Starting phenix.real_space_refine on Thu Nov 14 21:05:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8m_36074/11_2024/8j8m_36074_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8m_36074/11_2024/8j8m_36074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8m_36074/11_2024/8j8m_36074.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8m_36074/11_2024/8j8m_36074.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8m_36074/11_2024/8j8m_36074_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j8m_36074/11_2024/8j8m_36074_neut.cif" } resolution = 3.58 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= -0.001 sd= 0.039 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 4811 2.51 5 N 1188 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7362 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3656 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 22, 'TRANS': 446} Chain: "B" Number of atoms: 3579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3579 Classifications: {'peptide': 463} Link IDs: {'PTRANS': 24, 'TRANS': 438} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Time building chain proxies: 4.85, per 1000 atoms: 0.66 Number of scatterers: 7362 At special positions: 0 Unit cell: (99.645, 83.22, 125.925, 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 1336 8.00 N 1188 7.00 C 4811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS B 164 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN A 507 " " NAG D 1 " - " ASN A 382 " " NAG E 1 " - " ASN A 366 " " NAG F 1 " - " ASN A 425 " Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 1.1 seconds 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1718 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 4 sheets defined 58.8% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 178 through 207 removed outlier: 3.672A pdb=" N ARG A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TRP A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 removed outlier: 5.276A pdb=" N ASP A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N TYR A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 252 " --> pdb=" O ARG A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 301 Processing helix chain 'A' and resid 324 through 340 removed outlier: 4.371A pdb=" N GLU A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE A 337 " --> pdb=" O ASP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 356 through 372 removed outlier: 3.747A pdb=" N PHE A 360 " --> pdb=" O ASP A 356 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE A 371 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 372 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.552A pdb=" N ASP A 408 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 409 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 428 Processing helix chain 'A' and resid 450 through 459 removed outlier: 3.817A pdb=" N PHE A 459 " --> pdb=" O GLN A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 516 removed outlier: 4.218A pdb=" N GLU A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASP A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.800A pdb=" N SER A 532 " --> pdb=" O SER A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 540 Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.593A pdb=" N ILE B 59 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 79 removed outlier: 3.648A pdb=" N VAL B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 81 through 110 Processing helix chain 'B' and resid 115 through 123 removed outlier: 3.732A pdb=" N LEU B 121 " --> pdb=" O TYR B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 139 removed outlier: 3.796A pdb=" N ALA B 129 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 158 removed outlier: 3.702A pdb=" N GLN B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 167 through 189 removed outlier: 3.581A pdb=" N SER B 189 " --> pdb=" O VAL B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 221 removed outlier: 3.661A pdb=" N ALA B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.724A pdb=" N PHE B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALA B 253 " --> pdb=" O SER B 249 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TYR