Starting phenix.real_space_refine on Wed Feb 14 21:29:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngh_12314/02_2024/7ngh_12314.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngh_12314/02_2024/7ngh_12314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngh_12314/02_2024/7ngh_12314.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngh_12314/02_2024/7ngh_12314.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngh_12314/02_2024/7ngh_12314.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ngh_12314/02_2024/7ngh_12314.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= 0.000 sd= 0.020 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 52 5.16 5 C 6785 2.51 5 N 1672 2.21 5 O 1806 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 225": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 7": "NH1" <-> "NH2" Residue "B ARG 8": "NH1" <-> "NH2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 294": "OE1" <-> "OE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "C ARG 8": "NH1" <-> "NH2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 173": "NH1" <-> "NH2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "D PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 60": "OD1" <-> "OD2" Residue "D ARG 76": "NH1" <-> "NH2" Residue "D TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 501": "OD1" <-> "OD2" Residue "C ASP 501": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10315 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3108 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain breaks: 1 Chain: "B" Number of atoms: 3178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3178 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain: "C" Number of atoms: 3108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3108 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain breaks: 1 Chain: "D" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 894 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 3, 'TRANS': 111} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 5.59, per 1000 atoms: 0.54 Number of scatterers: 10315 At special positions: 0 Unit cell: (102.212, 109.296, 103.224, 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 52 16.00 O 1806 8.00 N 1672 7.00 C 6785 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 100 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.29 Conformation dependent library (CDL) restraints added in 1.8 seconds 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2464 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 3 sheets defined 80.2% alpha, 3.6% 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 8 through 12 removed outlier: 3.732A pdb=" N TYR A 12 " --> pdb=" O TYR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 35 removed outlier: 3.816A pdb=" N GLY A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 45 Processing helix chain 'A' and resid 45 through 73 removed outlier: 3.663A pdb=" N GLY A 49 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 60 " --> pdb=" O LEU A 56 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N MET A 61 " --> pdb=" O LYS A 57 " (cutoff:3.500A) Proline residue: A 62 - end of helix Processing helix chain 'A' and resid 76 through 110 removed outlier: 3.643A pdb=" N TYR A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 143 through 151 Processing helix chain 'A' and resid 152 through 172 removed outlier: 3.933A pdb=" N ASN A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 222 removed outlier: 3.714A pdb=" N SER A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Proline residue: A 208 - end of helix Processing helix chain 'A' and resid 228 through 256 removed outlier: 3.948A pdb=" N LYS A 232 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE A 250 " --> pdb=" O VAL A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 278 removed outlier: 5.202A pdb=" N ASP A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N ALA A 270 " --> pdb=" O LYS A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 283 through 294 Processing helix chain 'A' and resid 298 through 313 removed outlier: 5.614A pdb=" N PHE A 304 " --> pdb=" O GLY A 300 " (cutoff:3.500A) Proline residue: A 307 - end of helix removed outlier: 3.712A pdb=" N THR A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 332 Processing helix chain 'A' and resid 337 through 355 removed outlier: 3.831A pdb=" N LEU A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU A 350 " --> pdb=" O LEU A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 373 removed outlier: 4.177A pdb=" N ALA A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N MET A 368 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 369 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 420 removed outlier: 3.593A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 393 " --> pdb=" O MET A 389 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ALA A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ILE A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY A 400 " --> pdb=" O ILE A 396 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET A 403 " --> pdb=" O MET A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.699A pdb=" N TRP A 428 " --> pdb=" O ASP A 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 13 through 36 Processing helix chain 'B' and resid 37 through 45 Processing helix chain 'B' and resid 45 through 58 removed outlier: 3.821A pdb=" N GLY B 49 " --> pdb=" O