Starting phenix.real_space_refine on Wed Sep 25 16:50:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/09_2024/8j5y_33733.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/09_2024/8j5y_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/09_2024/8j5y_33733.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/09_2024/8j5y_33733.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/09_2024/8j5y_33733.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5y_33733/09_2024/8j5y_33733.cif" } resolution = 3.07 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} 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: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 144 Time building chain proxies: 6.98, per 1000 atoms: 0.64 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: 2.74 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.14 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: 2.98 Time building geometry restraints manager: 3.09 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: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.310 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- 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= 0.296 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 : 12.97 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (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 TRP 0.056 0.003 TRP C 21 HIS 0.014 0.001 HIS C 54 PHE 0.025 0.002 PHE A 263 TYR 0.028 0.002 TYR A 230 ARG 0.006 0.001 ARG B 268 *********************** 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 fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 1.187 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: 0.2239 time to fit residues: 33.0170 Evaluate side-chains 60 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.0770 chunk 103 optimal weight: 0.0470 chunk 57 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 69 optimal weight: 40.0000 chunk 55 optimal weight: 30.0000 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 40.0000 chunk 64 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 overall best weight: 0.5636 ------------------------------------------------------------------------------- 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 578 ASN D 104 GLN D 113 HIS B 371 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0158 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11193 Z= 0.177 Angle : 0.668 8.323 15253 Z= 0.338 Chirality : 0.044 0.174 1711 Planarity : 0.005 0.080 1953 Dihedral : 4.650 25.103 1484 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.45 % Favored : 94.33 % Rotamer: Outliers : 0.78 % Allowed : 6.66 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.22), residues: 1375 helix: 0.31 (0.26), residues: 398 sheet: -1.29 (0.33), residues: 224 loop : -1.20 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 21 HIS 0.011 0.001 HIS C 54 PHE 0.013 0.001 PHE B 434 TYR 0.023 0.002 TYR B 230 ARG 0.008 0.001 ARG A 577 *********************** 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 fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1180 (pt) cc_final: 0.0788 (tp) REVERT: A 485 MET cc_start: 0.3815 (mmm) cc_final: 0.2861 (mtm) REVERT: A 489 ASP cc_start: 0.3237 (t0) cc_final: 0.2080 (p0) REVERT: A 581 GLU cc_start: -0.0742 (tt0) cc_final: -0.2988 (pp20) REVERT: C 114 THR cc_start: -0.0591 (t) cc_final: -0.2176 (p) REVERT: B 188 LEU cc_start: 0.4065 (tt) cc_final: 0.3340 (mt) REVERT: B 231 LEU cc_start: 0.0610 (mp) cc_final: 0.0087 (tp) REVERT: B 301 LEU cc_start: 0.1442 (pt) cc_final: 0.0308 (tp) outliers start: 9 outliers final: 3 residues processed: 78 average time/residue: 0.1959 time to fit residues: 23.8954 Evaluate side-chains 63 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 268 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.0980 chunk 102 optimal weight: 9.9990 chunk 84 optimal weight: 0.0870 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 110 optimal weight: 8.9990 chunk 122 optimal weight: 50.0000 chunk 42 optimal weight: 0.0000 chunk 99 optimal weight: 0.6980 overall best weight: 0.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS B 286 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0197 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11193 Z= 0.147 Angle : 0.592 8.230 15253 Z= 0.300 Chirality : 0.042 0.160 1711 Planarity : 0.004 0.067 1953 Dihedral : 4.289 28.985 1484 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.31 % Favored : 94.55 % Rotamer: Outliers : 1.56 % Allowed : 9.33 % Favored : 89.