Starting phenix.real_space_refine on Fri Feb 14 23:23:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j5y_33733/02_2025/8j5y_33733.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j5y_33733/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j5y_33733/02_2025/8j5y_33733.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j5y_33733/02_2025/8j5y_33733.map" model { file = "/net/cci-nas-00/data/ceres_data/8j5y_33733/02_2025/8j5y_33733.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j5y_33733/02_2025/8j5y_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-5592/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: 7.50, per 1000 atoms: 0.69 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: 2.35 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: 1.19 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: 3.25 Time building geometry restraints manager: 2.82 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: 1.530 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 26.870 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.107 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: 0.2234 time to fit residues: 32.8942 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 : 1.089 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5231 r_free = 0.5231 target = 0.303337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4870 r_free = 0.4870 target = 0.251492 restraints weight = 13257.965| |-----------------------------------------------------------------------------| r_work (start): 0.4739 rms_B_bonded: 3.22 r_work: 0.4371 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0055 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 to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1123 (pt) cc_final: 0.0868 (tp) REVERT: A 485 MET cc_start: 0.3696 (mmm) cc_final: 0.2972 (mtm) REVERT: A 489 ASP cc_start: 0.3307 (t0) cc_final: 0.2111 (p0) REVERT: A 581 GLU cc_start: -0.1031 (tt0) cc_final: -0.3142 (pp20) REVERT: C 114 THR cc_start: -0.1851 (t) cc_final: -0.2722 (p) REVERT: B 188 LEU cc_start: 0.3043 (tt) cc_final: 0.2654 (mt) REVERT: B 231 LEU cc_start: 0.1539 (mp) cc_final: 0.0640 (tp) REVERT: B 301 LEU cc_start: 0.2735 (pt) cc_final: 0.1053 (tp) outliers start: 9 outliers final: 3 residues processed: 78 average time/residue: 0.2064 time to fit residues: 25.0573 Evaluate side-chains 63 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 121 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 24 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 120 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 134 optimal weight: 6.9990 chunk 3 optimal weight: 50.0000 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 449 HIS ** A 615 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN B 286 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 GLN B 374 ASN B 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5205 r_free = 0.5205 target = 0.300171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4871 r_free = 0.4871 target = 0.250873 restraints weight = 14461.815| |-----------------------------------------------------------------------------| r_work (start): 0.4757 rms_B_bonded: 3.08 r_work: 0.4459 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0373 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 11193 Z= 0.287 Angle : 0.791 10.485 15253 Z= 0.407 Chirality : 0.048 0.284 1711 Planarity : 0.006 0.117 1953 Dihedral : 5.384 32.680 1484 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.11 % Favored : 93.67 % Rotamer: Outliers : 1.99 % Allowed : 10.29 % Favored : 87.73 % 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: -1.32 (0.22), residues: 1375 helix: 0.24 (0.26), residues: 395 sheet: -1.01 (0.35), residues: 214 loop : -1.45 (0.21), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 121 HIS 0.010 0.002 HIS C 54 PHE 0.035 0.002 PHE B 442 TYR 0.019 0.002 TYR C 159 ARG 0.009 0.001 ARG B 268 *********************** 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 88 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1227 (pt) cc_final: 0.0825 (tt) REVERT: A 443 LYS cc_start: 0.0330 (mttp) cc_final: 0.0104 (ptpt) REVERT: A 485 MET cc_start: 0.4504 (mmm) cc_final: 0.3496 (mtm) REVERT: A 489 ASP cc_start: 0.3523 (t0) cc_final: 0.2161 (p0) REVERT: C 