ILE B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 72 Processing helix chain 'B' and resid 76 through 110 removed outlier: 3.655A pdb=" N TYR B 90 " --> pdb=" O LYS B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 143 through 150 Processing helix chain 'B' and resid 152 through 172 removed outlier: 3.854A pdb=" N VAL B 156 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 222 Proline residue: B 208 - end of helix Processing helix chain 'B' and resid 228 through 257 removed outlier: 3.788A pdb=" N LYS B 232 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N PHE B 250 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE B 251 " --> pdb=" O ILE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 278 removed outlier: 5.860A pdb=" N ASP B 269 " --> pdb=" O ARG B 265 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ALA B 270 " --> pdb=" O LYS B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 283 through 294 Processing helix chain 'B' and resid 298 through 313 removed outlier: 3.583A pdb=" N PHE B 302 " --> pdb=" O ASP B 298 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE B 304 " --> pdb=" O GLY B 300 " (cutoff:3.500A) Proline residue: B 307 - end of helix removed outlier: 3.700A pdb=" N THR B 311 " --> pdb=" O PRO B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 333 Processing helix chain 'B' and resid 337 through 355 removed outlier: 4.443A pdb=" N LEU B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 349 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 removed outlier: 4.149A pdb=" N ALA B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N MET B 368 " --> pdb=" O ILE B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 392 removed outlier: 3.782A pdb=" N LEU B 385 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 386 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 420 removed outlier: 3.850A pdb=" N GLY B 400 " --> pdb=" O ILE B 396 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET B 403 " --> pdb=" O MET B 399 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 429 Processing helix chain 'C' and resid 13 through 36 Processing helix chain 'C' and resid 37 through 45 Processing helix chain 'C' and resid 45 through 58 removed outlier: 3.719A pdb=" N GLY C 49 " --> pdb=" O ILE C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.666A pdb=" N ILE C 75 " --> pdb=" O GLY C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 110 removed outlier: 3.596A pdb=" N TYR C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 143 through 151 Processing helix chain 'C' and resid 153 through 171 Processing helix chain 'C' and resid 175 through 222 Proline residue: C 208 - end of helix Processing helix chain 'C' and resid 228 through 256 removed outlier: 4.323A pdb=" N PHE C 250 " --> pdb=" O VAL C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 278 removed outlier: 5.639A pdb=" N ASP C 269 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ALA C 270 " --> pdb=" O LYS C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 283 through 295 Processing helix chain 'C' and resid 298 through 313 removed outlier: 3.540A pdb=" N PHE C 302 " --> pdb=" O ASP C 298 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N PHE C 304 " --> pdb=" O GLY C 300 " (cutoff:3.500A) Proline residue: C 307 - end of helix Processing helix chain 'C' and resid 314 through 333 removed outlier: 3.787A pdb=" N GLY C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 354 removed outlier: 4.569A pdb=" N LEU C 346 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 349 " --> pdb=" O VAL C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 365 Processing helix chain 'C' and resid 365 through 373 removed outlier: 3.873A pdb=" N VAL C 369 " --> pdb=" O MET C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 420 removed outlier: 4.025A pdb=" N LEU C 385 " --> pdb=" O SER C 381 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE C 393 " --> pdb=" O MET C 389 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY C 400 " --> pdb=" O ILE C 396 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N MET C 403 " --> pdb=" O MET C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 Processing helix chain 'D' and resid 66 through 69 Processing helix chain 'D' and resid 91 through 95 Processing sheet with id=AA1, first strand: chain 'D' and resid 8 through 11 Processing sheet with id=AA2, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.172A pdb=" N GLY D 14 " --> pdb=" O THR D 116 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET D 38 " --> pdb=" O ILE D 55 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N ARG D 42 " --> pdb=" O TRP D 51 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TRP D 51 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 14 through 16 removed outlier: 6.172A pdb=" N GLY D 14 " --> pdb=" O THR D 116 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2367 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: 3.16 Time building geometry restraints manager: 4.62 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: 3212 1.34 - 1.46: 1954 1.46 - 1.57: 5240 1.57 - 1.69: 0 1.69 - 1.81: 102 Bond restraints: 10508 Sorted by residual: bond pdb=" C VAL B 140 " pdb=" N PRO B 141 " ideal model delta sigma weight residual 1.334 1.314 0.019 1.11e-02 8.12e+03 3.07e+00 bond pdb=" C ASP A 259 " pdb=" N PRO A 260 " ideal model delta sigma weight residual 1.336 1.318 0.018 1.20e-02 6.94e+03 