Starting phenix.real_space_refine on Thu Jul 2 21:47:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7plv_13503/07_2026/7plv_13503.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plv_13503/07_2026/7plv_13503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2026/7plv_13503.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2026/7plv_13503.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2026/7plv_13503.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2026/7plv_13503.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2026/7plv_13503.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7plv_13503/07_2026/7plv_13503.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 63 5.16 5 C 6462 2.51 5 N 1722 2.21 5 O 1889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10139 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 4 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.31, per 1000 atoms: 0.23 Number of scatterers: 10139 At special positions: 0 Unit cell: (103.88, 131.44, 152.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 2 15.00 Mg 1 11.99 O 1889 8.00 N 1722 7.00 C 6462 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 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 323.3 milliseconds 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " Number of C-beta restraints generated: 2378 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 14 sheets defined 55.2% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.200A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.645A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.544A pdb=" N ARG A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 4.251A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.276A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.967A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 316 removed outlier: 3.855A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 311 " --> pdb=" O ASN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.531A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 removed outlier: 3.857A pdb=" N HIS A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 479 removed outlier: 3.552A pdb=" N GLN A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.612A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 515 removed outlier: 3.666A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 removed outlier: 3.598A pdb=" N ALA A 524 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 removed outlier: 3.649A pdb=" N ASN A 568 " --> pdb=" O PHE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.743A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 3.537A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.837A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 695 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.766A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 4.353A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.183A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 4.077A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.548A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 4.276A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.798A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.262A pdb=" N PHE C 255 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.600A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 296 removed outlier: 3.698A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.361A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.602A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.762A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.789A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 removed outlier: 4.661A pdb=" N LEU A 42 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.884A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.235A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.553A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.706A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.470A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241 524 hydrogen bonds defined for protein. 