Starting phenix.real_space_refine on Sat Aug 23 08:11:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5y_33733/08_2025/8j5y_33733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5y_33733/08_2025/8j5y_33733.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j5y_33733/08_2025/8j5y_33733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5y_33733/08_2025/8j5y_33733.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j5y_33733/08_2025/8j5y_33733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5y_33733/08_2025/8j5y_33733.map" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.009 sd= 0.090 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 27 5.16 5 C 7006 2.51 5 N 1856 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10905 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4122 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 9, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 489} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 161 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 139 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 3, 'PHE:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 3, 'TYR:plan': 2, 'ASP:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "C" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1362 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 2, 'PTRANS': 10, 'TRANS': 153} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1352 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 154} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4069 Classifications: {'peptide': 528} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'CIS': 9, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 488} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 215 Unresolved non-hydrogen angles: 272 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ASN:plan1': 4, 'TYR:plan': 4, 'GLU:plan': 8, 'GLN:plan1': 4, 'PHE:plan': 5, 'ARG:plan': 3, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 144 Time building chain proxies: 2.56, per 1000 atoms: 0.23 Number of scatterers: 10905 At special positions: 0 Unit cell: (110.7, 140.22, 86.92, 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 27 16.00 O 2016 8.00 N 1856 7.00 C 7006 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 - 3.00 Amino acid : True - 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: 1.01 Conformation dependent library (CDL) restraints added in 389.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 33.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 174 through 176 No H-bonds generated for 'chain 'A' and resid 174 through 176' Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.094A pdb=" N LEU A 181 " --> pdb=" O GLU A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 removed outlier: 4.280A pdb=" N TYR A 187 " --> pdb=" O ASP A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 235 removed outlier: 3.884A pdb=" N THR A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) Proline residue: A 225 - end of helix removed outlier: 3.533A pdb=" N LEU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS A 234 " --> pdb=" O TYR A 230 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 270 Processing helix chain 'A' and resid 329 through 332 removed outlier: 3.636A pdb=" N ASP A 332 " --> pdb=" O SER A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 329 through 332' Processing helix chain 'A' and resid 333 through 351 removed outlier: 3.602A pdb=" N LEU A 344 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N HIS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 381 removed outlier: 3.619A pdb=" N ILE A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N HIS A 375 " --> pdb=" O GLN A 371 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ARG A 378 " --> pdb=" O ASN A 374 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LYS A 379 " --> pdb=" O HIS A 375 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A 381 " --> pdb=" O ILE A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 435 through 449 removed outlier: 3.506A pdb=" N THR A 441 " --> pdb=" O SER A 437 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE A 442 " --> pdb=" O GLN A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 494 Processing helix chain 'A' and resid 495 through 500 Processing helix chain 'A' and resid 562 through 567 removed outlier: 3.619A pdb=" N GLN A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'C' and resid 11 through 23 removed outlier: 3.643A pdb=" N LEU C 15 " --> pdb=" O ASP C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 48 Processing helix chain 'C' and resid 53 through 69 Processing helix chain 'C' and resid 81 through 101 removed outlier: 3.634A pdb=" N ARG C 85 " --> pdb=" O SER C 81 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL C 89 " --> pdb=" O ARG C 85 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N MET C 90 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 99 " --> pdb=" O PHE C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 120 Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 127 through 134 removed outlier: 3.854A pdb=" N GLY C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N THR C 133 " --> pdb=" O ARG C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 159 removed outlier: 3.568A pdb=" N SER C 153 " --> pdb=" O ASN C 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 23 removed outlier: 3.763A pdb=" N GLU D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 18 " --> pdb=" O GLU D 14 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 48 removed outlier: 3.522A