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.22), residues: 1375 helix: 0.67 (0.26), residues: 402 sheet: -1.03 (0.34), residues: 222 loop : -1.24 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 121 HIS 0.009 0.001 HIS C 54 PHE 0.009 0.001 PHE B 434 TYR 0.018 0.001 TYR B 230 ARG 0.005 0.000 ARG A 577 *********************** 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 83 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1281 (pt) cc_final: 0.0737 (tt) REVERT: A 261 GLU cc_start: -0.0975 (OUTLIER) cc_final: -0.1525 (tt0) REVERT: A 485 MET cc_start: 0.4175 (mmm) cc_final: 0.3132 (mtm) REVERT: A 489 ASP cc_start: 0.3371 (t0) cc_final: 0.2187 (p0) REVERT: A 581 GLU cc_start: -0.0815 (tt0) cc_final: -0.2969 (pp20) REVERT: C 5 ARG cc_start: -0.0691 (mtm110) cc_final: -0.1623 (ptt-90) REVERT: C 114 THR cc_start: -0.0643 (t) cc_final: -0.2314 (p) REVERT: B 188 LEU cc_start: 0.4416 (tt) cc_final: 0.3373 (mt) REVERT: B 301 LEU cc_start: 0.1383 (pt) cc_final: 0.0384 (tp) outliers start: 18 outliers final: 11 residues processed: 80 average time/residue: 0.2338 time to fit residues: 27.3862 Evaluate side-chains 71 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain C residue 131 TRP Chi-restraints excluded: chain C residue 155 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 268 ARG Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 376 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 584 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 50.0000 chunk 93 optimal weight: 0.0670 chunk 64 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 131 optimal weight: 8.9990 chunk 117 optimal weight: 0.7980 chunk 35 optimal weight: 30.0000 chunk 109 optimal weight: 9.9990 overall best weight: 4.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 61 GLN C 149 ASN ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN ** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1007 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 11193 Z= 0.470 Angle : 1.055 16.640 15253 Z= 0.541 Chirality : 0.056 0.326 1711 Planarity : 0.008 0.129 1953 Dihedral : 6.361 38.359 1484 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.98 % Favored : 92.80 % Rotamer: Outliers : 1.90 % Allowed : 13.14 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.22), residues: 1375 helix: -0.20 (0.26), residues: 393 sheet: -1.17 (0.36), residues: 189 loop : -1.61 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 121 HIS 0.025 0.002 HIS C 158 PHE 0.094 0.003 PHE B 434 TYR 0.037 0.003 TYR D 88 ARG 0.015 0.001 ARG B 268 *********************** 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 79 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 57 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1309 (pt) cc_final: 0.0997 (tp) REVERT: A 249 ASN cc_start: 0.0551 (OUTLIER) cc_final: -0.0862 (m110) REVERT: A 261 GLU cc_start: -0.0929 (OUTLIER) cc_final: -0.1515 (tt0) REVERT: A 485 MET cc_start: 0.4749 (mmm) cc_final: 0.3529 (mtm) REVERT: A 500 GLU cc_start: 0.2016 (mm-30) cc_final: 0.1195 (mt-10) REVERT: C 9 TRP cc_start: 0.0335 (p90) cc_final: -0.0600 (p-90) REVERT: C 19 LYS cc_start: -0.0636 (ttpt) cc_final: -0.1440 (ttpt) REVERT: C 154 TRP cc_start: -0.0039 (t60) cc_final: -0.0319 (t60) REVERT: B 65 LEU cc_start: 0.0118 (OUTLIER) cc_final: -0.0443 (tt) REVERT: B 268 ARG cc_start: 0.1863 (OUTLIER) cc_final: -0.1476 (mtt-85) outliers start: 22 outliers final: 12 residues processed: 76 average time/residue: 0.2250 time to fit residues: 25.6156 Evaluate side-chains 64 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 365 ILE 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 103 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 210 SER Chi-restraints excluded: chain B residue 268 ARG 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 582 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 67 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 chunk 44 optimal weight: 50.0000 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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** C 104 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0756 moved from start: 0.5000 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= 0.165 Angle : 0.622 7.779 15253 Z= 0.320 Chirality : 0.043 0.162 1711 Planarity : 0.005 0.087 1953 Dihedral : 4.857 23.777 1484 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 1.82 % Allowed : 15.13 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.22), residues: 1375 helix: 0.30 (0.26), residues: 410 sheet: -0.84 (0.35), residues: 215 loop : -1.61 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 131 HIS 0.004 0.001 HIS B 560 PHE 0.019 0.001 PHE B 434 