9 TRP cc_start: -0.0470 (p90) cc_final: -0.1706 (p90) REVERT: C 15 LEU cc_start: -0.3070 (tp) cc_final: -0.3767 (mt) REVERT: B 79 MET cc_start: 0.1944 (tmm) cc_final: 0.0983 (tmm) REVERT: B 268 ARG cc_start: -0.0486 (OUTLIER) cc_final: -0.1834 (ttt180) REVERT: B 280 LEU cc_start: -0.0482 (OUTLIER) cc_final: -0.1489 (mt) REVERT: B 301 LEU cc_start: 0.2581 (pt) cc_final: 0.0836 (tp) outliers start: 23 outliers final: 16 residues processed: 86 average time/residue: 0.2513 time to fit residues: 31.2814 Evaluate side-chains 71 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 SER 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 268 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 376 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 582 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 110 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 3 optimal weight: 50.0000 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 122 optimal weight: 40.0000 chunk 62 optimal weight: 0.0870 chunk 84 optimal weight: 0.3980 chunk 127 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 chunk 117 optimal weight: 0.0060 overall best weight: 0.3974 ------------------------------------------------------------------------------- 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 172 HIS ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 371 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 = 0.5206 r_free = 0.5206 target = 0.299966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4896 r_free = 0.4896 target = 0.253793 restraints weight = 14219.585| |-----------------------------------------------------------------------------| r_work (start): 0.4795 rms_B_bonded: 2.91 r_work: 0.4454 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0300 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11193 Z= 0.156 Angle : 0.607 8.884 15253 Z= 0.310 Chirality : 0.043 0.167 1711 Planarity : 0.005 0.062 1953 Dihedral : 4.538 26.058 1484 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.67 % Favored : 94.25 % Rotamer: Outliers : 1.73 % Allowed : 13.05 % Favored : 85.22 % 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: 0.42 (0.26), residues: 411 sheet: -0.86 (0.35), residues: 213 loop : -1.39 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 131 HIS 0.007 0.001 HIS B 560 PHE 0.014 0.001 PHE B 434 TYR 0.016 0.001 TYR D 88 ARG 0.004 0.000 ARG A 577 *********************** 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 74 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 1.142 Fit side-chains revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1232 (pt) cc_final: 0.0836 (tt) REVERT: A 443 LYS cc_start: 0.0377 (mttp) cc_final: 0.0151 (ptpt) REVERT: A 485 MET cc_start: 0.4526 (mmm) cc_final: 0.3502 (mtm) REVERT: C 9 TRP cc_start: -0.0208 (p90) cc_final: -0.1129 (p90) REVERT: C 15 LEU cc_start: -0.3177 (tp) cc_final: -0.3886 (mt) REVERT: C 114 THR cc_start: -0.1286 (t) cc_final: -0.2193 (p) REVERT: B 124 LEU cc_start: -0.3209 (OUTLIER) cc_final: -0.3902 (mt) REVERT: B 268 ARG cc_start: -0.0967 (OUTLIER) cc_final: -0.2904 (mmt-90) REVERT: B 280 LEU cc_start: -0.0889 (OUTLIER) cc_final: -0.1812 (mt) REVERT: B 375 HIS cc_start: 0.2117 (m-70) cc_final: 0.1464 (t70) outliers start: 20 outliers final: 10 residues processed: 70 average time/residue: 0.2822 time to fit residues: 29.4049 Evaluate side-chains 63 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 50 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 131 TRP 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 124 LEU Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 418 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 124 optimal weight: 30.0000 chunk 78 optimal weight: 0.7980 chunk 59 optimal weight: 40.0000 chunk 62 optimal weight: 0.0270 chunk 1 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 26 optimal weight: 30.0000 chunk 42 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 17 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN ** 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 = 0.5199 r_free = 0.5199 target = 0.299234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4877 r_free = 0.4877 target = 0.253024 restraints weight = 14460.087| |-----------------------------------------------------------------------------| r_work (start): 0.4782 rms_B_bonded: 3.83 r_work: 0.4405 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0349 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11193 Z= 0.177 Angle : 0.623 13.854 15253 Z= 0.317 Chirality : 0.043 0.158 1711 Planarity : 0.005 0.075 1953 Dihedral : 4.473 22.521 1484 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.96 % Favored : 93.89 % Rotamer: Outliers : 2.25 % Allowed : 14.09 % Favored : 83.66 % 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: 0.40 (0.26), residues: 414 sheet: -0.78 (0.35), residues: 215 loop : -1.50 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 131 HIS 0.009 0.001 HIS B 172 PHE 0.020 0.001 PHE B 434 TYR 0.027 0.001 TYR D 88 ARG 0.005 0.000 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 77 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 51 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 216 LEU cc_start: 0.1168 (pt) cc_final: 0.0786 (tt) REVERT: A 443 LYS cc_start: 0.0283 (mttp) cc_final: 0.0081 (ptpt) REVERT: A 485 MET cc_start: 0.4670 (mmm) cc_final: 0.3637 (mtm) REVERT: C 9 TRP cc_start: -0.0647 (p90) cc_final: -0.1505 (p90) REVERT: C 15 LEU cc_start: -0.3246 (tp) cc_final: -0.3939 (mt) REVERT: C 114 THR cc_start: -0.1769 (t) cc_final: -0.2556 (p) REVERT: D 99 LEU cc_start: 0.2895 (OUTLIER) cc_final: 0.2370 (tp) REVERT: B 95 PHE cc_start: 0.3351 (p90) cc_final: 0.2522 (p90) REVERT: B 268 ARG cc_start: -0.1078 (OUTLIER) cc_final: -0.2269 (mmm160) REVERT: B 280 LEU cc_start: -0.1053 (OUTLIER) cc_final: -0.1749 (mm) REVERT: B 311 LEU cc_start: -0.1515 (OUTLIER) cc_final: -0.2078 (mt) REVERT: B 453 GLN cc_start: -0.0135 (OUTLIER) cc_final: -0.0629 (mp10) outliers start: 26 outliers final: 14 residues processed: 75 average time/residue: 0.2671 time to fit residues: 29.2964 Evaluate side-chains 67 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 1.150 ------------------------------------------------------------------------------- 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 121 LEU 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 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 166 ARG Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 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 52 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 112 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 chunk 106 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 50.0000 chunk 98 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 149 ASN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5222 r_free = 0.5222 target = 0.303580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.264718 restraints weight = 14974.670| |-----------------------------------------------------------------------------| r_work (start): 0.4853 rms_B_bonded: 3.24 r_work: 0.4503 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0489 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11193 Z= 0.258 Angle : 0.747 9.919 15253 Z= 0.384 Chirality : 0.046 0.165 1711 Planarity : 0.006 0.121 1953 Dihedral : 5.195 30.896 1484 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.84 % Favored : 93.02 % Rotamer: Outliers : 2.07 % Allowed : 15.47 % Favored : 82.45 % 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: -1.27 (0.22), residues: 1375 helix: 0.29 (0.26), residues: 398 sheet: -0.67 (0.36), residues: 202 loop : -1.54 (0.21), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 124 HIS 0.010 0.001 HIS B 172 PHE 0.040 0.002 PHE B 434 TYR 0.022 0.002 TYR C 51 ARG 0.011 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 75 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 1.133 Fit side-chains REVERT: A 216 LEU cc_start: 0.0628 (pt) cc_final: 0.0400 (tt) REVERT: A 249 ASN cc_start: 0.0266 (m-40) cc_final: -0.0671 (m110) REVERT: A 443 LYS cc_start: 0.0463 (mttp) cc_final: 0.0197 (ptpt) REVERT: A 485 MET cc_start: 0.4703 (mmm) cc_final: 0.3779 (mtm) REVERT: C 9 TRP cc_start: -0.0486 (p90) cc_final: -0.1902 (p90) REVERT: C 19 LYS cc_start: -0.1471 (ttpt) cc_final: -0.1890 (ttpt) REVERT: D 99 LEU cc_start: 0.2795 (OUTLIER) cc_final: 0.2277 (tp) REVERT: D 143 MET cc_start: 0.1180 (ptt) cc_final: 0.0887 (ptp) REVERT: B 78 THR cc_start: -0.2090 (OUTLIER) cc_final: -0.3387 (p) REVERT: B 