pdb=" N ALA D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 38 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER D 43 " --> pdb=" O GLN D 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU D 46 " --> pdb=" O GLN D 42 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LYS D 47 " --> pdb=" O SER D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 70 removed outlier: 3.524A pdb=" N THR D 59 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU D 70 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 101 removed outlier: 3.925A pdb=" N ARG D 85 " --> pdb=" O SER D 81 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 119 Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 140 through 159 Processing helix chain 'B' and resid 177 through 182 removed outlier: 3.973A pdb=" N LEU B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 235 Proline residue: B 225 - end of helix removed outlier: 3.713A pdb=" N LEU B 229 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASN B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 270 Processing helix chain 'B' and resid 333 through 351 removed outlier: 3.690A pdb=" N LEU B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 381 removed outlier: 3.766A pdb=" N ASN B 374 " --> pdb=" O MET B 370 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS B 375 " --> pdb=" O GLN B 371 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE B 376 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG B 378 " --> pdb=" O ASN B 374 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS B 381 " --> pdb=" O ILE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 393 removed outlier: 4.647A pdb=" N SER B 393 " --> pdb=" O THR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 448 removed outlier: 3.780A pdb=" N PHE B 442 " --> pdb=" O GLN B 438 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 444 " --> pdb=" O ARG B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 488 Processing helix chain 'B' and resid 491 through 500 removed outlier: 3.597A pdb=" N ILE B 495 " --> pdb=" O ASN B 491 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N LYS B 496 " --> pdb=" O PRO B 492 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER B 497 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU B 500 " --> pdb=" O LYS B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 169 Processing sheet with id=AA2, first strand: chain 'A' and resid 166 through 169 removed outlier: 4.325A pdb=" N ILE A 305 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA4, first strand: chain 'A' and resid 357 through 360 removed outlier: 7.247A pdb=" N ARG A 241 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N LEU A 386 " --> pdb=" O ARG A 241 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N MET A 243 " --> pdb=" O LEU A 386 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 281 removed outlier: 6.050A pdb=" N LYS A 299 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR A 319 " --> pdb=" O LYS A 299 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 467 through 470 removed outlier: 6.944A pdb=" N ILE A 551 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ILE A 545 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ASN A 553 " --> pdb=" O HIS A 543 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE A 536 " --> pdb=" O THR A 508 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N THR A 508 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR A 538 " --> pdb=" O ILE A 506 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 572 " --> pdb=" O TYR A 509 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N GLN A 482 " --> pdb=" O ARG A 577 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 518 through 520 Processing sheet with id=AA8, first strand: chain 'A' and resid 605 through 606 removed outlier: 3.502A pdb=" N THR A 606 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 5 " --> pdb=" O THR A 606 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AB2, first strand: chain 'B' and resid 168 through 169 Processing sheet with id=AB3, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.527A pdb=" N ILE B 104 " --> pdb=" O TYR B 111 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 241 through 244 removed outlier: 3.679A pdb=" N VAL B 244 " --> pdb=" O LEU B 359 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 278 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N ASN B 360 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B 280 " --> pdb=" O ASN B 360 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE B 295 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLN B 322 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU B 297 " --> pdb=" O LEU B 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 468 through 470 removed outlier: 6.754A pdb=" N ILE B 551 " --> pdb=" O ILE B 545 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE B 545 " --> pdb=" O ILE B 551 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B 553 " --> pdb=" O HIS B 543 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N PHE B 536 " --> pdb=" O THR B 508 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR B 508 " --> pdb=" O PHE B 536 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR B 538 " --> pdb=" O ILE B 506 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP B 573 " --> pdb=" O ILE B 478 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 480 " --> pdb=" O TRP B 573 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 517 through 520 348 hydrogen bonds defined for protein. 