B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 264 Processing helix chain 'B' and resid 269 through 300 removed outlier: 3.596A pdb=" N LEU B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Proline residue: B 275 - end of helix Proline residue: B 283 - end of helix removed outlier: 3.795A pdb=" N THR B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 300 " --> pdb=" O TYR B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 308 Processing helix chain 'B' and resid 310 through 320 Processing helix chain 'B' and resid 325 through 356 removed outlier: 3.795A pdb=" N VAL B 329 " --> pdb=" O TRP B 325 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N SER B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 356 " --> pdb=" O VAL B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 387 through 390 removed outlier: 3.566A pdb=" N SER B 390 " --> pdb=" O TYR B 387 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 387 through 390' Processing helix chain 'B' and resid 393 through 395 No H-bonds generated for 'chain 'B' and resid 393 through 395' Processing helix chain 'B' and resid 396 through 422 removed outlier: 3.534A pdb=" N PHE B 400 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE B 402 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B 409 " --> pdb=" O TRP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 454 Processing helix chain 'B' and resid 454 through 466 removed outlier: 3.726A pdb=" N ILE B 465 " --> pdb=" O GLY B 461 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 467 through 476 removed outlier: 4.359A pdb=" N VAL B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 482 through 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 225 through 227 removed outlier: 6.320A pdb=" N LEU A 225 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N CYS A 432 " --> pdb=" O THR A 464 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL A 466 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N TRP A 434 " --> pdb=" O VAL A 466 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N SER A 468 " --> pdb=" O TRP A 434 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 5.917A pdb=" N LEU A 260 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASP A 308 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 8.496A pdb=" N GLN A 347 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 307 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 8.712A pdb=" N ARG A 349 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 377 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N THR A 402 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA A 379 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 541 through 545 removed outlier: 4.203A pdb=" N SER A 553 " --> pdb=" O PHE A 545 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLY A 622 " --> pdb=" O SER A 599 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N SER A 599 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU A 624 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 597 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 594 " --> pdb=" O LEU A 610 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 575 through 576 379 hydrogen bonds defined for protein. 1113 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: 2.07 Time building geometry restraints manager: 2.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2229 1.34 - 1.45: 1114 1.45 - 1.57: 4161 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 7544 Sorted by residual: bond pdb=" CD2 TRP B 601 " pdb=" CE3 TRP B 601 " ideal model delta sigma weight residual 1.398 1.555 -0.157 1.60e-02 3.91e+03 9.64e+01 bond pdb=" CE2 TRP B 601 " pdb=" CZ2 TRP B 601 " ideal model delta sigma weight residual 1.394 1.549 -0.155 2.10e-02 2.27e+03 5.47e+01 bond pdb=" CZ2 TRP B 601 " pdb=" CH2 TRP B 601 " ideal model delta sigma weight residual 1.368 1.491 -0.123 1.90e-02 2.77e+03 4.17e+01 bond pdb=" CG TRP B 601 " pdb=" CD2 TRP B 601 " ideal model delta sigma weight residual 1.433 1.341 0.092 1.80e-02 3.09e+03 2.61e+01 bond pdb=" CE3 TRP B 601 " pdb=" CZ3 TRP B 601 " ideal model delta sigma weight residual 1.382 1.493 -0.111 3.00e-02 1.11e+03 