95 PHE cc_start: 0.3450 (p90) cc_final: 0.3179 (p90) REVERT: B 124 LEU cc_start: -0.3598 (OUTLIER) cc_final: -0.3840 (mm) outliers start: 24 outliers final: 14 residues processed: 74 average time/residue: 0.2446 time to fit residues: 26.6921 Evaluate side-chains 65 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 158 HIS 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 166 ARG Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 365 ILE Chi-restraints excluded: chain B residue 386 LEU Chi-restraints excluded: chain B residue 400 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 1 optimal weight: 30.0000 chunk 84 optimal weight: 0.0870 chunk 114 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 125 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 59 optimal weight: 30.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 C 104 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5227 r_free = 0.5227 target = 0.304701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4971 r_free = 0.4971 target = 0.265384 restraints weight = 14978.201| |-----------------------------------------------------------------------------| r_work (start): 0.4854 rms_B_bonded: 3.24 r_work: 0.4496 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0400 moved from start: 0.5772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11193 Z= 0.152 Angle : 0.601 10.571 15253 Z= 0.305 Chirality : 0.043 0.171 1711 Planarity : 0.005 0.074 1953 Dihedral : 4.476 21.923 1484 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.82 % Favored : 94.04 % Rotamer: Outliers : 1.64 % Allowed : 16.68 % 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 (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: -1.09 (0.22), residues: 1375 helix: 0.57 (0.26), residues: 403 sheet: -0.59 (0.36), residues: 210 loop : -1.51 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 131 HIS 0.006 0.001 HIS B 560 PHE 0.016 0.001 PHE B 434 TYR 0.010 0.001 TYR C 51 ARG 0.008 0.000 ARG B 268 *********************** 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 68 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 1.212 Fit side-chains revert: symmetry clash REVERT: A 249 ASN cc_start: -0.0085 (m-40) cc_final: -0.0897 (m110) REVERT: A 443 LYS cc_start: 0.0380 (mttp) cc_final: 0.0098 (ptpt) REVERT: A 485 MET cc_start: 0.4698 (mmm) cc_final: 0.3821 (mtm) REVERT: D 99 LEU cc_start: 0.2988 (OUTLIER) cc_final: 0.2365 (tp) REVERT: B 95 PHE cc_start: 0.3152 (p90) cc_final: 0.2925 (p90) REVERT: B 135 HIS cc_start: -0.0267 (OUTLIER) cc_final: -0.1191 (p90) outliers start: 19 outliers final: 15 residues processed: 66 average time/residue: 0.2338 time to fit residues: 23.4674 Evaluate side-chains 64 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 90 MET 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 C residue 158 HIS 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 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 268 ARG 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 10 optimal weight: 0.5980 chunk 109 optimal weight: 8.9990 chunk 100 optimal weight: 3.9990 chunk 38 optimal weight: 40.0000 chunk 22 optimal weight: 50.0000 chunk 35 optimal weight: 7.9990 chunk 8 optimal weight: 20.0000 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 30.0000 overall best weight: 4.5186 ------------------------------------------------------------------------------- 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 ASN B 180 HIS B 214 GLN ** B 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 449 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5204 r_free = 0.5204 target = 0.302175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4822 r_free = 0.4822 target = 0.256872 restraints weight = 15092.906| |-----------------------------------------------------------------------------| r_work (start): 0.4734 rms_B_bonded: 3.88 r_work: 0.4525 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.4525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0605 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 11193 Z= 0.441 Angle : 0.942 14.369 15253 Z= 0.482 Chirality : 0.051 0.208 1711 Planarity : 0.007 0.090 1953 Dihedral : 5.883 40.302 1484 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.15 % Favored : 91.71 % Rotamer: Outliers : 2.07 % Allowed : 17.11 % Favored : 80.81 % 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: -1.46 (0.22), residues: 1375 helix: 0.10 (0.26), residues: 391 sheet: -0.67 (0.37), residues: 187 loop : -1.65 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 222 HIS 0.017 0.002 HIS B 172 PHE 0.080 0.003 PHE B 434 TYR 0.042 0.003 TYR B 221 ARG 0.012 0.001 ARG B 268 *********************** 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 75 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 51 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 443 LYS cc_start: 0.0454 (mttp) cc_final: 0.0193 (ptpt) REVERT: A 485 MET cc_start: 0.4866 (mmm) cc_final: 0.4078 (mtm) REVERT: C 9 TRP cc_start: -0.0516 (p90) cc_final: -0.1351 (p90) REVERT: C 19 LYS cc_start: -0.1491 (ttpt) cc_final: -0.1834 (ttpt) REVERT: D 99 LEU cc_start: 0.2936 (OUTLIER) cc_final: 0.2372 (tp) REVERT: B 89 LEU cc_start: -0.3357 (OUTLIER) cc_final: -0.3659 (tt) REVERT: B 135 HIS cc_start: -0.0851 (OUTLIER) cc_final: -0.1642 (m170) REVERT: B 309 GLN cc_start: 0.2716 (tp40) cc_final: 0.1431 (pt0) REVERT: B 461 LEU cc_start: -0.0834 (OUTLIER) cc_final: -0.1327 (mp) outliers start: 24 outliers final: 18 residues processed: 72 average time/residue: 0.2590 time to fit residues: 27.2571 Evaluate side-chains 70 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 48 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 55 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 121 LEU 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 65 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 400 LEU Chi-restraints excluded: chain B residue 461 LEU 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 51 optimal weight: 0.5980 chunk 37 optimal weight: 0.0770 chunk 3 optimal weight: 40.0000 chunk 123 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 overall best weight: 1.9142 ------------------------------------------------------------------------------- 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 90 HIS B 286 GLN ** B 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.5206 r_free = 0.5206 target = 0.302503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.268434 restraints weight = 15349.907| |-----------------------------------------------------------------------------| r_work (start): 0.4889 rms_B_bonded: 2.86 r_work: 0.4589 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0555 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11193 Z= 0.223 Angle : 0.695 12.321 15253 Z= 0.352 Chirality : 0.045 0.202 1711 Planarity : 0.005 0.072 1953 Dihedral : 5.243 33.385 1484 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer: Outliers : 1.64 % Allowed : 17.72 % Favored : 80.64 % 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: -1.37 (0.22), residues: 1375 helix: 0.32 (0.26), residues: 399 sheet: -0.56 (0.40), residues: 165 loop : -1.69 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 222 HIS 0.009 0.001 HIS A 615 PHE 0.043 0.001 PHE B 434 TYR 0.017 0.002 TYR B 187 ARG 0.008 0.001 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 66 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 LYS cc_start: 0.0480 (mttp) cc_final: 0.0217 (ptpt) REVERT: A 485 MET cc_start: 0.4822 (mmm) cc_final: 0.4032 (mtm) REVERT: C 9 TRP cc_start: -0.0538 (p90) cc_final: -0.1516 (p-90) REVERT: C 18 LEU cc_start: -0.2009 (OUTLIER) cc_final: -0.2239 (tp) REVERT: D 99 LEU cc_start: 0.3051 (OUTLIER) cc_final: 0.2453 (tp) REVERT: B 135 HIS cc_start: -0.0819 (OUTLIER) cc_final: -0.1621 (m170) outliers start: 19 outliers final: 15 residues processed: 63 average time/residue: 0.2428 time to fit residues: 23.1410 Evaluate side-chains 63 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 1.132 ------------------------------------------------------------------------------- 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 18 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain C residue 121 LEU 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 135 HIS Chi-restraints excluded: chain B residue 211 ASP Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 286 GLN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 123 optimal weight: 9.9990 chunk 83 optimal weight: 40.0000 chunk 45 optimal weight: 50.0000 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 60 optimal weight: 30.0000 chunk 124 optimal weight: 10.