975 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.65 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3536 1.34 - 1.46: 2635 1.46 - 1.58: 4981 1.58 - 1.70: 1 1.70 - 1.82: 40 Bond restraints: 11193 Sorted by residual: bond pdb=" CB PRO C 122 " pdb=" CG PRO C 122 " ideal model delta sigma weight residual 1.492 1.582 -0.090 5.00e-02 4.00e+02 3.27e+00 bond pdb=" CB PRO D 122 " pdb=" CG PRO D 122 " ideal model delta sigma weight residual 1.492 1.579 -0.087 5.00e-02 4.00e+02 3.00e+00 bond pdb=" N ASP A 74 " pdb=" CA ASP A 74 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 2.94e+00 bond pdb=" CG LEU C 128 " pdb=" CD2 LEU C 128 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 bond pdb=" CG LEU C 155 " pdb=" CD1 LEU C 155 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 ... (remaining 11188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 14996 2.72 - 5.45: 222 5.45 - 8.17: 28 8.17 - 10.90: 6 10.90 - 13.62: 1 Bond angle restraints: 15253 Sorted by residual: angle pdb=" N PRO B 416 " pdb=" CA PRO B 416 " pdb=" CB PRO B 416 " ideal model delta sigma weight residual 103.25 111.91 -8.66 1.05e+00 9.07e-01 6.81e+01 angle pdb=" N PRO A 416 " pdb=" CA PRO A 416 " pdb=" CB PRO A 416 " ideal model delta sigma weight residual 103.25 111.80 -8.55 1.05e+00 9.07e-01 6.62e+01 angle pdb=" N PRO B 422 " pdb=" CA PRO B 422 " pdb=" CB PRO B 422 " ideal model delta sigma weight residual 103.25 111.23 -7.98 1.05e+00 9.07e-01 5.77e+01 angle pdb=" N PRO B 466 " pdb=" CA PRO B 466 " pdb=" CB PRO B 466 " ideal model delta sigma weight residual 103.25 111.09 -7.84 1.05e+00 9.07e-01 5.57e+01 angle pdb=" CA PRO D 122 " pdb=" N PRO D 122 " pdb=" CD PRO D 122 " ideal model delta sigma weight residual 112.00 103.93 8.07 1.40e+00 5.10e-01 3.32e+01 ... (remaining 15248 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 5989 17.53 - 35.05: 524 35.05 - 52.58: 85 52.58 - 70.11: 15 70.11 - 87.63: 11 Dihedral angle restraints: 6624 sinusoidal: 2556 harmonic: 4068 Sorted by residual: dihedral pdb=" CA HIS D 130 " pdb=" C HIS D 130 " pdb=" N TRP D 131 " pdb=" CA TRP D 131 " 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 388 " pdb=" C LEU A 388 " pdb=" N GLU A 389 " pdb=" CA GLU A 389 " ideal model delta harmonic sigma weight residual -180.00 -161.84 -18.16 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASP D 101 " pdb=" C ASP D 101 " pdb=" N PRO D 102 " pdb=" CA PRO D 102 " ideal model delta harmonic sigma weight residual 180.00 162.73 17.27 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 6621 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1183 0.040 - 0.080: 374 0.080 - 0.120: 120 0.120 - 0.160: 26 0.160 - 0.201: 8 Chirality restraints: 1711 Sorted by residual: chirality pdb=" CA PRO A 416 " pdb=" N PRO A 416 " pdb=" C PRO A 416 " pdb=" CB PRO A 416 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA PRO B 416 " pdb=" N PRO B 416 " pdb=" C PRO B 416 " pdb=" CB PRO B 416 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 9.92e-01 chirality pdb=" CA PRO B 422 " pdb=" N PRO B 422 " pdb=" C PRO B 422 " pdb=" CB PRO B 422 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 1708 not shown) Planarity restraints: 1953 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 121 " -0.087 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO D 122 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO D 122 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO D 122 " -0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 286 " -0.078 5.00e-02 4.00e+02 1.16e-01 2.14e+01 pdb=" N PRO B 287 " 0.200 5.00e-02 4.00e+02 pdb=" CA PRO B 287 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO B 287 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 121 " -0.070 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO C 122 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO C 122 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO C 122 " -0.056 5.00e-02 4.00e+02 ... (remaining 1950 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 326 2.70 - 3.25: 11259 3.25 - 3.80: 16965 3.80 - 4.35: 21951 4.35 - 4.90: 36280 Nonbonded interactions: 86781 Sorted by model distance: nonbonded pdb=" O GLU A 77 " pdb=" OH TYR A 204 " model vdw 2.153 3.040 nonbonded pdb=" O GLU B 77 " pdb=" OH TYR B 204 " model vdw 2.159 3.040 nonbonded pdb=" OE1 GLU C 17 " pdb=" NH1 ARG C 40 " model vdw 2.167 3.120 nonbonded pdb=" O GLY B 247 " pdb=" OG SER B 250 " model vdw 2.193 3.040 nonbonded pdb=" O SER B 590 " pdb=" OG1 THR B 593 " model vdw 2.205 3.040 ... (remaining 86776 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 65 through 67 or (resid 68 and (name N or name CA or name \ C or name O or name CB )) or resid 69 through 70 or (resid 71 through 72 and (na \ me N or name CA or name C or name O or name CB )) or resid 73 through 74 or (res \ id 75 and (name N or name CA or name C or name O or name CB )) or resid 76 throu \ gh 82 or (resid 83 through 87 and (name N or name CA or name C or name O or name \ CB )) or resid 88 through 105 or (resid 106 and (name N or name CA or name C or \ name O or name CB )) or resid 107 through 167 or (resid 168 and (name N or name \ CA or name C or name O or name CB )) or resid 169 through 192 or (resid 193 and \ (name N or name CA or name C or name O or name CB )) or resid 194 through 197 o \ r (resid 198 through 201 and (name N or name CA or name C or name O or name CB ) \ ) or resid 202 through 225 or (resid 226 and (name N or name CA or name C or nam \ e O or name CB )) or resid 227 through 275 or (resid 276 and (name N or name CA \ or name C or name O or name CB )) or resid 277 through 302 or resid 304 through \ 367 