.00 152.83 27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA GLU A 336 " pdb=" C GLU A 336 " pdb=" N LEU A 337 " pdb=" CA LEU A 337 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 5178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 715 0.037 - 0.073: 368 0.073 - 0.110: 118 0.110 - 0.147: 43 0.147 - 0.183: 20 Chirality restraints: 1264 Sorted by residual: chirality pdb=" CA THR B 479 " pdb=" N THR B 479 " pdb=" C THR B 479 " pdb=" CB THR B 479 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CB VAL B 393 " pdb=" CA VAL B 393 " pdb=" CG1 VAL B 393 " pdb=" CG2 VAL B 393 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" CA ILE A 273 " pdb=" N ILE A 273 " pdb=" C ILE A 273 " pdb=" CB ILE A 273 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 1261 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 165 " 0.041 5.00e-02 4.00e+02 6.30e-02 6.35e+00 pdb=" N PRO B 166 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 450 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.18e+00 pdb=" C GLN B 450 " -0.043 2.00e-02 2.50e+03 pdb=" O GLN B 450 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU B 451 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 283 " 0.041 5.00e-02 4.00e+02 6.06e-02 5.88e+00 pdb=" N PRO A 284 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " 0.033 5.00e-02 4.00e+02 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 88 2.51 - 3.11: 6623 3.11 - 3.70: 12008 3.70 - 4.30: 17374 4.30 - 4.90: 29268 Nonbonded interactions: 65361 Sorted by model distance: nonbonded pdb=" OH TYR A 274 " pdb=" OE2 GLU A 371 " model vdw 1.911 2.440 nonbonded pdb=" OE1 GLU A 491 " pdb=" OH TYR B 316 " model vdw 1.987 2.440 nonbonded pdb=" OH TYR A 409 " pdb=" OE1 GLN B 269 " model vdw 2.033 2.440 nonbonded pdb=" OE1 GLN B 509 " pdb=" NE2 HIS B 511 " model vdw 2.097 2.520 nonbonded pdb=" NH2 ARG A 325 " pdb=" O ALA B 498 " model vdw 2.128 2.520 ... (remaining 65356 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.390 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: 2.230 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 26.100 Find NCS groups from input model: 0.260 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 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 : 0.009 0.094 8388 Z= 0.583 Angle : 0.871 7.448 11306 Z= 0.493 Chirality : 0.052 0.183 1264 Planarity : 0.006 0.063 1456 Dihedral : 14.876 89.529 3227 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.19 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -2.73 (0.25), residues: 1011 helix: -0.89 (0.27), residues: 315 sheet: -2.20 (0.40), residues: 155 loop : -2.29 (0.25), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 276 HIS 0.006 0.002 HIS B 120 PHE 0.020 0.003 PHE A 471 TYR 0.028 0.003 TYR A 400 ARG 0.011 0.001 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 48 MET cc_start: 0.7074 (mmt) cc_final: 0.6819 (mmt) REVERT: A 265 LYS cc_start: 0.7524 (mtpt) cc_final: 0.7168 (mmtt) REVERT: B 40 MET cc_start: 0.7512 (ttp) cc_final: 0.7291 (ttm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2303 time to fit residues: 29.8059 Evaluate side-chains 61 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 58 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 HIS B 33 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8388 Z= 0.177 Angle : 0.583 7.476 11306 Z= 0.297 Chirality : 0.043 0.151 1264 Planarity : 0.005 0.053 1456 Dihedral : 5.029 22.630 1094 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.87 % Allowed : 6.39 % Favored : 92.74 % 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: -1.60 (0.26), residues: 1011 helix: 0.39 (0.29), residues: 314 sheet: -1.49 (0.39), residues: 173 loop : -1.85 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 247 HIS 0.004 0.001 HIS B 188 PHE 0.016 0.001 PHE A 487 TYR 0.012 0.001 TYR A 400 ARG 0.007 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8458 (mp) cc_final: 0.7945 (mt) REVERT: A 102 ILE cc_start: 0.8731 (mm) cc_final: 0.8387 (mt) REVERT: A 135 MET cc_start: 0.6264 (tpp) cc_final: 0.6060 (tpp) REVERT: A 265 LYS cc_start: 0.7496 (mtpt) cc_final: 0.7143 (mmtt) REVERT: B 192 PHE cc_start: 0.5622 (m-80) cc_final: 0.5413 (m-80) REVERT: B 210 MET cc_start: 0.8032 (ttm) cc_final: 0.7813 (tmm) REVERT: B 474 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5258 (pm20) outliers start: 8 outliers