1470 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1691 1.32 - 1.44: 2733 1.44 - 1.56: 5825 1.56 - 1.69: 3 1.69 - 1.81: 102 Bond restraints: 10354 Sorted by residual: bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.453 0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.374 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.200 0.063 2.00e-02 2.50e+03 9.91e+00 bond pdb=" CA TRP H 1 " pdb=" C TRP H 1 " ideal model delta sigma weight residual 1.525 1.468 0.057 2.10e-02 2.27e+03 7.45e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.15e+00 ... (remaining 10349 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 13739 2.49 - 4.98: 216 4.98 - 7.47: 20 7.47 - 9.96: 5 9.96 - 12.45: 2 Bond angle restraints: 13982 Sorted by residual: angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.07 10.63 1.80e+00 3.09e-01 3.49e+01 angle pdb=" N HYP H 6 " pdb=" CA HYP H 6 " pdb=" CB HYP H 6 " ideal model delta sigma weight residual 103.00 108.87 -5.87 1.10e+00 8.26e-01 2.85e+01 angle pdb=" CA EEP H 2 " pdb=" CB EEP H 2 " pdb=" CG EEP H 2 " ideal model delta sigma weight residual 115.99 103.54 12.45 3.00e+00 1.11e-01 1.72e+01 angle pdb=" CD2 TRP H 1 " pdb=" CE2 TRP H 1 " pdb=" CZ2 TRP H 1 " ideal model delta sigma weight residual 122.40 118.25 4.15 1.00e+00 1.00e+00 1.72e+01 angle pdb=" CA DTH H 4 " pdb=" C DTH H 4 " pdb=" N CYS H 5 " ideal model delta sigma weight residual 116.20 123.69 -7.49 2.00e+00 2.50e-01 1.40e+01 ... (remaining 13977 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.86: 6088 31.86 - 63.72: 115 63.72 - 95.58: 38 95.58 - 127.44: 1 127.44 - 159.30: 2 Dihedral angle restraints: 6244 sinusoidal: 2554 harmonic: 3690 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 99.30 -159.30 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.37 -145.37 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 177.96 122.04 1 2.00e+01 2.50e-03 3.67e+01 ... (remaining 6241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.022: 1526 1.022 - 2.044: 0 2.044 - 3.067: 0 3.067 - 4.089: 0 4.089 - 5.111: 2 Chirality restraints: 1528 Sorted by residual: chirality pdb=" CB DTH H 4 " pdb=" CA DTH H 4 " pdb=" OG1 DTH H 4 " pdb=" CG2 DTH H 4 " both_signs ideal model delta sigma weight residual False 2.55 -2.56 5.11 2.00e-01 2.50e+01 6.53e+02 chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False 2.53 -2.36 4.89 2.00e-01 2.50e+01 5.97e+02 chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1525 not shown) Planarity restraints: 1791 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " -0.174 9.50e-02 1.11e+02 9.87e-02 4.98e+01 pdb=" NE ARG A 213 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.116 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.041 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.164 9.50e-02 1.11e+02 9.42e-02 4.69e+01 pdb=" NE ARG A 677 " -0.048 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.112 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.040 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 196 " 0.125 9.50e-02 1.11e+02 7.29e-02 2.90e+01 pdb=" NE ARG C 196 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG C 196 " 0.089 2.00e-02 2.50e+03 pdb=" NH1 ARG C 196 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG C 196 " -0.025 2.00e-02 2.50e+03 ... (remaining 1788 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.37: 13 2.37 - 3.00: 5420 3.00 - 3.63: 14892 3.63 - 4.27: 22403 4.27 - 4.90: 37983 Nonbonded interactions: 80711 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.732 3.620 nonbonded pdb=" OH TYR C 218 " pdb=" OE2 GLU C 226 " model vdw 2.167 3.040 nonbonded pdb=" NH2 ARG B 37 " pdb=" O PRO B 43 " model vdw 2.173 3.120 nonbonded pdb=" OD1 ASN C 128 " pdb=" NZ LYS C 359 " model vdw 2.214 3.120 nonbonded pdb=" O ASN C 92 " pdb=" NH1 ARG C 95 " model vdw 2.218 3.120 ... (remaining 80706 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.010 Normalize map: mean=0, sd=1: 2.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.270 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 0.119 10356 Z= 0.216 Angle : 0.812 12.450 13988 Z= 0.483 Chirality : 0.187 5.111 1528 Planarity : 0.008 0.124 1789 Dihedral : 14.950 159.301 3860 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.21), residues: 1236 helix: -1.60 (0.17), residues: 611 sheet: 0.34 (0.36), residues: 162 loop : -0.39 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.118 0.012 ARG A 213 TYR 0.040 0.006 TYR C 306 PHE 0.034 0.002 PHE C 255 TRP 0.022 0.003 TRP A 374 HIS 0.010 0.002 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.22 (10354) covalent geometry : angle 0.80758 / 0.48 (13982) hydrogen bonds : bond 0.14107 / 9.16 ( 522) hydrogen bonds : angle 6.78962 / 4.85 ( 1470) link_TRANS : bond 0.00704 / 0.35 ( 2) link_TRANS : angle 3.99435 / 2.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.9310 (m-10) cc_final: 0.8758 (m-10) REVERT: B 66 ASP cc_start: 0.8944 (p0) cc_final: 0.8367 (p0) REVERT: C 44 MET cc_start: 0.7946 (mtp) cc_final: 0.7737 (ttt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0919 time to fit residues: 18.5518 Evaluate side-chains 85 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.1980 chunk 123 optimal weight: 0.2980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 GLN A 81 HIS A 264 GLN A 283 ASN A 463 GLN A 464 GLN ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN C 59 GLN C 280 ASN C 296 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043075 restraints weight = 45874.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.044696 restraints weight = 21914.