1.36e+01 ... (remaining 7539 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 9945 1.61 - 3.22: 249 3.22 - 4.83: 53 4.83 - 6.43: 19 6.43 - 8.04: 8 Bond angle restraints: 10274 Sorted by residual: angle pdb=" C PHE B 231 " pdb=" CA PHE B 231 " pdb=" CB PHE B 231 " ideal model delta sigma weight residual 116.54 110.91 5.63 1.15e+00 7.56e-01 2.40e+01 angle pdb=" CA ILE B 327 " pdb=" C ILE B 327 " pdb=" N PRO B 328 " ideal model delta sigma weight residual 120.83 118.02 2.81 5.90e-01 2.87e+00 2.27e+01 angle pdb=" N TRP B 325 " pdb=" CA TRP B 325 " pdb=" C TRP B 325 " ideal model delta sigma weight residual 114.31 109.78 4.53 1.29e+00 6.01e-01 1.23e+01 angle pdb=" CG TRP B 601 " pdb=" CD2 TRP B 601 " pdb=" CE3 TRP B 601 " ideal model delta sigma weight residual 133.90 130.50 3.40 1.00e+00 1.00e+00 1.16e+01 angle pdb=" N GLY B 321 " pdb=" CA GLY B 321 " pdb=" C GLY B 321 " ideal model delta sigma weight residual 115.59 111.10 4.49 1.32e+00 5.74e-01 1.16e+01 ... (remaining 10269 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.12: 4096 23.12 - 46.23: 306 46.23 - 69.35: 56 69.35 - 92.47: 30 92.47 - 115.58: 32 Dihedral angle restraints: 4520 sinusoidal: 1847 harmonic: 2673 Sorted by residual: dihedral pdb=" CB CYS A 211 " pdb=" SG CYS A 211 " pdb=" SG CYS B 164 " pdb=" CB CYS B 164 " ideal model delta sinusoidal sigma weight residual 93.00 -177.18 -89.82 1 1.00e+01 1.00e-02 9.57e+01 dihedral pdb=" O3 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" O4 NAG C 2 " ideal model delta sinusoidal sigma weight residual 295.45 179.87 115.58 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C2 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" C4 NAG C 2 " pdb=" O4 NAG C 2 " ideal model delta sinusoidal sigma weight residual 175.11 60.03 115.08 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 4517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.194: 1207 0.194 - 0.389: 3 0.389 - 0.583: 1 0.583 - 0.778: 0 0.778 - 0.972: 1 Chirality restraints: 1212 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.43 -0.97 2.00e-02 2.50e+03 2.36e+03 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-02 2.50e+03 1.37e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.89e+01 ... (remaining 1209 not shown) Planarity restraints: 1275 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 366 " 0.160 2.00e-02 2.50e+03 3.78e-01 1.78e+03 pdb=" CG ASN A 366 " -0.111 2.00e-02 2.50e+03 pdb=" OD1 ASN A 366 " 0.177 2.00e-02 2.50e+03 pdb=" ND2 ASN A 366 " -0.669 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " 0.443 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 425 " -0.217 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" CG ASN A 425 " 0.094 2.00e-02 2.50e+03 pdb=" OD1 ASN A 425 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN A 425 " 0.481 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.341 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.332 2.00e-02 2.50e+03 2.82e-01 9.96e+02 pdb=" C7 NAG D 2 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.178 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.495 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.068 2.00e-02 2.50e+03 ... (remaining 1272 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 717 2.74 - 3.28: 7868 3.28 - 3.82: 12483 3.82 - 4.36: 13722 4.36 - 4.90: 23686 Nonbonded interactions: 58476 Sorted by model distance: nonbonded pdb=" NE2 GLN B 145 " pdb=" OG SER B 342 " model vdw 2.203 3.120 nonbonded pdb=" OG1 THR A 460 " pdb=" OH TYR A 554 " model vdw 2.207 3.040 nonbonded pdb=" OH TYR A 469 " pdb=" O PRO A 488 " model vdw 2.220 3.040 nonbonded pdb=" OD1 ASP A 493 " pdb=" OG SER A 496 " model vdw 2.235 3.040 nonbonded pdb=" O TYR A 251 " pdb=" OG SER A 254 " model vdw 2.246 3.040 ... (remaining 58471 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 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.370 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.157 7544 Z= 0.312 Angle : 0.677 8.043 10274 Z= 0.347 Chirality : 0.053 0.972 1212 Planarity : 0.016 0.282 1271 Dihedral : 20.770 115.585 2799 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.89 % Allowed : 0.63 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.29), residues: 