final: 2 residues processed: 95 average time/residue: 0.2172 time to fit residues: 30.1201 Evaluate side-chains 79 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8388 Z= 0.180 Angle : 0.541 6.864 11306 Z= 0.271 Chirality : 0.042 0.147 1264 Planarity : 0.004 0.058 1456 Dihedral : 4.590 18.794 1094 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.41 % Allowed : 9.43 % Favored : 89.17 % 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: -1.27 (0.27), residues: 1011 helix: 0.61 (0.30), residues: 316 sheet: -1.16 (0.39), residues: 173 loop : -1.66 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 247 HIS 0.003 0.001 HIS B 188 PHE 0.045 0.001 PHE B 59 TYR 0.012 0.001 TYR A 400 ARG 0.003 0.000 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8420 (mp) cc_final: 0.7947 (mt) REVERT: A 102 ILE cc_start: 0.8741 (mm) cc_final: 0.8365 (mt) REVERT: A 135 MET cc_start: 0.6474 (tpp) cc_final: 0.6163 (tpp) REVERT: A 265 LYS cc_start: 0.7535 (mtpt) cc_final: 0.7172 (mmtt) REVERT: A 498 MET cc_start: 0.6475 (ttm) cc_final: 0.5942 (tpp) REVERT: B 15 ASP cc_start: 0.6466 (t70) cc_final: 0.6179 (t0) REVERT: B 210 MET cc_start: 0.8052 (ttm) cc_final: 0.7824 (tmm) REVERT: B 223 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7326 (mt-10) REVERT: B 267 ILE cc_start: 0.8674 (mm) cc_final: 0.8440 (mt) outliers start: 13 outliers final: 6 residues processed: 90 average time/residue: 0.1885 time to fit residues: 24.6578 Evaluate side-chains 85 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 43 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8388 Z= 0.198 Angle : 0.529 8.081 11306 Z= 0.266 Chirality : 0.041 0.145 1264 Planarity : 0.004 0.061 1456 Dihedral : 4.402 19.325 1094 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.52 % Allowed : 10.94 % Favored : 87.54 % 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: -1.06 (0.27), residues: 1011 helix: 0.66 (0.29), residues: 323 sheet: -0.93 (0.39), residues: 173 loop : -1.53 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 247 HIS 0.003 0.001 HIS B 188 PHE 0.024 0.002 PHE B 59 TYR 0.011 0.001 TYR A 400 ARG 0.002 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 86 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8406 (mp) cc_final: 0.7990 (mt) REVERT: A 102 ILE cc_start: 0.8787 (mm) cc_final: 0.8421 (mt) REVERT: A 135 MET cc_start: 0.6497 (tpp) cc_final: 0.6220 (tpp) REVERT: A 265 LYS cc_start: 0.7725 (mtpt) cc_final: 0.7324 (mmtt) REVERT: A 498 MET cc_start: 0.6463 (ttm) cc_final: 0.5865 (tpp) REVERT: B 15 ASP cc_start: 0.6574 (t70) cc_final: 0.6295 (t0) REVERT: B 210 MET cc_start: 0.8018 (ttm) cc_final: 0.7791 (tmm) REVERT: B 212 MET cc_start: 0.8057 (mmm) cc_final: 0.7596 (mmm) REVERT: B 223 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.7339 (mt-10) REVERT: B 267 ILE cc_start: 0.8760 (mm) cc_final: 0.8517 (mt) outliers start: 14 outliers final: 7 residues processed: 94 average time/residue: 0.1910 time to fit residues: 26.2137 Evaluate side-chains 84 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.0030 chunk 83 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8388 Z= 0.250 Angle : 0.552 9.511 11306 Z= 0.276 Chirality : 0.042 0.141 1264 Planarity : 0.004 0.061 1456 Dihedral : 4.433 18.007 1094 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.17 % Allowed : 11.59 % Favored : 86.24 % 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: -1.01 (0.27), residues: 1011 helix: 0.68 (0.29), residues: 323 sheet: -0.90 (0.38), residues: 184 loop : -1.48 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 247 HIS 0.003 0.001 HIS B 246 PHE 0.020 0.002 PHE B 18 TYR 0.012 0.001 TYR B 395 ARG 0.003 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 75 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8363 (mp) cc_final: 0.7998 (mt) REVERT: A 102 ILE cc_start: 0.8859 (mm) cc_final: 0.8525 (mt) REVERT: A 265 LYS cc_start: 0.7659 (mtpt) cc_final: 0.7276 (mmtt) REVERT: B 15 ASP cc_start: 0.6797 (t70) cc_final: 0.6318 (t0) REVERT: B 210 MET cc_start: 0.8032 (ttm) cc_final: 0.7773 (tmm) REVERT: B 212 MET cc_start: 0.8106 (mmm) cc_final: 0.7758 (mmm) REVERT: B 223 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7288 (mt-10) REVERT: B 267 ILE cc_start: 0.8803 (mm) cc_final: 0.8581 (mt) outliers start: 20 outliers final: 12 residues processed: 88 average time/residue: 0.1693 time to fit residues: 