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045831 restraints weight = 13523.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.046576 restraints weight = 9696.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.047128 restraints weight = 7648.159| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10356 Z= 0.130 Angle : 0.619 7.952 13988 Z= 0.324 Chirality : 0.042 0.154 1528 Planarity : 0.004 0.052 1789 Dihedral : 8.680 158.337 1386 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 0.92 % Allowed : 5.18 % Favored : 93.90 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.23), residues: 1236 helix: 0.44 (0.20), residues: 610 sheet: 0.87 (0.39), residues: 158 loop : 0.49 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 372 TYR 0.018 0.001 TYR A 787 PHE 0.026 0.002 PHE C 255 TRP 0.016 0.002 TRP A 484 HIS 0.011 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10354) covalent geometry : angle 0.61829 / 0.32 (13982) hydrogen bonds : bond 0.03988 / 2.64 ( 522) hydrogen bonds : angle 4.86830 / 3.48 ( 1470) link_TRANS : bond 0.00546 / 0.28 ( 2) link_TRANS : angle 1.28432 / 0.93 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9485 (ttpp) cc_final: 0.9216 (ptmm) REVERT: B 66 ASP cc_start: 0.8840 (p0) cc_final: 0.8363 (p0) REVERT: B 93 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8992 (t80) REVERT: A 503 MET cc_start: 0.8582 (mmt) cc_final: 0.8205 (mmt) REVERT: C 44 MET cc_start: 0.8726 (mtp) cc_final: 0.8400 (ttt) REVERT: C 123 MET cc_start: 0.9404 (tpp) cc_final: 0.9046 (mmm) outliers start: 10 outliers final: 3 residues processed: 99 average time/residue: 0.0856 time to fit residues: 12.4170 Evaluate side-chains 75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 535 CYS Chi-restraints excluded: chain C residue 211 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.058401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.042463 restraints weight = 46092.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.044082 restraints weight = 22014.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.045178 restraints weight = 13606.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045915 restraints weight = 9740.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.046446 restraints weight = 7715.478| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10356 Z= 0.143 Angle : 0.560 7.199 13988 Z= 0.290 Chirality : 0.041 0.206 1528 Planarity : 0.004 0.056 1789 Dihedral : 8.088 158.349 1386 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Rotamer: Outliers : 1.02 % Allowed : 6.19 % Favored : 92.79 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.23), residues: 1236 helix: 1.05 (0.21), residues: 614 sheet: 0.75 (0.38), residues: 160 loop : 0.63 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 290 TYR 0.016 0.001 TYR A 787 PHE 0.023 0.001 PHE C 255 TRP 0.015 0.001 TRP A 484 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (10354) covalent geometry : angle 0.55970 / 0.29 (13982) hydrogen bonds : bond 0.03617 / 2.39 ( 522) hydrogen bonds : angle 4.52437 / 3.21 ( 1470) link_TRANS : bond 0.00127 / 0.06 ( 2) link_TRANS : angle 0.63481 / 0.41 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 LYS cc_start: 0.9480 (ttpp) cc_final: 0.9249 (ptmm) REVERT: B 66 ASP cc_start: 0.8840 (p0) cc_final: 0.8373 (p0) REVERT: B 93 PHE cc_start: 0.9331 (OUTLIER) cc_final: 0.8956 (t80) REVERT: A 478 MET cc_start: 0.9453 (tpp) cc_final: 0.8973 (tpp) REVERT: A 503 MET cc_start: 0.8552 (mmt) cc_final: 0.8178 (mmt) REVERT: A 682 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8945 (mm) REVERT: C 44 MET cc_start: 0.8826 (mtp) cc_final: 0.8543 (tpp) REVERT: C 123 MET cc_start: 0.9439 (tpp) cc_final: 0.9100 (mmm) REVERT: C 125 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7753 (mp0) REVERT: C 236 LEU cc_start: 0.8879 (mp) cc_final: 0.8663 (mt) REVERT: C 305 MET cc_start: 0.8763 (mmm) cc_final: 0.8412 (mmm) outliers start: 11 outliers final: 4 residues processed: 86 average time/residue: 0.0688 time to fit residues: 8.7841 Evaluate side-chains 76 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 107 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 410 ASN ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 HIS ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.057355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.041371 restraints weight = 46356.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.042962 restraints weight = 22152.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.044044 restraints weight = 13685.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044770 restraints weight = 9801.