or (resid 368 and (name N or name CA or name C or name O or name CB )) or re \ sid 369 through 405 or (resid 406 through 417 and (name N or name CA or name C o \ r name O or name CB )) or resid 418 through 421 or (resid 422 through 423 and (n \ ame N or name CA or name C or name O or name CB )) or resid 424 through 465 or ( \ resid 466 and (name N or name CA or name C or name O or name CB )) or resid 467 \ through 526 or (resid 527 and (name N or name CA or name C or name O or name CB \ )) or resid 528 through 618)) selection = (chain 'B' and (resid 65 through 261 or (resid 262 and (name N or name CA or nam \ e C or name O or name CB )) or resid 263 through 369 or (resid 370 and (name N o \ r name CA or name C or name O or name CB )) or resid 371 through 399 or (resid 4 \ 00 and (name N or name CA or name C or name O or name CB )) or resid 401 through \ 517 or (resid 518 and (name N or name CA or name C or name O or name CB )) or r \ esid 519 through 569 or (resid 570 through 571 and (name N or name CA or name C \ or name O or name CB )) or resid 572 through 611 or (resid 612 and (name N or na \ me CA or name C or name O or name CB )) or resid 613 through 618)) } ncs_group { reference = (chain 'C' and (resid 2 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 through 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 or (resid 29 throug \ h 30 and (name N or name CA or name C or name O or name CB )) or resid 31 throug \ h 167)) selection = (chain 'D' and (resid 2 through 134 or (resid 135 and (name N or name CA or name \ C or name O or name CB )) or resid 136 through 167)) } 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: 2.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.840 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0038 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 11193 Z= 0.199 Angle : 0.842 13.621 15253 Z= 0.475 Chirality : 0.046 0.201 1711 Planarity : 0.006 0.126 1953 Dihedral : 13.879 87.632 3986 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.04 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.55 (0.21), residues: 1375 helix: -0.28 (0.26), residues: 386 sheet: -1.64 (0.36), residues: 192 loop : -1.23 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 268 TYR 0.028 0.002 TYR A 230 PHE 0.025 0.002 PHE A 263 TRP 0.056 0.003 TRP C 21 HIS 0.014 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00449 (11193) covalent geometry : angle 0.84169 (15253) hydrogen bonds : bond 0.19935 ( 342) hydrogen bonds : angle 7.80291 ( 975) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.376 Fit side-chains REVERT: C 114 THR cc_start: -0.0995 (t) cc_final: -0.2581 (p) REVERT: D 126 VAL cc_start: -0.1066 (t) cc_final: -0.1311 (p) REVERT: B 188 LEU cc_start: 0.3229 (tt) cc_final: 0.2813 (mt) REVERT: B 301 LEU cc_start: 0.1475 (pt) cc_final: 0.0297 (tp) REVERT: B 552 MET cc_start: 0.0198 (mtm) cc_final: -0.0168 (ppp) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.0960 time to fit residues: 14.2074 Evaluate side-chains 60 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.0170 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 40.0000 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 0.0870 chunk 55 optimal weight: 20.0000 overall best weight: 1.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN A 375 HIS ** A 396 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 HIS ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN B 98 GLN B 286 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN B 435 HIS ** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5238 r_free = 0.5238 target = 0.304896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4892 r_free = 0.4892 target = 0.253940 restraints weight = 13357.811| |-----------------------------------------------------------------------------| r_work (start): 0.4749 rms_B_bonded: 3.16 r_work: 0.4421 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0235 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 11193 Z= 0.183 Angle : 0.756 10.128 15253 Z= 0.388 Chirality : 0.047 0.195 1711 Planarity : 0.006 0.109 1953 Dihedral : 5.055 23.225 1484 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.96 % Favored : 93.82 % Rotamer: Outliers : 0.95 % Allowed : 6.91 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.22), residues: 1375 helix: 0.14 (0.25), residues: 396 sheet: -1.25 (0.34), residues: 220 loop : -1.22 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 5 TYR 0.019 0.002 TYR B 230 PHE 0.030 0.002 PHE B 434 TRP 0.025 0.002 TRP B 121 HIS 0.008 0.001 HIS C 54 Details of bonding type rmsd covalent geometry : bond 0.00387 (11193) covalent geometry : angle 0.75647 (15253) hydrogen bonds : bond 0.04228 ( 342) hydrogen bonds : angle 5.81660 ( 975) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 485 MET cc_start: 0.4010 (mmm) cc_final: 0.3213 (mtm) REVERT: A 489 ASP cc_start: 0.3337 (t0) cc_final: 0.2138 (p0) REVERT: A 581 GLU cc_start: -0.0870 (tt0) cc_final: -0.3128 (pp20) REVERT: C 5 ARG cc_start: 0.0511 (mtm110) cc_final: -0.0465 (ptt90) REVERT: C 9 TRP cc_start: -0.0683 (p90) cc_final: -0.1589 (p90) REVERT: C 114 THR cc_start: -0.1850 (t) cc_final: -0.2811 (p) REVERT: B 301 LEU cc_start: 0.2582 (pt) cc_final: 0.0904 (tp) REVERT: B 311 LEU cc_start: -0.2121 (OUTLIER) cc_final: -0.2894 (mp) outliers start: 11 outliers final: 8 residues processed: 78 average time/residue: 0.0854 time to fit residues: 10.4176 Evaluate side-chains 64 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 560 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 85 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 