TYR 0.010 0.001 TYR A 230 ARG 0.008 0.001 ARG B 268 *********************** 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 78 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 57 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 ARG cc_start: -0.0296 (mmm160) cc_final: -0.1579 (mtm-85) REVERT: A 216 LEU cc_start: 0.1323 (pt) cc_final: 0.0804 (tt) REVERT: A 249 ASN cc_start: 0.0384 (m-40) cc_final: -0.0967 (m110) REVERT: A 261 GLU cc_start: -0.1081 (OUTLIER) cc_final: -0.1663 (tt0) REVERT: A 485 MET cc_start: 0.4718 (mmm) cc_final: 0.3482 (mtm) REVERT: A 500 GLU cc_start: 0.1813 (mm-30) cc_final: 0.1241 (mt-10) REVERT: C 15 LEU cc_start: -0.0859 (tp) cc_final: -0.2365 (mt) REVERT: D 99 LEU cc_start: 0.2988 (OUTLIER) cc_final: 0.2644 (tp) REVERT: B 124 LEU cc_start: -0.0807 (OUTLIER) cc_final: -0.1152 (mt) REVERT: B 166 ARG cc_start: -0.0818 (OUTLIER) cc_final: -0.1846 (ptm160) REVERT: B 375 HIS cc_start: 0.2811 (m-70) cc_final: 0.2382 (p90) outliers start: 21 outliers final: 9 residues processed: 76 average time/residue: 0.2428 time to fit residues: 27.0709 Evaluate side-chains 66 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 131 TRP 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 124 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 418 VAL Chi-restraints excluded: chain B residue 453 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 30.0000 chunk 32 optimal weight: 40.0000 chunk 131 optimal weight: 0.0870 chunk 109 optimal weight: 20.0000 chunk 60 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 overall best weight: 3.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN B 172 HIS B 214 GLN B 286 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1082 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 11193 Z= 0.350 Angle : 0.852 11.626 15253 Z= 0.435 Chirality : 0.049 0.228 1711 Planarity : 0.006 0.079 1953 Dihedral : 5.835 36.478 1484 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.85 % Favored : 92.00 % Rotamer: Outliers : 2.07 % Allowed : 16.16 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1375 helix: 0.19 (0.27), residues: 385 sheet: -0.85 (0.37), residues: 197 loop : -1.61 (0.21), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 222 HIS 0.011 0.001 HIS A 615 PHE 0.059 0.002 PHE B 434 TYR 0.024 0.002 TYR C 51 ARG 0.010 0.001 ARG B 268 *********************** 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 70 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 46 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1378 (pt) cc_final: 0.0885 (tt) REVERT: A 261 GLU cc_start: -0.0958 (OUTLIER) cc_final: -0.1548 (tt0) REVERT: A 485 MET cc_start: 0.4897 (mmm) cc_final: 0.3610 (mtm) REVERT: C 9 TRP cc_start: 0.0101 (p90) cc_final: -0.0782 (p-90) REVERT: C 19 LYS cc_start: -0.0453 (ttpt) cc_final: -0.1201 (ttpt) REVERT: D 99 LEU cc_start: 0.2902 (OUTLIER) cc_final: 0.2565 (tp) REVERT: B 124 LEU cc_start: -0.1197 (OUTLIER) cc_final: -0.1651 (mm) REVERT: B 165 LEU cc_start: 0.0635 (OUTLIER) cc_final: 0.0279 (mt) REVERT: B 166 ARG cc_start: -0.0635 (OUTLIER) cc_final: -0.2811 (mpt-90) REVERT: B 461 LEU cc_start: -0.1335 (OUTLIER) cc_final: -0.1788 (mp) outliers start: 24 outliers final: 14 residues processed: 69 average time/residue: 0.2364 time to fit residues: 24.9420 Evaluate side-chains 64 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 44 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP 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 78 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 165 LEU Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 172 HIS 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 461 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 1.9990 chunk 74 optimal weight: 40.0000 chunk 96 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 82 optimal weight: 40.0000 chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 0.0570 overall best weight: 2.