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.045248 restraints weight = 7759.737| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10356 Z= 0.181 Angle : 0.572 9.016 13988 Z= 0.292 Chirality : 0.041 0.200 1528 Planarity : 0.004 0.058 1789 Dihedral : 7.802 159.477 1386 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.76 % Allowed : 6.93 % Favored : 91.31 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.24), residues: 1236 helix: 1.27 (0.21), residues: 620 sheet: 0.79 (0.39), residues: 160 loop : 0.57 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 542 TYR 0.017 0.001 TYR A 787 PHE 0.021 0.001 PHE C 255 TRP 0.011 0.001 TRP C 79 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.18 (10354) covalent geometry : angle 0.57187 / 0.29 (13982) hydrogen bonds : bond 0.03525 / 2.32 ( 522) hydrogen bonds : angle 4.43983 / 3.13 ( 1470) link_TRANS : bond 0.00281 / 0.13 ( 2) link_TRANS : angle 0.45855 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9319 (OUTLIER) cc_final: 0.8965 (t80) REVERT: A 132 MET cc_start: 0.7984 (ttm) cc_final: 0.7651 (tpt) REVERT: A 305 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8473 (tpp) REVERT: A 478 MET cc_start: 0.9437 (tpp) cc_final: 0.8878 (tpp) REVERT: A 484 TRP cc_start: 0.7693 (m-10) cc_final: 0.7429 (m-90) REVERT: A 503 MET cc_start: 0.8610 (mmt) cc_final: 0.8280 (mmt) REVERT: A 682 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.8923 (mm) REVERT: C 123 MET cc_start: 0.9422 (tpp) cc_final: 0.8892 (mmm) REVERT: C 125 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7808 (mp0) REVERT: C 167 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8467 (mp0) REVERT: C 236 LEU cc_start: 0.8908 (mp) cc_final: 0.8707 (mt) REVERT: C 305 MET cc_start: 0.8776 (mmm) cc_final: 0.8406 (mmm) outliers start: 19 outliers final: 7 residues processed: 87 average time/residue: 0.0687 time to fit residues: 9.0324 Evaluate side-chains 77 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 565 LEU Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 250 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 24 optimal weight: 0.0470 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 12 optimal weight: 0.0030 overall best weight: 0.5088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.058590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.042532 restraints weight = 45706.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.044180 restraints weight = 21695.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.045284 restraints weight = 13333.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.045977 restraints weight = 9535.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.046527 restraints weight = 7604.435| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10356 Z= 0.104 Angle : 0.533 9.833 13988 Z= 0.269 Chirality : 0.040 0.179 1528 Planarity : 0.003 0.055 1789 Dihedral : 7.545 159.443 1386 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.39 % Allowed : 8.23 % Favored : 90.39 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1236 helix: 1.46 (0.21), residues: 623 sheet: 0.86 (0.39), residues: 158 loop : 0.67 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 542 TYR 0.017 0.001 TYR A 787 PHE 0.018 0.001 PHE C 255 TRP 0.011 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (10354) covalent geometry : angle 0.53305 / 0.27 (13982) hydrogen bonds : bond 0.03158 / 2.09 ( 522) hydrogen bonds : angle 4.23641 / 2.99 ( 1470) link_TRANS : bond 0.00192 / 0.10 ( 2) link_TRANS : angle 0.49695 / 0.30 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.9359 (m-10) cc_final: 0.8936 (m-10) REVERT: B 93 PHE cc_start: 0.9309 (OUTLIER) cc_final: 0.8967 (t80) REVERT: A 132 MET cc_start: 0.7946 (ttm) cc_final: 0.7696 (tpp) REVERT: A 177 MET cc_start: 0.8302 (ptt) cc_final: 0.8072 (ppp) REVERT: A 305 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8444 (tpp) REVERT: A 478 MET cc_start: 0.9406 (tpp) cc_final: 0.9072 (tpp) REVERT: A 503 MET cc_start: 0.8566 (mmt) cc_final: 0.8258 (mmt) REVERT: A 564 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8602 (t80) REVERT: A 682 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8940 (mm) REVERT: C 123 MET cc_start: 0.9361 (tpp) cc_final: 0.8963 (mmm) REVERT: C 125 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: C 167 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: C 227 MET cc_start: 0.8982 (tpt) cc_final: 0.8706 (tpt) REVERT: C 305 MET cc_start: 0.8776 (mmm) cc_final: 0.8406 (mmm) outliers start: 15 outliers final: 4 residues processed: 83 average time/residue: 0.0746 time to fit residues: 9.3447 Evaluate side-chains 73 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 269 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 90 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 36 optimal weight: 0.0870 chunk 51 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.043152 restraints weight = 45786.