chunk 45 optimal weight: 50.0000 chunk 100 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 578 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 HIS ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS B 374 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5210 r_free = 0.5210 target = 0.301969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.257412 restraints weight = 14638.972| |-----------------------------------------------------------------------------| r_work (start): 0.4775 rms_B_bonded: 3.58 r_work: 0.4399 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.4399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0398 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 11193 Z= 0.193 Angle : 0.782 14.252 15253 Z= 0.397 Chirality : 0.048 0.228 1711 Planarity : 0.006 0.084 1953 Dihedral : 5.378 30.632 1484 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 2.77 % Allowed : 11.24 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.22), residues: 1375 helix: -0.02 (0.25), residues: 410 sheet: -1.03 (0.35), residues: 212 loop : -1.48 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 268 TYR 0.020 0.002 TYR B 182 PHE 0.039 0.002 PHE B 434 TRP 0.018 0.002 TRP B 121 HIS 0.009 0.001 HIS A 615 Details of bonding type rmsd covalent geometry : bond 0.00425 (11193) covalent geometry : angle 0.78185 (15253) hydrogen bonds : bond 0.04807 ( 342) hydrogen bonds : angle 5.58265 ( 975) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 58 time to evaluate : 0.350 Fit side-chains revert: symmetry clash REVERT: A 107 ASN cc_start: 0.0353 (OUTLIER) cc_final: 0.0139 (p0) REVERT: A 216 LEU cc_start: 0.1353 (pt) cc_final: 0.1033 (tt) REVERT: A 443 LYS cc_start: 0.0353 (mttp) cc_final: 0.0126 (ptpt) REVERT: A 485 MET cc_start: 0.4527 (mmm) cc_final: 0.3520 (mtm) REVERT: A 500 GLU cc_start: 0.1599 (mm-30) cc_final: 0.1064 (mt-10) REVERT: C 9 TRP cc_start: -0.0558 (p90) cc_final: -0.1810 (p90) REVERT: C 15 LEU cc_start: -0.3325 (tp) cc_final: -0.3979 (mt) REVERT: D 51 TYR cc_start: 0.0092 (m-80) cc_final: -0.0212 (m-10) REVERT: B 268 ARG cc_start: -0.0816 (OUTLIER) cc_final: -0.2667 (mmp-170) REVERT: B 280 LEU cc_start: 0.0056 (OUTLIER) cc_final: -0.0431 (mt) REVERT: B 301 LEU cc_start: 0.2406 (pt) cc_final: 0.1053 (tp) outliers start: 32 outliers final: 17 residues processed: 87 average time/residue: 0.0976 time to fit residues: 12.3109 Evaluate side-chains 68 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 48 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 48 optimal weight: 40.0000 chunk 52 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** 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 = 0.5202 r_free = 0.5202 target = 0.300942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.248377 restraints weight = 14239.800| |-----------------------------------------------------------------------------| r_work (start): 0.4704 rms_B_bonded: 4.38 r_work: 0.4440 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.4440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0437 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11193 Z= 0.161 Angle : 0.692 11.591 15253 Z= 0.351 Chirality : 0.045 0.177 1711 Planarity : 0.005 0.085 1953 Dihedral : 5.003 26.013 1484 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.67 % Rotamer: Outliers : 2.51 % Allowed : 13.48 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.45 (0.22), residues: 1375 helix: 0.04 (0.25), residues: 420 sheet: -1.00 (0.35), residues: 218 loop : -1.55 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 268 TYR 0.015 0.002 TYR D 88 PHE 0.030 0.001 PHE B 434 TRP 0.012 0.002 TRP A 121 HIS 0.008 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00348 (11193) covalent geometry : angle 0.69224 (15253) hydrogen bonds : bond 0.04369 ( 342) hydrogen bonds : angle 5.35251 ( 975) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 53 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1097 (pt) cc_final: 0.0831 (tt) REVERT: A 443 LYS cc_start: 0.0416 (mttp) cc_final: 0.0157 (ptpt) REVERT: A 485 MET cc_start: 0.4765 (mmm) cc_final: 0.3667 (mtm) REVERT: A 500 GLU cc_start: 0.1743 (mm-30) cc_final: 0.1167 (mt-10) REVERT: C 9 TRP cc_start: -0.0642 (p90) cc_final: -0.1784 (p90) REVERT: C 15 LEU cc_start: -0.3022 (tp) cc_final: -0.3827 (mt) REVERT: C 114 THR cc_start: -0.1718 (t) cc_final: -0.2493 (p) REVERT: D 51 TYR cc_start: 0.0125 (OUTLIER) cc_final: -0.0446 (m-10) REVERT: D 143 MET cc_start: -0.0347 (ptm) cc_final: -0.0608 (ptt) REVERT: B 95 PHE cc_start: 0.3446 (p90) cc_final: 0.2802 (p90) outliers start: 29 outliers final: 20 residues processed: 78 average time/residue: 0.1065 time to fit residues: 12.0815 Evaluate side-chains 69 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 117 optimal weight: 4.9990 chunk 37 optimal weight: 40.0000 chunk 89 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 55 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 71 optimal weight: 40.0000 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 30.