2.29e+00 bond pdb=" CA VAL B 358 " pdb=" CB VAL B 358 " ideal model delta sigma weight residual 1.546 1.534 0.013 8.80e-03 1.29e+04 2.06e+00 bond pdb=" N VAL C 226 " pdb=" CA VAL C 226 " ideal model delta sigma weight residual 1.474 1.456 0.019 1.57e-02 4.06e+03 1.41e+00 bond pdb=" CA ASN A 313 " pdb=" CB ASN A 313 " ideal model delta sigma weight residual 1.525 1.509 0.016 1.47e-02 4.63e+03 1.14e+00 ... (remaining 10503 not shown) Histogram of bond angle deviations from ideal: 98.77 - 105.83: 253 105.83 - 112.89: 5946 112.89 - 119.94: 3507 119.94 - 127.00: 4500 127.00 - 134.06: 89 Bond angle restraints: 14295 Sorted by residual: angle pdb=" N VAL C 227 " pdb=" CA VAL C 227 " pdb=" C VAL C 227 " ideal model delta sigma weight residual 113.71 109.09 4.62 9.50e-01 1.11e+00 2.36e+01 angle pdb=" N LEU B 59 " pdb=" CA LEU B 59 " pdb=" C LEU B 59 " ideal model delta sigma weight residual 114.62 110.76 3.86 1.14e+00 7.69e-01 1.15e+01 angle pdb=" C VAL B 246 " pdb=" N ILE B 247 " pdb=" CA ILE B 247 " ideal model delta sigma weight residual 122.63 118.76 3.87 1.19e+00 7.06e-01 1.06e+01 angle pdb=" N ALA A 207 " pdb=" CA ALA A 207 " pdb=" C ALA A 207 " ideal model delta sigma weight residual 109.81 116.42 -6.61 2.21e+00 2.05e-01 8.96e+00 angle pdb=" N ALA C 207 " pdb=" CA ALA C 207 " pdb=" C ALA C 207 " ideal model delta sigma weight residual 109.81 116.31 -6.50 2.21e+00 2.05e-01 8.66e+00 ... (remaining 14290 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5686 17.82 - 35.65: 427 35.65 - 53.47: 62 53.47 - 71.30: 7 71.30 - 89.12: 2 Dihedral angle restraints: 6184 sinusoidal: 2304 harmonic: 3880 Sorted by residual: dihedral pdb=" CA GLN B 128 " pdb=" C GLN B 128 " pdb=" N PRO B 129 " pdb=" CA PRO B 129 " ideal model delta harmonic sigma weight residual 180.00 157.98 22.02 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA LEU A 59 " pdb=" C LEU A 59 " pdb=" N VAL A 60 " pdb=" CA VAL A 60 " ideal model delta harmonic sigma weight residual -180.00 -160.00 -20.00 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CA VAL D 104 " pdb=" C VAL D 104 " pdb=" N GLY D 105 " pdb=" CA GLY D 105 " ideal model delta harmonic sigma weight residual -180.00 -160.77 -19.23 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 6181 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1003 0.028 - 0.055: 462 0.055 - 0.083: 178 0.083 - 0.110: 96 0.110 - 0.138: 20 Chirality restraints: 1759 Sorted by residual: chirality pdb=" CA ASN D 81 " pdb=" N ASN D 81 " pdb=" C ASN D 81 " pdb=" CB ASN D 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA PRO C 208 " pdb=" N PRO C 208 " pdb=" C PRO C 208 " pdb=" CB PRO C 208 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA PRO B 379 " pdb=" N PRO B 379 " pdb=" C PRO B 379 " pdb=" CB PRO B 379 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1756 not shown) Planarity restraints: 1760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 245 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" C ILE B 245 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE B 245 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 246 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 244 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.92e+00 pdb=" C GLN B 244 " 0.030 2.00e-02 2.50e+03 pdb=" O GLN B 244 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE B 245 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 128 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO B 129 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 129 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 129 " 0.023 5.00e-02 4.00e+02 ... (remaining 1757 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 618 2.71 - 3.26: 12742 3.26 - 3.81: 18665 3.81 - 4.35: 21741 4.35 - 4.90: 35412 Nonbonded interactions: 89178 Sorted by model distance: nonbonded pdb=" O ILE C 63 " pdb=" OG SER C 67 " model vdw 2.169 2.440 nonbonded pdb=" O ALA C 363 " pdb=" OH TYR C 387 " model vdw 2.177 2.440 nonbonded pdb=" O ALA A 363 " pdb=" OH TYR A 387 " model vdw 2.180 2.440 nonbonded pdb=" O ARG A 7 " pdb=" NH1 ARG A 7 " model vdw 2.180 2.520 nonbonded pdb=" O ILE B 63 " pdb=" OG SER B 67 " model vdw 2.183 2.440 ... (remaining 89173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 5 through 117 or resid 129 through 430 or resid 501)) selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.030 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 30.290 Find NCS groups from input model: 0.630 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: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 : 0.005 0.037 10508 Z= 0.349 Angle : 0.644 7.765 14295 Z= 0.366 Chirality : 0.040 0.138 1759 Planarity : 0.004 0.042 1760 Dihedral : 12.536 89.120 3717 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 6.64 % Favored : 93.36 % 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: -2.00 (0.21), residues: 1359 helix: -1.02 (0.15), residues: 1020 sheet: -2.42 (0.59), residues: 57 loop : -1.49 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 428 HIS 0.003 0.001 HIS D 39 PHE 0.016 0.001 PHE A 302 TYR 0.010 0.001 TYR A 169 ARG 0.003 0.000 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 LYS cc_start: 0.9378 (mtmm) cc_final: 0.9009 (mtmm) REVERT: A 243 LEU cc_start: 0.9719 (tp) cc_final: 0.9503 (tp) REVERT: A 271 MET cc_start: 0.9288 (mtp) cc_final: 0.9012 (mtm) REVERT: A 288 MET cc_start: 0.9318 (mtp) cc_final: 0.9080 (mtp) REVERT: A 321 GLN cc_start: 0.9521 (mm-40) cc_final: 