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.044781 restraints weight = 21633.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.045868 restraints weight = 13241.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046616 restraints weight = 9417.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.047154 restraints weight = 7395.968| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10356 Z= 0.098 Angle : 0.537 10.403 13988 Z= 0.269 Chirality : 0.041 0.216 1528 Planarity : 0.003 0.055 1789 Dihedral : 7.366 158.986 1386 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.11 % Allowed : 8.32 % Favored : 90.57 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.24), residues: 1236 helix: 1.57 (0.21), residues: 624 sheet: 0.89 (0.38), residues: 158 loop : 0.68 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.017 0.001 TYR A 787 PHE 0.016 0.001 PHE C 255 TRP 0.008 0.001 TRP A 484 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (10354) covalent geometry : angle 0.53695 / 0.27 (13982) hydrogen bonds : bond 0.03014 / 1.99 ( 522) hydrogen bonds : angle 4.12554 / 2.90 ( 1470) link_TRANS : bond 0.00185 / 0.10 ( 2) link_TRANS : angle 0.51594 / 0.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 PHE cc_start: 0.9502 (m-10) cc_final: 0.9236 (m-10) REVERT: B 19 PHE cc_start: 0.7902 (m-80) cc_final: 0.7541 (m-80) REVERT: B 93 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8971 (t80) REVERT: A 132 MET cc_start: 0.7887 (ttm) cc_final: 0.7676 (tpp) REVERT: A 305 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8398 (tpp) REVERT: A 478 MET cc_start: 0.9383 (tpp) cc_final: 0.9065 (tpp) REVERT: A 503 MET cc_start: 0.8519 (mmt) cc_final: 0.8241 (mmt) REVERT: A 564 PHE cc_start: 0.9191 (OUTLIER) cc_final: 0.8577 (t80) REVERT: A 682 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.8944 (mm) REVERT: C 118 LYS cc_start: 0.9296 (tppt) cc_final: 0.8904 (tppt) REVERT: C 123 MET cc_start: 0.9259 (tpp) cc_final: 0.8916 (mmm) REVERT: C 125 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: C 167 GLU cc_start: 0.8808 (OUTLIER) cc_final: 0.8339 (mp0) REVERT: C 305 MET cc_start: 0.8761 (mmm) cc_final: 0.8369 (mmm) outliers start: 12 outliers final: 4 residues processed: 81 average time/residue: 0.0913 time to fit residues: 10.8376 Evaluate side-chains 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 93 optimal weight: 0.0570 chunk 113 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 53 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 110 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.043067 restraints weight = 45190.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.044687 restraints weight = 21577.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.045789 restraints weight = 13278.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046532 restraints weight = 9426.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.047016 restraints weight = 7412.443| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10356 Z= 0.105 Angle : 0.531 11.288 13988 Z= 0.266 Chirality : 0.040 0.176 1528 Planarity : 0.003 0.055 1789 Dihedral : 7.266 157.648 1386 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.02 % Allowed : 8.78 % Favored : 90.20 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1236 helix: 1.65 (0.21), residues: 624 sheet: 0.90 (0.38), residues: 158 loop : 0.70 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 542 TYR 0.019 0.001 TYR A 787 PHE 0.016 0.001 PHE C 255 TRP 0.009 0.001 TRP A 781 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (10354) covalent geometry : angle 0.53081 / 0.27 (13982) hydrogen bonds : bond 0.02996 / 1.96 ( 522) hydrogen bonds : angle 4.08596 / 2.86 ( 1470) link_TRANS : bond 0.00138 / 0.07 ( 2) link_TRANS : angle 0.49487 / 0.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 93 PHE cc_start: 0.9258 (OUTLIER) cc_final: 0.8980 (t80) REVERT: A 132 MET cc_start: 0.7929 (ttm) cc_final: 0.7721 (tpp) REVERT: A 305 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8432 (tpp) REVERT: A 503 MET cc_start: 0.8519 (mmt) cc_final: 0.8247 (mmt) REVERT: A 564 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8560 (t80) REVERT: A 682 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8904 (mm) REVERT: C 44 MET cc_start: 0.8732 (tpp) cc_final: 0.8526 (tpp) REVERT: C 123 MET cc_start: 0.9240 (tpp) cc_final: 0.8904 (mmm) REVERT: C 125 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: C 167 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: C 227 MET cc_start: 0.8906 (tpt) cc_final: 0.8677 (tpt) REVERT: C 305 MET cc_start: 0.8762 (mmm) cc_final: 0.8371 (mmm) outliers start: 11 outliers final: 4 residues processed: 82 average time/residue: 0.0810 time to fit residues: 9.5763 Evaluate side-chains 72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 682 LEU Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 101 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 HIS ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** 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 = 0.3306 r_free = 0.3306 target = 0.058490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.042411 restraints weight = 45903.