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5198 r_free = 0.5198 target = 0.299849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.253274 restraints weight = 14914.174| |-----------------------------------------------------------------------------| r_work (start): 0.4760 rms_B_bonded: 4.13 r_work: 0.4427 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.4427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0431 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11193 Z= 0.167 Angle : 0.718 9.988 15253 Z= 0.366 Chirality : 0.045 0.180 1711 Planarity : 0.006 0.106 1953 Dihedral : 5.110 29.983 1484 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.76 % Favored : 93.09 % Rotamer: Outliers : 3.37 % Allowed : 14.95 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.22), residues: 1375 helix: 0.24 (0.26), residues: 400 sheet: -0.89 (0.35), residues: 215 loop : -1.58 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 268 TYR 0.031 0.002 TYR D 88 PHE 0.034 0.001 PHE B 434 TRP 0.021 0.002 TRP D 131 HIS 0.008 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00370 (11193) covalent geometry : angle 0.71818 (15253) hydrogen bonds : bond 0.04410 ( 342) hydrogen bonds : angle 5.38438 ( 975) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 55 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1232 (pt) cc_final: 0.0998 (tp) REVERT: A 443 LYS cc_start: 0.0501 (mttp) cc_final: 0.0214 (ptpt) REVERT: A 485 MET cc_start: 0.4828 (mmm) cc_final: 0.3762 (mtm) REVERT: A 500 GLU cc_start: 0.1676 (mm-30) cc_final: 0.1188 (mt-10) REVERT: C 9 TRP cc_start: -0.0720 (p90) cc_final: -0.1301 (p90) REVERT: C 19 LYS cc_start: -0.1376 (ttpt) cc_final: -0.1793 (ttpt) REVERT: D 51 TYR cc_start: 0.0054 (OUTLIER) cc_final: -0.0828 (m-10) REVERT: D 99 LEU cc_start: 0.2654 (OUTLIER) cc_final: 0.2117 (tp) REVERT: B 95 PHE cc_start: 0.3299 (p90) cc_final: 0.2916 (p90) REVERT: B 135 HIS cc_start: -0.0682 (OUTLIER) cc_final: -0.1375 (p90) REVERT: B 269 ASP cc_start: -0.0260 (OUTLIER) cc_final: -0.0765 (p0) outliers start: 39 outliers final: 22 residues processed: 88 average time/residue: 0.0966 time to fit residues: 12.3660 Evaluate side-chains 78 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 52 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 131 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 72 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 24 optimal weight: 30.0000 chunk 3 optimal weight: 50.0000 chunk 34 optimal weight: 9.9990 chunk 108 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 309 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN B 107 ASN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5203 r_free = 0.5203 target = 0.301568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4860 r_free = 0.4860 target = 0.257510 restraints weight = 15250.899| |-----------------------------------------------------------------------------| r_work (start): 0.4755 rms_B_bonded: 4.21 r_work: 0.4501 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0573 moved from start: 0.6735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 11193 Z= 0.220 Angle : 0.825 12.291 15253 Z= 0.423 Chirality : 0.049 0.209 1711 Planarity : 0.007 0.133 1953 Dihedral : 5.795 35.218 1484 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.71 % Favored : 92.15 % Rotamer: Outliers : 3.63 % Allowed : 15.47 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.65 (0.22), residues: 1375 helix: -0.01 (0.26), residues: 401 sheet: -0.65 (0.39), residues: 181 loop : -1.85 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 268 TYR 0.039 0.002 TYR B 221 PHE 0.055 0.002 PHE B 434 TRP 0.023 0.002 TRP B 222 HIS 0.023 0.002 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00492 (11193) covalent geometry : angle 0.82514 (15253) hydrogen bonds : bond 0.05218 ( 342) hydrogen bonds : angle 5.86330 ( 975) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 47 time to evaluate : 0.333 Fit side-chains REVERT: A 443 LYS cc_start: 0.0507 (mttp) cc_final: 0.0231 (ptpt) REVERT: A 485 MET cc_start: 0.4903 (mmm) cc_final: 0.4041 (mtm) REVERT: C 2 ILE cc_start: -0.1907 (OUTLIER) cc_final: -0.2591 (pt) REVERT: C 9 TRP cc_start: -0.0666 (p90) cc_final: -0.1496 (p-90) REVERT: C 19 LYS cc_start: -0.1660 (ttpt) cc_final: -0.2014 (ttpt) REVERT: C 90 MET cc_start: 0.0927 (OUTLIER) cc_final: -0.0725 (mmm) REVERT: D 99 LEU cc_start: 0.2871 (OUTLIER) cc_final: 0.2173 (tp) REVERT: D 115 LEU cc_start: 0.0332 (OUTLIER) cc_final: 0.0073 (mm) REVERT: B 124 LEU cc_start: -0.3407 (OUTLIER) cc_final: -0.3658 (mm) REVERT: B 135 HIS cc_start: -0.0747 (OUTLIER) cc_final: -0.1689 (m170) REVERT: B 166 ARG cc_start: -0.1952 (OUTLIER) cc_final: -0.3033 (mmm-85) outliers start: 42 outliers final: 30 residues processed: 85 average time/residue: 0.1054 time to fit residues: 13.1917 Evaluate side-chains 81 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 44 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 5 optimal weight: 10.0000 chunk 124 optimal weight: 40.0000 chunk 104 optimal weight: 0.8980 chunk 22 optimal weight: 20.0000 chunk 96 optimal weight: 0.9990 chunk 36 optimal weight: 50.0000 chunk 88 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 chunk 58 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 HIS B 286 GLN B 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5191 r_free = 0.5191 target = 0.299685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4843 r_free = 0.4843 target = 0.255383 restraints weight = 15373.657| |-----------------------------------------------------------------------------| r_work (start): 0.4774 rms_B_bonded: 4.11 r_work: 0.4480 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.4480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0478 moved from start: 0.6881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11193 Z= 0.159 Angle : 0.697 11.819 15253 Z= 0.355 Chirality : 0.045 0.173 1711 Planarity : 0.006 0.113 1953 Dihedral : 5.283 30.877 1484 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.84 % Favored : 93.02 % Rotamer: Outliers : 3.11 % Allowed : 16.68 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.22), residues: 