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN B 172 HIS ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1086 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11193 Z= 0.279 Angle : 0.761 11.468 15253 Z= 0.388 Chirality : 0.047 0.221 1711 Planarity : 0.006 0.065 1953 Dihedral : 5.652 35.529 1484 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer: Outliers : 2.16 % Allowed : 17.37 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.22), residues: 1375 helix: 0.30 (0.27), residues: 382 sheet: -0.78 (0.40), residues: 179 loop : -1.65 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 617 HIS 0.010 0.001 HIS A 615 PHE 0.056 0.002 PHE B 434 TYR 0.018 0.002 TYR B 221 ARG 0.008 0.001 ARG B 257 *********************** 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 75 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 50 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1328 (pt) cc_final: 0.0794 (tt) REVERT: A 261 GLU cc_start: -0.0947 (OUTLIER) cc_final: -0.1570 (tt0) REVERT: A 485 MET cc_start: 0.4951 (mmm) cc_final: 0.3876 (mtm) REVERT: C 9 TRP cc_start: 0.0115 (p90) cc_final: -0.0862 (p-90) REVERT: D 99 LEU cc_start: 0.2703 (OUTLIER) cc_final: 0.2341 (tp) REVERT: B 78 THR cc_start: -0.1930 (OUTLIER) cc_final: -0.3172 (p) REVERT: B 89 LEU cc_start: -0.0865 (OUTLIER) cc_final: -0.1276 (tt) REVERT: B 124 LEU cc_start: -0.0903 (OUTLIER) cc_final: -0.1369 (mm) REVERT: B 135 HIS cc_start: 0.0394 (OUTLIER) cc_final: -0.1280 (m90) REVERT: B 165 LEU cc_start: 0.0840 (OUTLIER) cc_final: 0.0367 (mt) outliers start: 25 outliers final: 15 residues processed: 73 average time/residue: 0.2325 time to fit residues: 24.9930 Evaluate side-chains 70 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 48 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain C residue 121 LEU 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 78 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 124 LEU 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 268 ARG 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 83 optimal weight: 40.0000 chunk 89 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 12 optimal weight: 0.0870 chunk 103 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0937 moved from start: 0.6680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11193 Z= 0.160 Angle : 0.613 10.364 15253 Z= 0.313 Chirality : 0.043 0.173 1711 Planarity : 0.004 0.050 1953 Dihedral : 4.797 25.237 1484 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.89 % Favored : 93.96 % Rotamer: Outliers : 1.82 % Allowed : 17.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1375 helix: 0.58 (0.26), residues: 400 sheet: -0.64 (0.40), residues: 184 loop : -1.54 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 131 HIS 0.006 0.001 HIS A 615 PHE 0.018 0.001 PHE B 434 TYR 0.013 0.001 TYR B 279 ARG 0.005 0.001 ARG C 94 *********************** 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 71 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 50 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 261 GLU cc_start: -0.1097 (OUTLIER) cc_final: -0.1698 (tt0) REVERT: A 331 GLN cc_start: 0.0257 (OUTLIER) cc_final: -0.1822 (tt0) REVERT: A 485 MET cc_start: 0.4917 (mmm) cc_final: 0.3919 (mtm) REVERT: C 9 TRP cc_start: 0.0064 (p90) cc_final: -0.0985 (p-90) REVERT: C 45 ARG cc_start: 0.2690 (ttp-170) cc_final: 0.1531 (ttp-170) REVERT: D 99 LEU cc_start: 0.3087 (OUTLIER) cc_final: 0.2623 (tp) REVERT: B 89 LEU cc_start: -0.0997 (OUTLIER) cc_final: -0.1405 (tt) REVERT: B 135 HIS cc_start: 0.0326 (OUTLIER) cc_final: -0.0641 (m90) outliers start: 21 outliers final: 11 residues processed: 70 average time/residue: 0.2484 time to fit residues: 25.3510 Evaluate side-chains 62 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP 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 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 401 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 125 optimal weight: 20.0000 chunk 73 optimal weight: 30.0000 chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 37 optimal weight: 50.0000 chunk 110 optimal weight: 6.9990 chunk 115 optimal weight: 0.0570 chunk 121 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 129 optimal weight: 0.0570 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 449 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0992 moved from start: 0.6923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11193 Z= 0.179 Angle : 0.642 9.488 15253 Z= 0.326 Chirality : 0.043 0.168 1711 Planarity : 0.005 0.051 1953 Dihedral : 4.823 28.416 1484 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.47 % Favored : 93.38 % Rotamer: Outliers : 1.90 % Allowed : 17.98 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.22), residues: 1375 helix: 0.61 (0.27), residues: 396 sheet: -0.51 (0.40), residues: 184 loop : -1.49 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 131 HIS 0.006 0.001 HIS B 172 PHE 0.026 0.001 PHE B 434 TYR 0.012 0.001 TYR B 230 ARG 0.005 0.000 ARG B 268 *********************** 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 71 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 49 time to evaluate : 1.026 Fit side-chains REVERT: A 261 GLU cc_start: -0.1326 (OUTLIER) cc_final: -0.1894 (tt0) REVERT: A 331 