928 helix: 1.64 (0.25), residues: 498 sheet: -0.59 (0.58), residues: 63 loop : -1.04 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 478 HIS 0.004 0.001 HIS A 221 PHE 0.022 0.001 PHE A 320 TYR 0.013 0.001 TYR B 318 ARG 0.003 0.000 ARG B 421 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 0.902 Fit side-chains REVERT: A 508 MET cc_start: 0.7810 (mpp) cc_final: 0.7484 (mpp) REVERT: B 120 MET cc_start: 0.8447 (ttp) cc_final: 0.7933 (tmm) REVERT: B 132 LYS cc_start: 0.8921 (tptp) cc_final: 0.8695 (tptp) REVERT: B 305 MET cc_start: 0.9077 (mtt) cc_final: 0.8713 (mtt) REVERT: B 365 MET cc_start: 0.8216 (mpp) cc_final: 0.7951 (mpp) outliers start: 7 outliers final: 2 residues processed: 93 average time/residue: 0.1481 time to fit residues: 20.4547 Evaluate side-chains 59 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 327 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 77 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 438 GLN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN ** B 261 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 HIS B 505 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7544 Z= 0.227 Angle : 0.750 11.350 10274 Z= 0.337 Chirality : 0.046 0.300 1212 Planarity : 0.004 0.046 1271 Dihedral : 20.355 116.388 1160 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.27 % Allowed : 7.99 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.29), residues: 928 helix: 1.80 (0.24), residues: 505 sheet: -0.64 (0.59), residues: 63 loop : -0.95 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 478 HIS 0.005 0.001 HIS B 367 PHE 0.021 0.002 PHE B 439 TYR 0.014 0.001 TYR B 117 ARG 0.003 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 1.085 Fit side-chains REVERT: A 508 MET cc_start: 0.7763 (mpp) cc_final: 0.7183 (mpp) REVERT: B 305 MET cc_start: 0.9070 (mtt) cc_final: 0.8835 (mtt) REVERT: B 365 MET cc_start: 0.8223 (mpp) cc_final: 0.7874 (mpp) outliers start: 10 outliers final: 5 residues processed: 64 average time/residue: 0.1376 time to fit residues: 13.8021 Evaluate side-chains 53 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 28 optimal weight: 0.0980 chunk 67 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7544 Z= 0.165 Angle : 0.695 9.599 10274 Z= 0.307 Chirality : 0.045 0.294 1212 Planarity : 0.004 0.042 1271 Dihedral : 16.943 111.138 1156 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.40 % Allowed : 11.04 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.29), residues: 928 helix: 2.01 (0.24), residues: 500 sheet: -0.72 (0.60), residues: 65 loop : -0.93 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 405 HIS 0.004 0.001 HIS B 367 PHE 0.015 0.001 PHE B 439 TYR 0.012 0.001 TYR B 117 ARG 0.002 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.7894 (mpp) cc_final: 0.7305 (mpp) REVERT: B 365 MET cc_start: 0.8164 (mpp) cc_final: 0.7841 (mpp) outliers start: 11 outliers final: 9 residues processed: 63 average time/residue: 0.1362 time to fit residues: 13.4074 Evaluate side-chains 59 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 79 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 GLN ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7544 Z= 0.165 Angle : 0.685 12.931 10274 Z= 0.304 Chirality : 0.045 0.326 1212 Planarity : 0.003 0.039 1271 Dihedral : 15.145 111.682 1156 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 1.78 % Allowed : 13.83 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.29), residues: 928 helix: 2.11 (0.24), residues: 500 sheet: -0.66 (0.60), residues: 65 loop : -0.88 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 405 HIS 0.002 0.001 HIS B 367 PHE 0.013 0.001 PHE B 379 TYR 0.011 0.001 TYR B 117 ARG 0.002 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.833 Fit side-chains revert: symmetry clash REVERT: A 508 MET cc_start: 0.7975 (mpp) cc_final: 0.7327 (mpp) REVERT: B 365 MET cc_start: 0.8188 (mpp) cc_final: 0.7966 (mpp) outliers start: 14 outliers final: 10 residues processed: 63 average time/residue: 0.1366 time to fit residues: 13.3734 Evaluate side-chains 62 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 79 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7544 Z= 