22.3282 Evaluate side-chains 86 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 393 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 94 optimal weight: 0.1980 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8388 Z= 0.240 Angle : 0.553 9.642 11306 Z= 0.274 Chirality : 0.042 0.139 1264 Planarity : 0.004 0.060 1456 Dihedral : 4.364 18.614 1094 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.06 % Allowed : 12.46 % Favored : 85.48 % 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 (0.27), residues: 1011 helix: 0.70 (0.29), residues: 324 sheet: -0.95 (0.39), residues: 171 loop : -1.45 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 247 HIS 0.003 0.001 HIS B 188 PHE 0.020 0.002 PHE B 345 TYR 0.011 0.001 TYR A 400 ARG 0.003 0.000 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 LEU cc_start: 0.8377 (mp) cc_final: 0.8001 (mt) REVERT: A 102 ILE cc_start: 0.8811 (mm) cc_final: 0.8586 (mt) REVERT: A 135 MET cc_start: 0.6382 (tpp) cc_final: 0.6181 (tpp) REVERT: A 265 LYS cc_start: 0.7679 (mtpt) cc_final: 0.7311 (mmtt) REVERT: B 212 MET cc_start: 0.8080 (mmm) cc_final: 0.7806 (mmm) REVERT: B 223 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7305 (mt-10) REVERT: B 267 ILE cc_start: 0.8777 (mm) cc_final: 0.8565 (mt) REVERT: B 474 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.5440 (pm20) outliers start: 19 outliers final: 12 residues processed: 94 average time/residue: 0.1755 time to fit residues: 24.3502 Evaluate side-chains 88 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 450 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8388 Z= 0.183 Angle : 0.531 8.783 11306 Z= 0.261 Chirality : 0.041 0.139 1264 Planarity : 0.004 0.060 1456 Dihedral : 4.221 18.197 1094 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.95 % Allowed : 13.43 % Favored : 84.62 % 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: -0.80 (0.27), residues: 1011 helix: 0.94 (0.29), residues: 324 sheet: -1.02 (0.39), residues: 167 loop : -1.31 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 247 HIS 0.003 0.001 HIS B 188 PHE 0.033 0.001 PHE B 59 TYR 0.010 0.001 TYR A 400 ARG 0.002 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 SER cc_start: 0.8711 (t) cc_final: 0.8450 (m) REVERT: A 83 LEU cc_start: 0.8378 (mp) cc_final: 0.8020 (mt) REVERT: A 102 ILE cc_start: 0.8972 (mm) cc_final: 0.8767 (mt) REVERT: A 135 MET cc_start: 0.6390 (tpp) cc_final: 0.6155 (tpp) REVERT: A 265 LYS cc_start: 0.7729 (mtpt) cc_final: 0.7333 (mmtt) REVERT: A 498 MET cc_start: 0.6518 (ttm) cc_final: 0.5816 (tpp) REVERT: B 210 MET cc_start: 0.7996 (ttm) cc_final: 0.7728 (tmm) REVERT: B 223 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: B 267 ILE cc_start: 0.8769 (mm) cc_final: 0.8558 (mt) REVERT: B 474 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5332 (pm20) outliers start: 18 outliers final: 11 residues processed: 92 average time/residue: 0.1707 time to fit residues: 23.5170 Evaluate side-chains 91 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 78 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 5.9990 chunk 19 optimal weight: 0.0270 chunk 18 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 2.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8388 Z= 0.285 Angle : 0.589 10.340 11306 Z= 0.289 Chirality : 0.042 0.138 1264 Planarity : 0.004 0.060 1456 Dihedral : 4.412 19.801 1094 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.06 % Allowed : 13.65 % Favored : 84.29 % 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: -0.95 (0.27), residues: 1011 helix: 0.73 (0.29), residues: 324 sheet: -1.04 (0.39), residues: 178 loop : -1.37 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 247 HIS 0.003 0.001 HIS B 131 PHE 0.026 0.002 PHE B 59 TYR 0.012 0.002 TYR A 400 ARG 0.003 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 ILE cc_start: 0.8955 (mm) cc_final: 0.8725 (mt) REVERT: A 134 MET cc_start: 0.7627 (pmm) cc_final: 0.7381 (pmm) REVERT: A 135 MET cc_start: 0.6557 (tpp) cc_final: 0.6265 (tpp) REVERT: A 265 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7421 (mmtt) REVERT: B 212 MET cc_start: 0.8151 (mmm) cc_final: 0.7668 (mmm) REVERT: B 223 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7282 (mt-10) REVERT: B 267 ILE cc_start: 0.8856 (mm) cc_final: 0.8648 (mt) REVERT: B 474 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5396 (pm20) outliers start: 19 outliers final: 11 residues processed: 92 average time/residue: 0.1791 time to fit residues: 24.4572 Evaluate side-chains 88 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 75 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 446 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 414 HIS Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN B 269 GLN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8388 Z= 0.171 Angle : 0.550 9.667 11306 Z= 0.268 Chirality : 0.041 0.167 1264 Planarity : 0.004 0.061 1456 Dihedral : 4.179 18.474 1094 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.52 % Allowed : 14.73 % Favored : 83.75 % 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: -0.70 (0.27), residues: 1011 helix: 1.03 (0.29), residues: 325 sheet: -0.94 (0.39), residues: 167 loop : -1.28 (0.28), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 247 HIS 0.003 0.001 HIS B 188 PHE 0.023 0.001 PHE B 59 TYR 0.010 0.001 TYR A 400 ARG 0.002 0.000 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 SER cc_start: 0.8683 (t) cc_final: 0.8413 (m) REVERT: A 265 LYS cc_start: 0.7764 (mtpt) cc_final: 0.7368 (mmtt) REVERT: A 498 MET cc_start: 0.6603 (ttm) cc_final: 0.6288 (tmm) REVERT: B 210 MET cc_start: 0.8131 (ttm) cc_final: 0.7760 (tmm) REVERT: B 223 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7285 (mt-10) REVERT: B 267 ILE cc_start: 0.8792 (mm) cc_final: 0.8573 (mt) REVERT: B 474 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5185 (pm20) outliers start: 14 outliers final: 9 residues processed: 92 average time/residue: 0.1687 time to fit residues: 23.2395 Evaluate side-chains 90 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.0970 chunk 66 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 80 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8388 Z= 0.220 Angle : 0.583 9.304 11306 Z= 0.281 Chirality : 0.042 0.172 1264 Planarity : 0.004 0.061 1456 Dihedral : 4.267 19.115 1094 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.30 % Allowed : 15.60 % Favored : 83.10 % 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: -0.76 (0.27), residues: 1011 helix: 0.98 (0.29), residues: 324 sheet: -0.87 (0.39), residues: 174 loop : -1.35 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 247 HIS 0.003 0.001 HIS B 131 PHE 0.023 0.001 PHE B 59 TYR 0.011 0.001 TYR A 400 ARG 0.003 0.000 ARG A 318 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 84 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 SER cc_start: 0.8679 (t) cc_final: 0.8403 (m) REVERT: A 265 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7410 (mmtt) REVERT: B 210 MET cc_start: 0.8127 (ttm) cc_final: 0.7749 (tmm) REVERT: B 223 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7260 (mt-10) REVERT: B 267 ILE cc_start: 0.8816 (mm) cc_final: 0.8605 (mt) REVERT: B 474 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5257 (pm20) outliers start: 12 outliers final: 9 residues processed: 92 average time/residue: 0.1750 time to fit residues: 24.0355 Evaluate side-chains 91 residues out of total 924 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ASP Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 58 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 393 VAL Chi-restraints excluded: chain B residue 474 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 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 = 0.4034 r_free = 0.4034 target = 0.116392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.094819 restraints weight = 18946.573| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.02 r_work: 0.3565 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8388 Z= 0.151 Angle : 0.553 9.290 11306 Z= 0.268 Chirality : 0.041 0.173 1264 Planarity : 0.004 0.061 1456 Dihedral : 4.039 17.985 1094 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.52 % Allowed : 15.82 % Favored : 82.67 % 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: -0.49 (0.27), residues: 1011 helix: 1.18 (0.30), residues: 322 sheet: -0.79 (0.40), residues: 173 loop : -1.13 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 247 HIS 0.003 0.001 HIS B 188 PHE 0.030 0.001 PHE B 491 TYR 0.009 0.001 TYR A 400 ARG 0.002 0.000 ARG B 394 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1792.27 seconds wall clock time: 33 minutes 30.88 seconds (2010.88 seconds total)