GLN cc_start: 0.0332 (OUTLIER) cc_final: -0.1908 (tt0) REVERT: A 485 MET cc_start: 0.4842 (mmm) cc_final: 0.3848 (mtm) REVERT: C 9 TRP cc_start: 0.0075 (p90) cc_final: -0.1122 (p90) REVERT: C 19 LYS cc_start: -0.0531 (ttpt) cc_final: -0.1296 (ttpt) REVERT: D 99 LEU cc_start: 0.3016 (OUTLIER) cc_final: 0.2618 (tp) REVERT: B 89 LEU cc_start: -0.1035 (OUTLIER) cc_final: -0.1425 (tt) REVERT: B 135 HIS cc_start: 0.0547 (OUTLIER) cc_final: -0.1015 (m90) outliers start: 22 outliers final: 15 residues processed: 71 average time/residue: 0.2251 time to fit residues: 23.6997 Evaluate side-chains 66 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 46 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 561 THR Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 131 TRP 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 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 359 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 4.9990 chunk 61 optimal weight: 0.4980 chunk 89 optimal weight: 0.8980 chunk 135 optimal weight: 0.0040 chunk 124 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 11 optimal weight: 40.0000 chunk 83 optimal weight: 30.0000 chunk 66 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 1.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN C 42 GLN B 322 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1050 moved from start: 0.7296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11193 Z= 0.210 Angle : 0.692 14.331 15253 Z= 0.351 Chirality : 0.045 0.169 1711 Planarity : 0.005 0.051 1953 Dihedral : 5.003 30.455 1484 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer: Outliers : 1.73 % Allowed : 18.84 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.23), residues: 1375 helix: 0.57 (0.27), residues: 391 sheet: -0.55 (0.39), residues: 184 loop : -1.49 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 131 HIS 0.015 0.001 HIS B 310 PHE 0.034 0.001 PHE B 434 TYR 0.018 0.001 TYR B 324 ARG 0.006 0.001 ARG B 268 ********************** 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 74 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 54 time to evaluate : 1.147 Fit side-chains REVERT: A 248 LYS cc_start: -0.0733 (pttt) cc_final: -0.1503 (pttm) REVERT: A 261 GLU cc_start: -0.1277 (OUTLIER) cc_final: -0.1832 (tt0) REVERT: A 485 MET cc_start: 0.4869 (mmm) cc_final: 0.3859 (mtm) REVERT: C 9 TRP cc_start: 0.0076 (p90) cc_final: -0.1122 (p90) REVERT: C 19 LYS cc_start: -0.0568 (ttpt) cc_final: -0.1179 (ttpt) REVERT: D 99 LEU cc_start: 0.2959 (OUTLIER) cc_final: 0.2510 (tp) REVERT: B 89 LEU cc_start: -0.0876 (OUTLIER) cc_final: -0.1276 (tt) REVERT: B 135 HIS cc_start: 0.0685 (OUTLIER) cc_final: -0.0853 (m90) outliers start: 20 outliers final: 15 residues processed: 74 average time/residue: 0.2308 time to fit residues: 25.3411 Evaluate side-chains 69 residues out of total 1257 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 50 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU 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 105 GLN Chi-restraints excluded: chain C residue 131 TRP 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 78 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 359 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 0.6980 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 chunk 94 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 HIS C 78 HIS ** D 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.305948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.264726 restraints weight = 15356.089| |-----------------------------------------------------------------------------| r_work (start): 0.4798 rms_B_bonded: 3.18 r_work: 0.4605 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0734 moved from start: 0.8211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11193 Z= 0.336 Angle : 0.866 14.186 15253 Z= 0.445 Chirality : 0.050 0.245 1711 Planarity : 0.006 0.057 1953 Dihedral : 6.171 39.985 1484 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.24 % Favored : 90.62 % Rotamer: Outliers : 1.82 % Allowed : 19.01 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 1.61 % Twisted Proline : 1.25 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.22), residues: 1375 helix: 0.11 (0.26), residues: 390 sheet: -0.39 (0.46), residues: 130 loop : -1.72 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP B 189 HIS 0.014 0.002 HIS A 615 PHE 0.056 0.002 PHE B 434 TYR 0.020 0.002 TYR B 456 ARG 0.010 0.001 ARG A 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2208.50 seconds wall clock time: 40 minutes 25.77 seconds (2425.77 seconds total)