0.386 Angle : 0.777 11.178 10274 Z= 0.364 Chirality : 0.047 0.294 1212 Planarity : 0.004 0.044 1271 Dihedral : 14.485 111.703 1156 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 1.78 % Allowed : 16.24 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.28), residues: 928 helix: 1.83 (0.24), residues: 504 sheet: -0.92 (0.62), residues: 65 loop : -0.94 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 405 HIS 0.004 0.001 HIS A 266 PHE 0.020 0.002 PHE B 344 TYR 0.012 0.002 TYR B 117 ARG 0.006 0.001 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 48 time to evaluate : 0.841 Fit side-chains REVERT: A 508 MET cc_start: 0.8069 (mpp) cc_final: 0.7459 (mpp) REVERT: B 305 MET cc_start: 0.9031 (mtt) cc_final: 0.8794 (mtt) REVERT: B 365 MET cc_start: 0.8331 (mpp) cc_final: 0.8109 (mpp) outliers start: 14 outliers final: 11 residues processed: 58 average time/residue: 0.1351 time to fit residues: 12.4535 Evaluate side-chains 56 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 396 VAL Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 89 optimal weight: 0.0870 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 539 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7544 Z= 0.164 Angle : 0.678 13.737 10274 Z= 0.307 Chirality : 0.044 0.288 1212 Planarity : 0.003 0.039 1271 Dihedral : 14.079 112.847 1156 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.27 % Allowed : 17.01 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.29), residues: 928 helix: 2.13 (0.24), residues: 503 sheet: -0.65 (0.62), residues: 65 loop : -0.83 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 405 HIS 0.003 0.001 HIS B 367 PHE 0.014 0.001 PHE B 379 TYR 0.014 0.001 TYR A 251 ARG 0.001 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.857 Fit side-chains REVERT: A 508 MET cc_start: 0.8202 (mpp) cc_final: 0.7518 (mpp) REVERT: B 305 MET cc_start: 0.8959 (mtt) cc_final: 0.8748 (mtt) REVERT: B 365 MET cc_start: 0.8194 (mpp) cc_final: 0.7958 (mpp) outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 0.1596 time to fit residues: 13.6465 Evaluate side-chains 56 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 66 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 8.9990 chunk 50 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 88 optimal weight: 0.0050 chunk 55 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7544 Z= 0.158 Angle : 0.677 13.964 10274 Z= 0.306 Chirality : 0.043 0.289 1212 Planarity : 0.003 0.040 1271 Dihedral : 13.624 113.668 1156 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 1.14 % Allowed : 17.51 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 928 helix: 2.09 (0.24), residues: 510 sheet: -0.55 (0.63), residues: 65 loop : -0.82 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 405 HIS 0.002 0.001 HIS B 367 PHE 0.017 0.001 PHE B 379 TYR 0.012 0.001 TYR A 251 ARG 0.001 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.835 Fit side-chains REVERT: A 508 MET cc_start: 0.8256 (mpp) cc_final: 0.7542 (mpp) REVERT: B 289 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8296 (m-10) REVERT: B 305 MET cc_start: 0.8970 (mtt) cc_final: 0.8742 (mtt) REVERT: B 365 MET cc_start: 0.8239 (mpp) cc_final: 0.7986 (mpp) outliers start: 9 outliers final: 6 residues processed: 56 average time/residue: 0.1501 time to fit residues: 13.0960 Evaluate side-chains 54 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 80 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7544 Z= 0.181 Angle : 0.664 12.671 10274 Z= 0.301 Chirality : 0.043 0.287 1212 Planarity : 0.003 0.039 1271 Dihedral : 13.418 113.478 1156 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.14 % Allowed : 18.78 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.29), residues: 928 helix: 2.17 (0.24), residues: 510 sheet: -0.54 (0.64), residues: 65 loop : -0.83 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 405 HIS 0.002 0.001 HIS A 620 PHE 0.025 0.001 PHE B 439 TYR 0.009 0.001 TYR B 117 ARG 0.002 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.974 Fit side-chains REVERT: A 508 MET cc_start: 0.8214 (mpp) cc_final: 0.7517 (mpp) REVERT: B 289 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8261 (m-10) REVERT: B 305 