0.9225 (mm110) REVERT: A 394 ASP cc_start: 0.9031 (p0) cc_final: 0.8710 (p0) REVERT: A 403 MET cc_start: 0.8974 (tmm) cc_final: 0.8105 (tmm) REVERT: B 50 ASP cc_start: 0.9078 (m-30) cc_final: 0.8751 (m-30) REVERT: B 180 LYS cc_start: 0.9560 (mmmm) cc_final: 0.9246 (mmmm) REVERT: B 271 MET cc_start: 0.9245 (mtp) cc_final: 0.8613 (mpp) REVERT: B 399 MET cc_start: 0.9225 (ptp) cc_final: 0.8956 (ptp) REVERT: C 97 MET cc_start: 0.8854 (tpp) cc_final: 0.8373 (tpp) REVERT: C 219 MET cc_start: 0.9598 (tpp) cc_final: 0.9048 (tpp) REVERT: C 244 GLN cc_start: 0.9505 (tm-30) cc_final: 0.8940 (tm-30) REVERT: C 271 MET cc_start: 0.9159 (mtm) cc_final: 0.8485 (mtp) REVERT: C 295 MET cc_start: 0.9319 (mmm) cc_final: 0.9013 (mmm) REVERT: C 321 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8845 (mm-40) REVERT: C 365 MET cc_start: 0.8896 (ptp) cc_final: 0.8677 (ptp) REVERT: C 403 MET cc_start: 0.9153 (tmm) cc_final: 0.8935 (tmm) REVERT: D 24 LEU cc_start: 0.9341 (mm) cc_final: 0.9134 (mm) REVERT: D 40 TRP cc_start: 0.9280 (m100) cc_final: 0.8381 (m100) REVERT: D 42 ARG cc_start: 0.9255 (ttp-170) cc_final: 0.8991 (ttp80) REVERT: D 55 ILE cc_start: 0.9258 (tt) cc_final: 0.9002 (tt) REVERT: D 84 TYR cc_start: 0.9112 (m-10) cc_final: 0.8891 (m-10) REVERT: D 85 LEU cc_start: 0.9517 (tt) cc_final: 0.9239 (tt) REVERT: D 99 TYR cc_start: 0.9452 (m-10) cc_final: 0.9212 (m-10) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2074 time to fit residues: 41.5084 Evaluate side-chains 110 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 ASN ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10508 Z= 0.199 Angle : 0.634 8.523 14295 Z= 0.320 Chirality : 0.041 0.182 1759 Planarity : 0.004 0.040 1760 Dihedral : 4.504 38.605 1470 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.55 % Allowed : 13.09 % Favored : 86.36 % 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: -0.05 (0.23), residues: 1359 helix: 0.46 (0.16), residues: 1047 sheet: -2.30 (0.60), residues: 59 loop : -1.10 (0.43), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 428 HIS 0.003 0.001 HIS D 39 PHE 0.026 0.001 PHE A 302 TYR 0.012 0.001 TYR D 63 ARG 0.001 0.000 ARG D 101 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 136 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9278 (m-30) cc_final: 0.8992 (m-30) REVERT: A 150 LYS cc_start: 0.9275 (mtmm) cc_final: 0.8941 (mtmm) REVERT: A 271 MET cc_start: 0.9253 (mtp) cc_final: 0.8694 (mtt) REVERT: A 321 GLN cc_start: 0.9588 (mm-40) cc_final: 0.9269 (mm110) REVERT: A 403 MET cc_start: 0.8845 (tmm) cc_final: 0.7995 (tmm) REVERT: B 50 ASP cc_start: 0.9085 (m-30) cc_final: 0.8589 (m-30) REVERT: B 171 MET cc_start: 0.8827 (mmp) cc_final: 0.8392 (mmm) REVERT: B 180 LYS cc_start: 0.9543 (mmmm) cc_final: 0.9217 (mmmm) REVERT: B 271 MET cc_start: 0.9223 (mtp) cc_final: 0.8701 (mtp) REVERT: B 368 MET cc_start: 0.8958 (tmm) cc_final: 0.8676 (tmm) REVERT: B 399 MET cc_start: 0.9086 (ptp) cc_final: 0.8715 (ptp) REVERT: C 97 MET cc_start: 0.8901 (tpp) cc_final: 0.8543 (tpp) REVERT: C 174 ASN cc_start: 0.9256 (p0) cc_final: 0.8987 (p0) REVERT: C 219 MET cc_start: 0.9520 (tpp) cc_final: 0.9027 (tpp) REVERT: C 244 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9031 (tm-30) REVERT: C 271 MET cc_start: 0.9025 (mtm) cc_final: 0.8381 (mtp) REVERT: C 321 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8757 (mm110) REVERT: C 365 MET cc_start: 0.8934 (ptp) cc_final: 0.8539 (ptp) REVERT: D 24 LEU cc_start: 0.9442 (mm) cc_final: 0.9073 (mm) REVERT: D 40 TRP cc_start: 0.9258 (m100) cc_final: 0.8099 (m100) REVERT: D 55 ILE cc_start: 0.9287 (tt) cc_final: 0.8818 (tt) REVERT: D 56 GLU cc_start: 0.8755 (pt0) cc_final: 0.8282 (pt0) REVERT: D 69 LYS cc_start: 0.9440 (mmmt) cc_final: 0.9086 (mmmt) REVERT: D 85 LEU cc_start: 0.9359 (tt) cc_final: 0.8887 (tt) REVERT: D 99 TYR cc_start: 0.9445 (m-10) cc_final: 0.9204 (m-10) REVERT: D 108 TYR cc_start: 0.9346 (m-10) cc_final: 0.9023 (m-10) outliers start: 6 outliers final: 1 residues processed: 141 average time/residue: 0.1987 time to fit residues: 41.5066 Evaluate side-chains 120 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 119 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 122 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10508 Z= 0.257 Angle : 0.632 9.031 14295 Z= 0.319 Chirality : 0.041 0.179 1759 Planarity : 0.004 0.051 1760 Dihedral : 4.487 40.647 1470 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.92 % Allowed : 15.02 % Favored : 84.06 % 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: 0.55 (0.23), residues: 1359 helix: 0.94 (0.16), residues: 1038 sheet: -2.16 (0.60), residues: 59 loop : -1.02 (0.43), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 51 HIS 0.003 0.001 HIS D 39 PHE 0.024 0.001 PHE A 302 TYR 0.011 0.001 TYR C 387 ARG 0.004 0.000 ARG D 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 128 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9287 (m-30) cc_final: 0.9084 (m-30) REVERT: A 97 MET cc_start: 0.9493 (mmm) cc_final: 0.9288 (mmt) REVERT: A 150 LYS cc_start: 0.9200 (mtmm) cc_final: 0.8908 (mtmm) REVERT: A 271 MET cc_start: 0.9267 (mtp) cc_final: 0.8712 (mtt) REVERT: A 321 GLN cc_start: 0.9559 (mm-40) cc_final: 0.9244 (mm110) REVERT: A 403 MET cc_start: 0.8857 (tmm) cc_final: 0.7982 (tmm) REVERT: B 50 ASP cc_start: 0.9065 (m-30) cc_final: 0.8516 (m-30) REVERT: B 171 MET cc_start: 0.8848 (mmp) cc_final: 0.8411 (mmm) REVERT: B 180 LYS cc_start: 0.9542 (mmmm) cc_final: 0.9226 (mmmm) REVERT: B 271 MET cc_start: 0.9275 (mtp) cc_final: 0.8763 (mtp) REVERT: B 371 GLN cc_start: 0.9137 (pp30) cc_final: 0.8933 (pp30) REVERT: C 97 MET cc_start: 0.8917 (tpp) cc_final: 0.8464 (tpp) REVERT: C 219 MET cc_start: 0.9545 (tpp) cc_final: 0.8879 (tpp) REVERT: C 244 GLN cc_start: 0.9536 (tm-30) cc_final: 0.9067 (tm-30) REVERT: C 271 MET cc_start: 0.8958 (mtm) cc_final: 0.7622 (mtp) REVERT: C 321 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8582 (mm110) REVERT: C 365 MET cc_start: 0.8904 (ptp) cc_final: 0.8627 (ptp) REVERT: C 403 MET cc_start: 0.9067 (tmm) cc_final: 0.8742 (tpp) REVERT: D 24 LEU cc_start: 0.9353 (mm) cc_final: 0.8976 (mm) REVERT: D 40 TRP cc_start: 0.9219 (m100) cc_final: 0.8112 (m100) REVERT: D 55 ILE cc_start: 0.9284 (tt) cc_final: 0.8908 (tt) REVERT: D 69 LYS cc_start: 0.9442 (mmmt) cc_final: 0.9192 (mmmt) REVERT: D 72 PHE cc_start: 0.9402 (m-80) cc_final: 0.9178 (m-80) REVERT: D 85 LEU cc_start: 0.9187 (tt) cc_final: 0.8928 (tt) REVERT: D 99 TYR cc_start: 0.9424 (m-10) cc_final: 0.9126 (m-10) REVERT: D 108 TYR cc_start: 0.9269 (m-10) cc_final: 0.8914 (m-80) outliers start: 10 outliers final: 4 residues processed: 136 average time/residue: 0.2309 time to fit residues: 46.7387 Evaluate side-chains 116 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 112 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 288 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 HIS A 341 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10508 Z= 0.188 Angle : 0.613 9.396 14295 Z= 0.306 Chirality : 0.041 0.194 1759 Planarity : 0.004 0.056 1760 Dihedral : 4.368 39.232 1470 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.84 % Allowed : 16.04 % Favored : 82.12 % 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: 0.90 (0.24), residues: 1359 helix: 1.17 (0.16), residues: 1035 sheet: -1.85 (0.63), residues: 59 loop : -0.84 (0.42), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 51 HIS 0.002 0.001 HIS D 39 PHE 0.019 0.001 PHE A 302 TYR 0.010 0.001 TYR C 387 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9286 (m-30) cc_final: 0.8896 (m-30) REVERT: A 150 LYS cc_start: 0.9148 (mtmm) cc_final: 0.8878 (mtmm) REVERT: A 271 MET cc_start: 0.9258 (mtp) cc_final: 0.8702 (mtt) REVERT: A 321 GLN cc_start: 0.9571 (mm-40) cc_final: 0.9248 (mm110) REVERT: A 394 ASP cc_start: 0.8997 (p0) cc_final: 0.8628 (p0) REVERT: A 403 MET cc_start: 0.8824 (tmm) cc_final: 0.7932 (tmm) REVERT: B 30 LEU cc_start: 0.9841 (OUTLIER) cc_final: 0.9623 (mm) REVERT: B 50 ASP cc_start: 0.9064 (m-30) cc_final: 0.8469 (m-30) REVERT: B 171 MET cc_start: 0.8787 (mmp) cc_final: 0.8410 (mmm) REVERT: B 180 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9210 (mmmm) REVERT: B 271 MET cc_start: 0.9262 (mtp) cc_final: 0.8761 (mtp) REVERT: B 371 GLN cc_start: 0.9147 (pp30) cc_final: 0.8929 (pp30) REVERT: C 97 MET cc_start: 0.8952 (tpp) cc_final: 0.8466 (tpp) REVERT: C 219 MET cc_start: 0.9539 (tpp) cc_final: 0.8953 (tpp) REVERT: C 244 GLN cc_start: 0.9515 (tm-30) cc_final: 0.9049 (tm-30) REVERT: C 271 MET cc_start: 0.8966 (mtm) cc_final: 0.7826 (mtt) REVERT: C 295 MET cc_start: 0.9401 (mmp) cc_final: 0.9134 (mmp) REVERT: C 403 MET cc_start: 0.9007 (tmm) cc_final: 0.8786 (tpt) REVERT: C 406 VAL cc_start: 0.9501 (p) cc_final: 0.9179 (p) REVERT: D 24 LEU cc_start: 0.9332 (mm) cc_final: 0.8959 (mm) REVERT: D 40 TRP cc_start: 0.9126 (m100) cc_final: 0.7962 (m100) REVERT: D 55 ILE cc_start: 0.9304 (tt) cc_final: 0.8928 (tt) REVERT: D 72 PHE cc_start: 0.9396 (m-80) cc_final: 0.9143 (m-80) REVERT: D 85 LEU cc_start: 0.9201 (tt) cc_final: 0.8907 (tt) REVERT: D 99 TYR cc_start: 0.9369 (m-10) cc_final: 0.9052 (m-10) REVERT: D 108 TYR cc_start: 0.9260 (m-10) cc_final: 0.8967 (m-10) outliers start: 20 outliers final: 7 residues processed: 146 average time/residue: 0.2044 time to fit residues: 44.1939 Evaluate side-chains 126 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 118 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 288 MET Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 ASN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN D 78 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10508 Z= 0.177 Angle : 0.642 12.550 14295 Z= 0.313 Chirality : 0.040 0.185 1759 Planarity : 0.004 0.056 1760 Dihedral : 4.311 34.252 1470 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 1.94 % Allowed : 18.06 % Favored : 80.00 % 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: 1.03 (0.23), residues: 1359 helix: 1.24 (0.16), residues: 1031 sheet: -1.50 (0.63), residues: 59 loop : -0.73 (0.43), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 106 HIS 0.003 0.001 HIS D 39 PHE 0.016 0.001 PHE A 302 TYR 0.012 0.001 TYR C 387 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9280 (m-30) cc_final: 0.8996 (m-30) REVERT: A 97 MET cc_start: 0.9516 (mmm) cc_final: 0.9274 (mmt) REVERT: A 150 LYS cc_start: 0.9158 (mtmm) cc_final: 0.8864 (mtmm) REVERT: A 271 MET cc_start: 0.9255 (mtp) cc_final: 0.8972 (mtm) REVERT: A 321 GLN cc_start: 0.9573 (mm-40) cc_final: 0.9234 (mm110) REVERT: A 394 ASP cc_start: 0.8934 (p0) cc_final: 0.8593 (p0) REVERT: A 403 MET cc_start: 0.8828 (tmm) cc_final: 0.7934 (tmm) REVERT: B 50 ASP cc_start: 0.9056 (m-30) cc_final: 0.8451 (m-30) REVERT: B 171 MET cc_start: 0.8768 (mmp) cc_final: 0.8398 (mmm) REVERT: B 180 LYS cc_start: 0.9510 (mmmm) cc_final: 0.9204 (mmmm) REVERT: B 271 MET cc_start: 0.9224 (mtp) cc_final: 0.8763 (mtp) REVERT: B 368 MET cc_start: 0.9051 (tmm) cc_final: 0.8694 (tmm) REVERT: C 30 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9111 (tt) REVERT: C 97 MET cc_start: 0.8960 (tpp) cc_final: 0.8698 (tpp) REVERT: C 219 MET cc_start: 0.9534 (tpp) cc_final: 0.9140 (tpt) REVERT: C 244 GLN cc_start: 0.9508 (tm-30) cc_final: 0.9055 (tm-30) REVERT: C 271 MET cc_start: 0.8994 (mtm) cc_final: 0.7962 (mtt) REVERT: C 365 MET cc_start: 0.9189 (ptp) cc_final: 0.8988 (ptm) REVERT: D 24 LEU cc_start: 0.9291 (mm) cc_final: 0.8944 (mm) REVERT: D 40 TRP cc_start: 0.9035 (m100) cc_final: 0.7632 (m100) REVERT: D 55 ILE cc_start: 0.9280 (tt) cc_final: 0.8720 (tt) REVERT: D 69 LYS cc_start: 0.9438 (mmmt) cc_final: 0.9000 (mmmt) REVERT: D 72 PHE cc_start: 0.9414 (m-80) cc_final: 0.9130 (m-80) REVERT: D 85 LEU cc_start: 0.9172 (tt) cc_final: 0.8873 (tt) REVERT: D 99 TYR cc_start: 0.9352 (m-10) cc_final: 0.9126 (m-10) REVERT: D 108 TYR cc_start: 0.9220 (m-10) cc_final: 0.8967 (m-10) outliers start: 21 outliers final: 6 residues processed: 155 average time/residue: 0.1882 time to fit residues: 43.7075 Evaluate side-chains 136 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 129 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10508 Z= 0.214 Angle : 0.662 10.314 14295 Z= 0.324 Chirality : 0.041 0.207 1759 Planarity : 0.004 0.056 1760 Dihedral : 4.274 35.106 1470 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.66 % Allowed : 19.72 % Favored : 78.62 % 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: 1.11 (0.23), residues: 1359 helix: 1.26 (0.16), residues: 1037 sheet: -1.37 (0.63), residues: 59 loop : -0.65 (0.43), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 106 HIS 0.002 0.001 HIS D 39 PHE 0.015 0.001 PHE A 302 TYR 0.011 0.001 TYR C 387 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 138 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9285 (m-30) cc_final: 0.8982 (m-30) REVERT: A 271 MET cc_start: 0.9269 (mtp) cc_final: 0.8996 (mtm) REVERT: A 321 GLN cc_start: 0.9545 (mm-40) cc_final: 0.9228 (mm110) REVERT: A 394 ASP cc_start: 0.8955 (p0) cc_final: 0.8599 (p0) REVERT: A 403 MET cc_start: 0.8840 (tmm) cc_final: 0.7931 (tmm) REVERT: B 50 ASP cc_start: 0.9064 (m-30) cc_final: 0.8449 (m-30) REVERT: B 171 MET cc_start: 0.8797 (mmp) cc_final: 0.8327 (mmm) REVERT: B 180 LYS cc_start: 0.9512 (mmmm) cc_final: 0.9205 (mmmm) REVERT: B 271 MET cc_start: 0.9222 (mtp) cc_final: 0.8750 (mtp) REVERT: B 321 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8861 (mm-40) REVERT: B 368 MET cc_start: 0.9035 (tmm) cc_final: 0.8701 (tmm) REVERT: C 97 MET cc_start: 0.8981 (tpp) cc_final: 0.8464 (tpp) REVERT: C 219 MET cc_start: 0.9541 (tpp) cc_final: 0.8938 (tpp) REVERT: C 244 GLN cc_start: 0.9501 (tm-30) cc_final: 0.9052 (tm-30) REVERT: C 271 MET cc_start: 0.8950 (mtm) cc_final: 0.8213 (mtp) REVERT: D 6 VAL cc_start: 0.9072 (OUTLIER) cc_final: 0.8675 (p) REVERT: D 24 LEU cc_start: 0.9275 (mm) cc_final: 0.8949 (mm) REVERT: D 36 GLN cc_start: 0.8977 (pt0) cc_final: 0.8353 (pm20) REVERT: D 40 TRP cc_start: 0.9076 (m100) cc_final: 0.7707 (m100) REVERT: D 55 ILE cc_start: 0.9044 (tt) cc_final: 0.8744 (tt) REVERT: D 72 PHE cc_start: 0.9417 (m-80) cc_final: 0.9146 (m-80) REVERT: D 85 LEU cc_start: 0.9189 (tt) cc_final: 0.8884 (tt) REVERT: D 99 TYR cc_start: 0.9357 (m-10) cc_final: 0.9119 (m-10) REVERT: D 108 TYR cc_start: 0.9210 (m-10) cc_final: 0.8921 (m-10) outliers start: 18 outliers final: 8 residues processed: 153 average time/residue: 0.1959 time to fit residues: 44.5202 Evaluate side-chains 134 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 78 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 0.0170 chunk 72 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 80 optimal weight: 0.7980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10508 Z= 0.173 Angle : 0.674 11.198 14295 Z= 0.323 Chirality : 0.041 0.202 1759 Planarity : 0.004 0.057 1760 Dihedral : 4.232 31.746 1470 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.75 % Allowed : 20.55 % Favored : 77.70 % 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: 1.12 (0.23), residues: 1359 helix: 1.25 (0.16), residues: 1038 sheet: -1.19 (0.67), residues: 54 loop : -0.58 (0.43), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 51 HIS 0.001 0.000 HIS D 39 PHE 0.015 0.001 PHE A 302 TYR 0.011 0.001 TYR C 387 ARG 0.002 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9287 (m-30) cc_final: 0.8979 (m-30) REVERT: A 97 MET cc_start: 0.9525 (mmm) cc_final: 0.9272 (mmt) REVERT: A 321 GLN cc_start: 0.9560 (mm-40) cc_final: 0.9236 (mm110) REVERT: A 365 MET cc_start: 0.9032 (tmm) cc_final: 0.8787 (tmm) REVERT: A 394 ASP cc_start: 0.8924 (p0) cc_final: 0.8546 (p0) REVERT: A 403 MET cc_start: 0.8792 (tmm) cc_final: 0.8295 (tmm) REVERT: B 50 ASP cc_start: 0.9040 (m-30) cc_final: 0.8412 (m-30) REVERT: B 167 ILE cc_start: 0.9723 (mt) cc_final: 0.9245 (tt) REVERT: B 171 MET cc_start: 0.8747 (mmp) cc_final: 0.8311 (mmm) REVERT: B 180 LYS cc_start: 0.9500 (mmmm) cc_final: 0.9200 (mmmm) REVERT: B 219 MET cc_start: 0.8613 (ttp) cc_final: 0.8079 (tmm) REVERT: B 271 MET cc_start: 0.9202 (mtp) cc_final: 0.8762 (mtp) REVERT: B 368 MET cc_start: 0.9041 (tmm) cc_final: 0.8699 (tmm) REVERT: C 97 MET cc_start: 0.8952 (tpp) cc_final: 0.8640 (tpp) REVERT: C 219 MET cc_start: 0.9532 (tpp) cc_final: 0.9122 (tpt) REVERT: C 244 GLN cc_start: 0.9488 (tm-30) cc_final: 0.9075 (tm-30) REVERT: C 271 MET cc_start: 0.8918 (mtm) cc_final: 0.8251 (mtp) REVERT: C 306 LEU cc_start: 0.9659 (OUTLIER) cc_final: 0.9420 (mm) REVERT: D 6 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8581 (p) REVERT: D 24 LEU cc_start: 0.9246 (mm) cc_final: 0.8908 (mm) REVERT: D 40 TRP cc_start: 0.9025 (m100) cc_final: 0.7736 (m100) REVERT: D 85 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8882 (tt) REVERT: D 99 TYR cc_start: 0.9351 (m-10) cc_final: 0.9043 (m-10) REVERT: D 108 TYR cc_start: 0.9217 (m-10) cc_final: 0.8982 (m-10) outliers start: 19 outliers final: 9 residues processed: 156 average time/residue: 0.1999 time to fit residues: 45.8985 Evaluate side-chains 138 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 0.9990 chunk 12 optimal weight: 0.0170 chunk 102 optimal weight: 0.8980 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 8.