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN ** C 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 GLN ** B 316 ASN ** 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 = 0.5236 r_free = 0.5236 target = 0.305857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4873 r_free = 0.4873 target = 0.262522 restraints weight = 14961.341| |-----------------------------------------------------------------------------| r_work (start): 0.4770 rms_B_bonded: 3.79 r_work: 0.4576 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.4576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0645 moved from start: 0.7553 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= 0.336 Angle : 0.851 11.098 15253 Z= 0.433 Chirality : 0.049 0.209 1711 Planarity : 0.006 0.068 1953 Dihedral : 5.932 38.821 1484 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.95 % Favored : 90.91 % Rotamer: Outliers : 2.33 % Allowed : 17.37 % Favored : 80.29 % 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: -1.58 (0.22), residues: 1375 helix: 0.09 (0.26), residues: 394 sheet: -0.45 (0.42), residues: 150 loop : -1.81 (0.21), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 189 HIS 0.011 0.002 HIS A 615 PHE 0.067 0.002 PHE B 434 TYR 0.028 0.002 TYR B 187 ARG 0.011 0.001 ARG B 440 ********************** 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 78 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 51 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 443 LYS cc_start: 0.0381 (mttp) cc_final: 0.0169 (ptpt) REVERT: A 485 MET cc_start: 0.4777 (mmm) cc_final: 0.4012 (mtm) REVERT: A 489 ASP cc_start: 0.3107 (t0) cc_final: 0.2073 (p0) REVERT: C 9 TRP cc_start: -0.0735 (p90) cc_final: -0.1891 (p90) REVERT: C 90 MET cc_start: 0.0097 (OUTLIER) cc_final: -0.1116 (mmm) REVERT: C 143 MET cc_start: 0.0429 (tpt) cc_final: 0.0143 (tpt) REVERT: D 99 LEU cc_start: 0.2982 (OUTLIER) cc_final: 0.2333 (tp) REVERT: B 135 HIS cc_start: -0.0709 (OUTLIER) cc_final: -0.1280 (m-70) REVERT: B 166 ARG cc_start: -0.1426 (OUTLIER) cc_final: -0.3163 (mmt90) outliers start: 27 outliers final: 19 residues processed: 75 average time/residue: 0.2457 time to fit residues: 27.0658 Evaluate side-chains 68 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 45 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 18 LEU 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 158 HIS 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 135 HIS Chi-restraints excluded: chain B residue 166 ARG Chi-restraints excluded: chain B residue 211 ASP 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 56 optimal weight: 0.0010 chunk 25 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 35 optimal weight: 50.0000 chunk 104 optimal weight: 0.8980 chunk 1 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 40 optimal weight: 50.0000 chunk 61 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- 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** D 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5226 r_free = 0.5226 target = 0.305858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4929 r_free = 0.4929 target = 0.268362 restraints weight = 14949.314| |-----------------------------------------------------------------------------| r_work (start): 0.4855 rms_B_bonded: 3.88 r_work: 0.4596 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0580 moved from start: 0.7484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11193 Z= 0.174 Angle : 0.661 11.829 15253 Z= 0.334 Chirality : 0.044 0.180 1711 Planarity : 0.005 0.052 1953 Dihedral : 5.011 30.094 1484 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.69 % Favored : 93.16 % Rotamer: Outliers : 1.73 % Allowed : 17.89 % Favored : 80.38 % 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: -1.29 (0.22), residues: 1375 helix: 0.41 (0.26), residues: 400 sheet: -0.40 (0.40), residues: 165 loop : -1.69 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 131 HIS 0.008 0.001 HIS B 310 PHE 0.029 0.001 PHE B 434 TYR 0.011 0.001 TYR C 51 ARG 0.006 0.001 ARG A 610 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6170.14 seconds wall clock time: 110 minutes 8.67 seconds (6608.67 seconds total)