MET cc_start: 0.8992 (mtt) cc_final: 0.8777 (mtt) REVERT: B 365 MET cc_start: 0.8245 (mpp) cc_final: 0.7972 (mpp) outliers start: 9 outliers final: 7 residues processed: 51 average time/residue: 0.1373 time to fit residues: 11.4092 Evaluate side-chains 55 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 137 LEU Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 285 VAL Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 84 optimal weight: 0.0770 chunk 49 optimal weight: 7.9990 chunk 35 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 25 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 7544 Z= 0.150 Angle : 0.646 12.191 10274 Z= 0.292 Chirality : 0.043 0.282 1212 Planarity : 0.003 0.040 1271 Dihedral : 13.154 113.307 1156 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.02 % Allowed : 18.53 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.29), residues: 928 helix: 2.21 (0.24), residues: 510 sheet: -0.51 (0.63), residues: 65 loop : -0.81 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 405 HIS 0.002 0.001 HIS A 620 PHE 0.019 0.001 PHE B 439 TYR 0.009 0.001 TYR A 251 ARG 0.002 0.000 ARG B 348 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.846 Fit side-chains REVERT: A 508 MET cc_start: 0.8207 (mpp) cc_final: 0.7495 (mpp) REVERT: A 565 LEU cc_start: 0.9132 (tt) cc_final: 0.8919 (tp) REVERT: B 289 TYR cc_start: 0.8731 (OUTLIER) cc_final: 0.8288 (m-10) REVERT: B 305 MET cc_start: 0.8993 (mtt) cc_final: 0.8786 (mtt) REVERT: B 365 MET cc_start: 0.8246 (mpp) cc_final: 0.7987 (mpp) outliers start: 8 outliers final: 4 residues processed: 55 average time/residue: 0.1416 time to fit residues: 12.2803 Evaluate side-chains 52 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 0.0270 chunk 91 optimal weight: 0.2980 chunk 84 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7544 Z= 0.146 Angle : 0.667 13.250 10274 Z= 0.298 Chirality : 0.043 0.282 1212 Planarity : 0.003 0.040 1271 Dihedral : 12.937 113.178 1156 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.63 % Allowed : 19.16 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.29), residues: 928 helix: 2.25 (0.24), residues: 510 sheet: -0.39 (0.64), residues: 65 loop : -0.75 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 405 HIS 0.002 0.000 HIS B 367 PHE 0.018 0.001 PHE B 439 TYR 0.022 0.001 TYR A 251 ARG 0.002 0.000 ARG B 348 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1856 Ramachandran restraints generated. 928 Oldfield, 0 Emsley, 928 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.842 Fit side-chains REVERT: A 508 MET cc_start: 0.8207 (mpp) cc_final: 0.7491 (mpp) REVERT: A 565 LEU cc_start: 0.9140 (tt) cc_final: 0.8919 (tp) REVERT: B 289 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.8311 (m-10) REVERT: B 305 MET cc_start: 0.8993 (mtt) cc_final: 0.8763 (mtt) REVERT: B 365 MET cc_start: 0.8237 (mpp) cc_final: 0.7958 (mpp) outliers start: 5 outliers final: 4 residues processed: 51 average time/residue: 0.1407 time to fit residues: 11.5335 Evaluate side-chains 51 residues out of total 788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 289 TYR Chi-restraints excluded: chain B residue 400 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.076345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056083 restraints weight = 31410.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.057980 restraints weight = 17173.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.059106 restraints weight = 12683.629| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7544 Z= 0.174 Angle : 0.668 13.219 10274 Z= 0.302 Chirality : 0.043 0.283 1212 Planarity : 0.003 0.040 1271 Dihedral : 12.839 113.033 1156 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.89 % Allowed : 19.29 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.29), residues: 928 helix: 2.28 (0.24), residues: 510 sheet: -0.43 (0.64), residues: 65 loop : -0.74 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 405 HIS 0.004 0.001 HIS B 367 PHE 0.017 0.001 PHE B 439 TYR 0.018 0.001 TYR A 251 ARG 0.002 0.000 ARG B 348 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1378.46 seconds wall clock time: 26 minutes 7.43 seconds (1567.43 seconds total)