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10508 Z= 0.183 Angle : 0.694 11.391 14295 Z= 0.332 Chirality : 0.041 0.200 1759 Planarity : 0.004 0.056 1760 Dihedral : 4.213 26.645 1470 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.12 % Allowed : 21.29 % Favored : 76.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.23), residues: 1359 helix: 1.25 (0.16), residues: 1041 sheet: -1.20 (0.66), residues: 54 loop : -0.54 (0.43), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 51 HIS 0.001 0.000 HIS D 39 PHE 0.017 0.001 PHE A 302 TYR 0.012 0.001 TYR C 387 ARG 0.004 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 141 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9283 (m-30) cc_final: 0.8964 (m-30) REVERT: A 97 MET cc_start: 0.9504 (mmm) cc_final: 0.9266 (mmt) REVERT: A 150 LYS cc_start: 0.9274 (mtpp) cc_final: 0.8897 (mtmm) REVERT: A 271 MET cc_start: 0.9202 (mtm) cc_final: 0.8883 (mtt) REVERT: A 321 GLN cc_start: 0.9562 (mm-40) cc_final: 0.9235 (mm110) REVERT: A 365 MET cc_start: 0.9033 (tmm) cc_final: 0.8781 (tmm) REVERT: A 394 ASP cc_start: 0.8921 (p0) cc_final: 0.8576 (p0) REVERT: A 403 MET cc_start: 0.8806 (tmm) cc_final: 0.8307 (tmm) REVERT: B 50 ASP cc_start: 0.9026 (m-30) cc_final: 0.8384 (m-30) REVERT: B 171 MET cc_start: 0.8733 (mmp) cc_final: 0.8274 (mmm) REVERT: B 180 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9211 (mmmm) REVERT: B 219 MET cc_start: 0.8630 (ttp) cc_final: 0.8195 (tmm) REVERT: B 271 MET cc_start: 0.8892 (mtp) cc_final: 0.8351 (mtt) REVERT: B 368 MET cc_start: 0.9049 (tmm) cc_final: 0.8707 (tmm) REVERT: C 61 MET cc_start: 0.7796 (mtp) cc_final: 0.7535 (mtp) REVERT: C 97 MET cc_start: 0.8971 (tpp) cc_final: 0.8691 (tpp) REVERT: C 174 ASN cc_start: 0.9306 (p0) cc_final: 0.9032 (p0) REVERT: C 219 MET cc_start: 0.9546 (tpp) cc_final: 0.9082 (tpt) REVERT: C 244 GLN cc_start: 0.9459 (tm-30) cc_final: 0.9083 (tm-30) REVERT: C 271 MET cc_start: 0.8925 (mtm) cc_final: 0.8201 (mtt) REVERT: C 306 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9416 (mm) REVERT: C 389 MET cc_start: 0.9472 (ptm) cc_final: 0.9125 (ppp) REVERT: C 403 MET cc_start: 0.9202 (tpt) cc_final: 0.8940 (tpt) REVERT: D 24 LEU cc_start: 0.9225 (mm) cc_final: 0.8885 (mm) REVERT: D 40 TRP cc_start: 0.8997 (m100) cc_final: 0.7873 (m100) REVERT: D 85 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8854 (tt) REVERT: D 99 TYR cc_start: 0.9311 (m-10) cc_final: 0.8997 (m-10) REVERT: B 501 ASP cc_start: 0.6598 (m-30) cc_final: 0.6114 (m-30) outliers start: 23 outliers final: 15 residues processed: 157 average time/residue: 0.1834 time to fit residues: 43.2938 Evaluate side-chains 147 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 120 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 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 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 GLN D 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10508 Z= 0.206 Angle : 0.712 10.978 14295 Z= 0.338 Chirality : 0.043 0.324 1759 Planarity : 0.004 0.056 1760 Dihedral : 4.147 25.467 1470 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.21 % Allowed : 21.47 % Favored : 76.31 % 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: 1.15 (0.23), residues: 1359 helix: 1.28 (0.16), residues: 1041 sheet: -1.04 (0.67), residues: 54 loop : -0.72 (0.42), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 51 HIS 0.001 0.000 HIS D 39 PHE 0.013 0.001 PHE A 302 TYR 0.014 0.001 TYR C 387 ARG 0.002 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 2.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9289 (m-30) cc_final: 0.8971 (m-30) REVERT: A 97 MET cc_start: 0.9486 (mmm) cc_final: 0.9260 (mmt) REVERT: A 150 LYS cc_start: 0.9266 (mtpp) cc_final: 0.8892 (mtmm) REVERT: A 271 MET cc_start: 0.9219 (mtm) cc_final: 0.8892 (mtt) REVERT: A 321 GLN cc_start: 0.9557 (mm-40) cc_final: 0.9246 (mm110) REVERT: A 365 MET cc_start: 0.9065 (tmm) cc_final: 0.8606 (tmm) REVERT: A 394 ASP cc_start: 0.8935 (p0) cc_final: 0.8592 (p0) REVERT: A 403 MET cc_start: 0.8825 (tmm) cc_final: 0.8308 (tmm) REVERT: B 50 ASP cc_start: 0.9050 (m-30) cc_final: 0.8408 (m-30) REVERT: B 61 MET cc_start: 0.8507 (mmt) cc_final: 0.8194 (mmt) REVERT: B 128 GLN cc_start: 0.8357 (mp10) cc_final: 0.8132 (mp10) REVERT: B 171 MET cc_start: 0.8730 (mmp) cc_final: 0.8197 (mmm) REVERT: B 180 LYS cc_start: 0.9509 (mmmm) cc_final: 0.9220 (mmmm) REVERT: B 219 MET cc_start: 0.8635 (ttp) cc_final: 0.8259 (tmm) REVERT: B 271 MET cc_start: 0.8934 (mtp) cc_final: 0.8608 (mtm) REVERT: B 368 MET cc_start: 0.9043 (tmm) cc_final: 0.8707 (tmm) REVERT: C 97 MET cc_start: 0.8984 (tpp) cc_final: 0.8679 (tpp) REVERT: C 219 MET cc_start: 0.9554 (tpp) cc_final: 0.9055 (tpt) REVERT: C 244 GLN cc_start: 0.9460 (tm-30) cc_final: 0.9089 (tm-30) REVERT: C 271 MET cc_start: 0.8943 (mtm) cc_final: 0.8109 (mtp) REVERT: C 306 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9450 (mm) REVERT: C 389 MET cc_start: 0.9471 (ptm) cc_final: 0.9126 (ppp) REVERT: C 403 MET cc_start: 0.9227 (tpt) cc_final: 0.8979 (tpt) REVERT: D 24 LEU cc_start: 0.9246 (mm) cc_final: 0.8907 (mm) REVERT: D 40 TRP cc_start: 0.9059 (m100) cc_final: 0.7831 (m100) REVERT: D 85 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8832 (tt) REVERT: D 99 TYR cc_start: 0.9337 (m-10) cc_final: 0.9003 (m-10) REVERT: D 108 TYR cc_start: 0.8539 (m-10) cc_final: 0.8314 (m-10) REVERT: B 501 ASP cc_start: 0.6701 (m-30) cc_final: 0.6236 (m-30) outliers start: 24 outliers final: 16 residues processed: 149 average time/residue: 0.1928 time to fit residues: 43.2006 Evaluate side-chains 144 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain D residue 7 GLN Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 78 ASN Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 0.0770 chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 134 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 overall best weight: 1.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10508 Z= 0.200 Angle : 0.725 13.084 14295 Z= 0.343 Chirality : 0.043 0.305 1759 Planarity : 0.004 0.056 1760 Dihedral : 4.166 25.901 1470 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.66 % Allowed : 22.86 % Favored : 75.48 % 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: 1.19 (0.23), residues: 1359 helix: 1.31 (0.16), residues: 1037 sheet: -1.02 (0.67), residues: 54 loop : -0.69 (0.42), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 51 HIS 0.001 0.000 HIS D 39 PHE 0.017 0.001 PHE A 302 TYR 0.013 0.001 TYR C 387 ARG 0.003 0.000 ARG B 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 131 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9285 (m-30) cc_final: 0.8964 (m-30) REVERT: A 97 MET cc_start: 0.9484 (mmm) cc_final: 0.9258 (mmt) REVERT: A 150 LYS cc_start: 0.9245 (mtpp) cc_final: 0.8853 (mtmm) REVERT: A 271 MET cc_start: 0.9126 (mtm) cc_final: 0.8801 (mtt) REVERT: A 321 GLN cc_start: 0.9558 (mm-40) cc_final: 0.9241 (mm110) REVERT: A 365 MET cc_start: 0.9067 (tmm) cc_final: 0.8613 (tmm) REVERT: A 394 ASP cc_start: 0.8930 (p0) cc_final: 0.8572 (p0) REVERT: A 403 MET cc_start: 0.8818 (tmm) cc_final: 0.8301 (tmm) REVERT: B 50 ASP cc_start: 0.9033 (m-30) cc_final: 0.8385 (m-30) REVERT: B 171 MET cc_start: 0.8737 (mmp) cc_final: 0.8228 (mmm) REVERT: B 180 LYS cc_start: 0.9514 (mmmm) cc_final: 0.9222 (mmmm) REVERT: B 219 MET cc_start: 0.8596 (ttp) cc_final: 0.8268 (tmm) REVERT: B 271 MET cc_start: 0.8914 (mtp) cc_final: 0.8599 (mtm) REVERT: B 368 MET cc_start: 0.9026 (tmm) cc_final: 0.8700 (tmm) REVERT: C 61 MET cc_start: 0.7685 (mtp) cc_final: 0.7432 (mtp) REVERT: C 97 MET cc_start: 0.8984 (tpp) cc_final: 0.8676 (tpp) REVERT: C 174 ASN cc_start: 0.9313 (p0) cc_final: 0.9039 (p0) REVERT: C 219 MET cc_start: 0.9546 (tpp) cc_final: 0.9012 (tpt) REVERT: C 244 GLN cc_start: 0.9455 (tm-30) cc_final: 0.9092 (tm-30) REVERT: C 271 MET cc_start: 0.8943 (mtm) cc_final: 0.8112 (mtp) REVERT: C 306 LEU cc_start: 0.9677 (OUTLIER) cc_final: 0.9430 (mm) REVERT: C 389 MET cc_start: 0.9462 (ptm) cc_final: 0.9116 (ppp) REVERT: C 403 MET cc_start: 0.9217 (tpt) cc_final: 0.8971 (tpt) REVERT: D 24 LEU cc_start: 0.9250 (mm) cc_final: 0.8913 (mm) REVERT: D 40 TRP cc_start: 0.9067 (m100) cc_final: 0.7841 (m100) REVERT: D 85 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8852 (tt) REVERT: D 99 TYR cc_start: 0.9355 (m-10) cc_final: 0.9013 (m-10) REVERT: D 108 TYR cc_start: 0.8643 (m-10) cc_final: 0.8386 (m-10) REVERT: B 501 ASP cc_start: 0.6665 (m-30) cc_final: 0.6210 (m-30) outliers start: 18 outliers final: 14 residues processed: 143 average time/residue: 0.1914 time to fit residues: 41.1643 Evaluate side-chains 142 residues out of total 1085 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 358 VAL Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain D residue 80 LYS Chi-restraints excluded: chain D residue 85 LEU Chi-restraints excluded: chain D residue 87 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 0.0470 chunk 98 optimal weight: 2.9990 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.048537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.038520 restraints weight = 57984.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.039848 restraints weight = 27962.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.040746 restraints weight = 17157.342| |-----------------------------------------------------------------------------| r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10508 Z= 0.186 Angle : 0.719 14.161 14295 Z= 0.339 Chirality : 0.042 0.291 1759 Planarity : 0.004 0.057 1760 Dihedral : 4.107 26.444 1470 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.57 % Allowed : 22.86 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.23), residues: 1359 helix: 1.26 (0.16), residues: 1035 sheet: -0.97 (0.68), residues: 54 loop : -0.64 (0.42), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 51 HIS 0.001 0.000 HIS D 39 PHE 0.013 0.001 PHE B 302 TYR 0.012 0.001 TYR C 387 ARG 0.003 0.000 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1888.20 seconds wall clock time: 35 minutes 28.31 seconds (2128.31 seconds total)