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.044037 restraints weight = 21969.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045134 restraints weight = 13590.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.045886 restraints weight = 9747.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.046361 restraints weight = 7683.515| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10356 Z= 0.124 Angle : 0.556 12.367 13988 Z= 0.275 Chirality : 0.040 0.160 1528 Planarity : 0.003 0.055 1789 Dihedral : 7.257 156.202 1386 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.20 % Allowed : 9.33 % Favored : 89.46 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.24), residues: 1236 helix: 1.75 (0.21), residues: 625 sheet: 0.93 (0.39), residues: 155 loop : 0.63 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 64 TYR 0.020 0.001 TYR A 787 PHE 0.016 0.001 PHE B 12 TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS C 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 (10354) covalent geometry : angle 0.55619 / 0.28 (13982) hydrogen bonds : bond 0.03048 / 2.00 ( 522) hydrogen bonds : angle 4.09450 / 2.86 ( 1470) link_TRANS : bond 0.00092 / 0.05 ( 2) link_TRANS : angle 0.42755 / 0.29 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8130 (m-80) cc_final: 0.7732 (m-80) REVERT: B 93 PHE cc_start: 0.9270 (OUTLIER) cc_final: 0.9009 (t80) REVERT: A 132 MET cc_start: 0.7996 (ttm) cc_final: 0.7744 (tpp) REVERT: A 177 MET cc_start: 0.8467 (tmm) cc_final: 0.8175 (tmm) REVERT: A 305 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.8463 (tpp) REVERT: A 478 MET cc_start: 0.9217 (tpp) cc_final: 0.8897 (tpp) REVERT: A 503 MET cc_start: 0.8551 (mmt) cc_final: 0.8249 (mmt) REVERT: A 564 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8621 (t80) REVERT: C 44 MET cc_start: 0.8778 (tpp) cc_final: 0.8557 (tpp) REVERT: C 123 MET cc_start: 0.9274 (tpp) cc_final: 0.8817 (mmm) REVERT: C 125 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: C 167 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: C 227 MET cc_start: 0.8937 (tpt) cc_final: 0.8701 (tpt) REVERT: C 305 MET cc_start: 0.8768 (mmm) cc_final: 0.8378 (mmm) outliers start: 13 outliers final: 5 residues processed: 76 average time/residue: 0.0720 time to fit residues: 8.1159 Evaluate side-chains 75 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain C residue 167 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 13 optimal weight: 6.9990 chunk 99 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 120 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.058247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.042489 restraints weight = 45562.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.044088 restraints weight = 21752.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.045178 restraints weight = 13333.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.045931 restraints weight = 9513.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046395 restraints weight = 7455.318| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10356 Z= 0.126 Angle : 0.555 12.999 13988 Z= 0.274 Chirality : 0.040 0.159 1528 Planarity : 0.003 0.055 1789 Dihedral : 7.174 151.709 1386 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.20 % Allowed : 9.52 % Favored : 89.28 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.24), residues: 1236 helix: 1.76 (0.21), residues: 628 sheet: 0.91 (0.39), residues: 155 loop : 0.53 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.018 0.001 TYR A 787 PHE 0.023 0.001 PHE B 12 TRP 0.009 0.001 TRP C 79 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (10354) covalent geometry : angle 0.55518 / 0.27 (13982) hydrogen bonds : bond 0.03066 / 2.00 ( 522) hydrogen bonds : angle 4.08054 / 2.84 ( 1470) link_TRANS : bond 0.00091 / 0.05 ( 2) link_TRANS : angle 0.36901 / 0.26 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8127 (m-80) cc_final: 0.7922 (m-80) REVERT: B 61 LYS cc_start: 0.7601 (mmmt) cc_final: 0.6571 (pttt) REVERT: B 73 MET cc_start: 0.8230 (pmm) cc_final: 0.7986 (pmm) REVERT: B 93 PHE cc_start: 0.9232 (m-80) cc_final: 0.8997 (t80) REVERT: A 177 MET cc_start: 0.8393 (tmm) cc_final: 0.8061 (tmm) REVERT: A 305 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8443 (tpp) REVERT: A 478 MET cc_start: 0.9139 (tpp) cc_final: 0.8741 (tpp) REVERT: A 503 MET cc_start: 0.8543 (mmt) cc_final: 0.8254 (mmt) REVERT: A 564 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8671 (t80) REVERT: C 123 MET cc_start: 0.9249 (tpp) cc_final: 0.8826 (mmm) REVERT: C 167 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: C 227 MET cc_start: 0.8919 (tpt) cc_final: 0.8686 (tpt) REVERT: C 305 MET cc_start: 0.8758 (mmm) cc_final: 0.8368 (mmm) outliers start: 13 outliers final: 6 residues processed: 83 average time/residue: 0.0779 time to fit residues: 9.4719 Evaluate side-chains 72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 3 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 18 optimal weight: 0.1980 chunk 120 optimal weight: 0.5980 chunk 118 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.058553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.042730 restraints weight = 45029.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.044323 restraints weight = 21610.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.045400 restraints weight = 13324.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.046125 restraints weight = 9530.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046648 restraints weight = 7551.102| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10356 Z= 0.119 Angle : 0.577 13.305 13988 Z= 0.284 Chirality : 0.040 0.158 1528 Planarity : 0.003 0.055 1789 Dihedral : 7.085 147.250 1386 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.92 % Allowed : 10.17 % Favored : 88.91 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.24), residues: 1236 helix: 1.82 (0.21), residues: 627 sheet: 0.90 (0.39), residues: 155 loop : 0.46 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.022 0.001 TYR A 787 PHE 0.020 0.001 PHE B 12 TRP 0.020 0.001 TRP C 86 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (10354) covalent geometry : angle 0.57738 / 0.28 (13982) hydrogen bonds : bond 0.03029 / 1.98 ( 522) hydrogen bonds : angle 4.06695 / 2.83 ( 1470) link_TRANS : bond 0.00088 / 0.05 ( 2) link_TRANS : angle 0.40064 / 0.29 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2472 Ramachandran restraints generated. 1236 Oldfield, 0 Emsley, 1236 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 19 PHE cc_start: 0.8091 (m-80) cc_final: 0.7876 (m-10) REVERT: A 177 MET cc_start: 0.8383 (tmm) cc_final: 0.8052 (tmm) REVERT: A 305 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8431 (tpp) REVERT: A 478 MET cc_start: 0.9152 (tpp) cc_final: 0.8770 (tpp) REVERT: A 503 MET cc_start: 0.8546 (mmt) cc_final: 0.8213 (mmt) REVERT: A 564 PHE cc_start: 0.9211 (OUTLIER) cc_final: 0.8649 (t80) REVERT: C 123 MET cc_start: 0.9288 (tpp) cc_final: 0.8824 (mmm) REVERT: C 167 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8364 (mp0) REVERT: C 227 MET cc_start: 0.8898 (tpt) cc_final: 0.8662 (tpt) REVERT: C 305 MET cc_start: 0.8756 (mmm) cc_final: 0.8369 (mmm) REVERT: C 355 MET cc_start: 0.9112 (mmm) cc_final: 0.8861 (mmt) outliers start: 10 outliers final: 6 residues processed: 74 average time/residue: 0.0828 time to fit residues: 9.3611 Evaluate side-chains 72 residues out of total 1093 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 139 ILE Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 564 PHE Chi-restraints excluded: chain A residue 735 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 54 optimal weight: 0.3980 chunk 79 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.058439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042284 restraints weight = 46011.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.043914 restraints weight = 22023.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.045026 restraints weight = 13559.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.045765 restraints weight = 9738.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.046305 restraints weight = 7705.860| |-----------------------------------------------------------------------------| r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10356 Z= 0.129 Angle : 0.592 13.221 13988 Z= 0.290 Chirality : 0.041 0.164 1528 Planarity : 0.004 0.055 1789 Dihedral : 7.038 141.158 1386 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.83 % Allowed : 10.72 % Favored : 88.45 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.24), residues: 1236 helix: 1.83 (0.21), residues: 628 sheet: 0.88 (0.39), residues: 155 loop : 0.40 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 372 TYR 0.021 0.001 TYR A 787 PHE 0.017 0.001 PHE B 12 TRP 0.025 0.001 TRP C 86 HIS 0.005 0.001 HIS A 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (10354) covalent geometry : angle 0.59184 / 0.29 (13982) hydrogen bonds : bond 0.03059 / 2.00 ( 522) hydrogen bonds : angle 4.10469 / 2.86 ( 1470) link_TRANS : bond 0.00075 / 0.04 ( 2) link_TRANS : angle 0.38653 / 0.27 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1521.17 seconds wall clock time: 27 minutes 3.60 seconds (1623.60 seconds total)