1375 helix: 0.18 (0.26), residues: 395 sheet: -0.54 (0.39), residues: 187 loop : -1.80 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 268 TYR 0.018 0.001 TYR B 221 PHE 0.038 0.001 PHE B 434 TRP 0.021 0.002 TRP B 222 HIS 0.008 0.001 HIS A 615 Details of bonding type rmsd covalent geometry : bond 0.00349 (11193) covalent geometry : angle 0.69701 (15253) hydrogen bonds : bond 0.04356 ( 342) hydrogen bonds : angle 5.42643 ( 975) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 56 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 215 SER cc_start: 0.1485 (p) cc_final: 0.1271 (m) REVERT: A 443 LYS cc_start: 0.0478 (mttp) cc_final: 0.0212 (ptpt) REVERT: A 485 MET cc_start: 0.4939 (mmm) cc_final: 0.4116 (mtm) REVERT: A 610 ARG cc_start: -0.1200 (OUTLIER) cc_final: -0.2464 (ptt180) REVERT: C 2 ILE cc_start: -0.1713 (OUTLIER) cc_final: -0.2344 (pt) REVERT: C 9 TRP cc_start: -0.0793 (p90) cc_final: -0.1738 (p-90) REVERT: C 19 LYS cc_start: -0.1442 (ttpt) cc_final: -0.1750 (ttpt) REVERT: D 99 LEU cc_start: 0.2961 (OUTLIER) cc_final: 0.2173 (tp) REVERT: D 115 LEU cc_start: 0.0393 (OUTLIER) cc_final: 0.0172 (mm) REVERT: D 143 MET cc_start: -0.0200 (ptm) cc_final: -0.0590 (ptm) REVERT: B 135 HIS cc_start: -0.1091 (OUTLIER) cc_final: -0.2274 (m90) outliers start: 36 outliers final: 26 residues processed: 85 average time/residue: 0.0959 time to fit residues: 12.0300 Evaluate side-chains 85 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 54 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain C residue 2 ILE Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 127 SER Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 2 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 30.0000 chunk 4 optimal weight: 0.0970 chunk 126 optimal weight: 6.9990 chunk 131 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 21 optimal weight: 50.0000 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN B 286 GLN B 322 GLN B 449 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5197 r_free = 0.5197 target = 0.300224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.257100 restraints weight = 15012.245| |-----------------------------------------------------------------------------| r_work (start): 0.4821 rms_B_bonded: 3.73 r_work: 0.4490 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0451 moved from start: 0.6912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11193 Z= 0.116 Angle : 0.616 13.691 15253 Z= 0.313 Chirality : 0.043 0.178 1711 Planarity : 0.005 0.077 1953 Dihedral : 4.707 24.000 1484 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.11 % Favored : 93.75 % Rotamer: Outliers : 2.16 % Allowed : 17.55 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.22), residues: 1375 helix: 0.39 (0.26), residues: 408 sheet: -0.51 (0.39), residues: 191 loop : -1.65 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 268 TYR 0.012 0.001 TYR B 221 PHE 0.017 0.001 PHE B 434 TRP 0.012 0.001 TRP C 131 HIS 0.005 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00250 (11193) covalent geometry : angle 0.61584 (15253) hydrogen bonds : bond 0.03663 ( 342) hydrogen bonds : angle 4.97230 ( 975) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.332 Fit side-chains REVERT: A 215 SER cc_start: 0.1784 (p) cc_final: 0.1579 (m) REVERT: A 443 LYS cc_start: 0.0583 (mttp) cc_final: 0.0268 (ptpt) REVERT: A 485 MET cc_start: 0.4882 (mmm) cc_final: 0.4034 (mtm) REVERT: C 9 TRP cc_start: -0.0754 (p90) cc_final: -0.1789 (p-90) REVERT: C 19 LYS cc_start: -0.1379 (ttpt) cc_final: -0.1692 (ttpt) REVERT: D 99 LEU cc_start: 0.2899 (OUTLIER) cc_final: 0.2106 (tp) REVERT: D 115 LEU cc_start: 0.0553 (OUTLIER) cc_final: 0.0334 (mm) REVERT: D 143 MET cc_start: -0.0202 (ptm) cc_final: -0.0633 (ptm) REVERT: B 135 HIS cc_start: -0.1183 (OUTLIER) cc_final: -0.1998 (m170) REVERT: B 309 GLN cc_start: 0.3101 (tp40) cc_final: 0.1492 (pt0) REVERT: B 394 LYS cc_start: -0.0873 (OUTLIER) cc_final: -0.2763 (mtmm) outliers start: 25 outliers final: 18 residues processed: 81 average time/residue: 0.0834 time to fit residues: 10.1062 Evaluate side-chains 77 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain D residue 115 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 286 GLN Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 50.0000 chunk 33 optimal weight: 0.0070 chunk 106 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 30.0000 chunk 89 optimal weight: 0.0060 chunk 135 optimal weight: 6.9990 chunk 84 optimal weight: 0.0670 overall best weight: 0.7754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5198 r_free = 0.5198 target = 0.300175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4893 r_free = 0.4893 target = 0.257969 restraints weight = 14929.393| |-----------------------------------------------------------------------------| r_work (start): 0.4827 rms_B_bonded: 3.53 r_work: 0.4478 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0448 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11193 Z= 0.118 Angle : 0.611 13.591 15253 Z= 0.311 Chirality : 0.043 0.176 1711 Planarity : 0.005 0.072 1953 Dihedral : 4.602 24.220 1484 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.96 % Favored : 93.89 % Rotamer: Outliers : 2.25 % Allowed : 17.98 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.22), residues: 1375 helix: 0.50 (0.26), residues: 408 sheet: -0.38 (0.39), residues: 185 loop : -1.59 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 268 TYR 0.011 0.001 TYR B 380 PHE 0.016 0.001 PHE B 434 TRP 0.010 0.001 TRP C 131 HIS 0.005 0.001 HIS B 396 Details of bonding type rmsd covalent geometry : bond 0.00249 (11193) covalent geometry : angle 0.61075 (15253) hydrogen bonds : bond 0.03543 ( 342) hydrogen bonds : angle 4.90886 ( 975) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 54 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 215 SER cc_start: 0.1817 (p) cc_final: 0.1609 (m) REVERT: A 443 LYS cc_start: 0.0500 (mttp) cc_final: 0.0207 (ptpt) REVERT: A 485 MET cc_start: 0.4859 (mmm) cc_final: 0.3980 (mtm) REVERT: C 2 ILE cc_start: -0.1519 (mt) cc_final: -0.2223 (pt) REVERT: C 9 TRP cc_start: -0.0749 (p90) cc_final: -0.1574 (p90) REVERT: D 99 LEU cc_start: 0.2907 (OUTLIER) cc_final: 0.2116 (tp) REVERT: D 143 MET cc_start: -0.0310 (ptm) cc_final: -0.0742 (ptm) REVERT: B 135 HIS cc_start: -0.1071 (OUTLIER) cc_final: -0.1527 (m-70) REVERT: B 309 GLN cc_start: 0.3192 (tp40) cc_final: 0.1543 (pt0) REVERT: B 394 LYS cc_start: -0.0961 (OUTLIER) cc_final: -0.2812 (mtmm) outliers start: 26 outliers final: 20 residues processed: 77 average time/residue: 0.1002 time to fit residues: 11.5883 Evaluate side-chains 76 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 441 THR Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 20 optimal weight: 9.9990 chunk 105 optimal weight: 0.5980 chunk 47 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 36 optimal weight: 50.0000 chunk 12 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 122 optimal weight: 50.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 HIS A 286 GLN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5225 r_free = 0.5225 target = 0.305544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4968 r_free = 0.4968 target = 0.268843 restraints weight = 14763.489| |-----------------------------------------------------------------------------| r_work (start): 0.4866 rms_B_bonded: 3.24 r_work: 0.4598 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0607 moved from start: 0.7526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11193 Z= 0.186 Angle : 0.737 10.708 15253 Z= 0.375 Chirality : 0.046 0.179 1711 Planarity : 0.005 0.080 1953 Dihedral : 5.241 35.162 1484 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.64 % Favored : 92.22 % Rotamer: Outliers : 2.16 % Allowed : 17.98 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.31 (0.22), residues: 1375 helix: 0.35 (0.26), residues: 394 sheet: -0.14 (0.40), residues: 169 loop : -1.73 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 609 TYR 0.021 0.002 TYR B 221 PHE 0.046 0.002 PHE B 434 TRP 0.018 0.002 TRP B 189 HIS 0.011 0.001 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00417 (11193) covalent geometry : angle 0.73686 (15253) hydrogen bonds : bond 0.04404 ( 342) hydrogen bonds : angle 5.40822 ( 975) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2750 Ramachandran restraints generated. 1375 Oldfield, 0 Emsley, 1375 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.314 Fit side-chains REVERT: A 215 SER cc_start: 0.1966 (p) cc_final: 0.1736 (m) REVERT: A 248 LYS cc_start: -0.1906 (pttt) cc_final: -0.2383 (pttp) REVERT: A 443 LYS cc_start: 0.0589 (mttp) cc_final: 0.0292 (ptpt) REVERT: A 485 MET cc_start: 0.4915 (mmm) cc_final: 0.4059 (mtm) REVERT: C 2 ILE cc_start: -0.1335 (mt) cc_final: -0.2150 (pt) REVERT: C 9 TRP cc_start: -0.0697 (p90) cc_final: -0.1898 (p90) REVERT: D 99 LEU cc_start: 0.2839 (OUTLIER) cc_final: 0.2172 (tp) REVERT: B 135 HIS cc_start: -0.0526 (OUTLIER) cc_final: -0.1564 (m170) REVERT: B 166 ARG cc_start: -0.1668 (OUTLIER) cc_final: -0.3085 (mmt90) REVERT: B 309 GLN cc_start: 0.3299 (tp40) cc_final: 0.1613 (pt0) REVERT: B 394 LYS cc_start: -0.0619 (OUTLIER) cc_final: -0.1366 (tttt) outliers start: 25 outliers final: 21 residues processed: 77 average time/residue: 0.0898 time to fit residues: 10.4083 Evaluate side-chains 76 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain A residue 610 ARG Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain D residue 51 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 103 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 394 LYS Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 582 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 17 optimal weight: 30.0000 chunk 23 optimal weight: 50.0000 chunk 97 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5255 r_free = 0.5255 target = 0.307101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4935 r_free = 0.4935 target = 0.265073 restraints weight = 14902.124| |-----------------------------------------------------------------------------| r_work (start): 0.4833 rms_B_bonded: 3.93 r_work: 0.4531 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0459 moved from start: 0.7491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11193 Z= 0.113 Angle : 0.605 11.642 15253 Z= 0.309 Chirality : 0.043 0.177 1711 Planarity : 0.004 0.051 1953 Dihedral : 4.606 24.503 1484 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.04 % Favored : 93.82 % Rotamer: Outliers : 1.90 % Allowed : 18.06 % Favored : 80.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.22), residues: 1375 helix: 0.50 (0.26), residues: 410 sheet: -0.12 (0.42), residues: 163 loop : -1.61 (0.21), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 94 TYR 0.012 0.001 TYR B 380 PHE 0.015 0.001 PHE B 434 TRP 0.020 0.001 TRP D 131 HIS 0.006 0.001 HIS A 615 Details of bonding type rmsd covalent geometry : bond 0.00239 (11193) covalent geometry : angle 0.60505 (15253) hydrogen bonds : bond 0.03487 ( 342) hydrogen bonds : angle 4.91252 ( 975) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3129.39 seconds wall clock time: 54 minutes 17.89 seconds (3257.89 seconds total)