Starting phenix.real_space_refine on Thu Jul 2 23:47:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9neg_49308/07_2026/9neg_49308.cif Found real_map, /net/cci-nas-00/data/ceres_data/9neg_49308/07_2026/9neg_49308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9neg_49308/07_2026/9neg_49308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9neg_49308/07_2026/9neg_49308.map" model { file = "/net/cci-nas-00/data/ceres_data/9neg_49308/07_2026/9neg_49308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9neg_49308/07_2026/9neg_49308.cif" } resolution = 3.17 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= 0.018 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: 5 Type Number sf(0) Gaussians K 2 8.98 5 S 32 5.16 5 C 7121 2.51 5 N 1661 2.21 5 O 1780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 10596 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2530 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2526 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 314, 2524 Classifications: {'peptide': 314} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 297} Chain breaks: 5 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "D" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2525 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 16, 'TRANS': 296} Chain breaks: 5 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 27 Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 62 Unusual residues: {'ACE': 1} Classifications: {'peptide': 10, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 9} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 74 Unusual residues: {'ACE': 1} Classifications: {'peptide': 11, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'TRANS': 10} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 101 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'POV': 9} Classifications: {'undetermined': 9} Link IDs: {None: 7} Chain breaks: 1 Unresolved non-hydrogen bonds: 367 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 7} Unresolved non-hydrogen planarities: 71 Chain: "B" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 86 Ad-hoc single atom residues: {' K': 1} Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 6} Chain breaks: 1 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 294 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 8, 'POV:plan-2': 7, 'POV:plan-3': 5} Unresolved non-hydrogen planarities: 71 Chain: "C" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 77 Unusual residues: {'POV': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 346 Unresolved non-hydrogen dihedrals: 255 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'POV:plan-1': 6, 'POV:plan-2': 5, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 88 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 292 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'POV:plan-1': 7, 'POV:plan-2': 6, 'POV:plan-3': 6} Unresolved non-hydrogen planarities: 67 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.44, per 1000 atoms: 0.23 Number of scatterers: 10596 At special positions: 0 Unit cell: (107.07, 107.07, 113.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 2 19.00 S 32 16.00 O 1780 8.00 N 1661 7.00 C 7121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 362.3 milliseconds 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2412 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 4 sheets defined 69.7% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 112 through 117 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.571A pdb=" N ARG A 128 " --> pdb=" O ASP A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.982A pdb=" N ILE A 152 " --> pdb=" O SER A 148 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 181 removed outlier: 3.622A pdb=" N PHE A 173 " --> pdb=" O PRO A 169 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 removed outlier: 3.548A pdb=" N ASN A 188 " --> pdb=" O ASP A 184 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 248 removed outlier: 4.324A pdb=" N VAL A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 298 Processing helix chain 'A' and resid 311 through 319 Processing helix chain 'A' and resid 320 through 326 Processing helix chain 'A' and resid 358 through 368 Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.551A pdb=" N LEU A 375 " --> pdb=" O ILE A 372 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG A 377 " --> pdb=" O LYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 392 removed outlier: 3.732A pdb=" N GLN A 383 " --> pdb=" O SER A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 419 Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 441 Processing helix chain 'A' and resid 452 through 472 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.996A pdb=" N ILE A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 117 Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 148 through 159 removed outlier: 3.580A pdb=" N ILE B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR B 156 " --> pdb=" O ILE B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 181 removed outlier: 3.621A pdb=" N PHE B 173 " --> pdb=" O PRO B 169 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 178 " --> pdb=" O SER B 174 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 226 through 248 removed outlier: 3.749A pdb=" N ALA B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 298 Processing helix chain 'B' and resid 311 through 319 Processing helix chain 'B' and resid 320 through 326 Processing helix chain 'B' and resid 358 through 368 Processing helix chain 'B' and resid 369 through 377 removed outlier: 3.524A pdb=" N LEU B 375 " --> pdb=" O ILE B 372 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 392 removed outlier: 3.754A pdb=" N GLN B 383 " --> pdb=" O SER B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 419 Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 441 Processing helix chain 'B' and resid 452 through 472 Processing helix chain 'B' and resid 473 through 489 removed outlier: 3.931A pdb=" N ILE B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 120 through 125 removed outlier: 4.253A pdb=" N ASP C 125 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 129 removed outlier: 3.513A pdb=" N ARG C 129 " --> pdb=" O PRO C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 126 through 129' Processing helix chain 'C' and resid 148 through 159 removed outlier: 3.839A pdb=" N ILE C 152 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 181 removed outlier: 3.568A pdb=" N TYR C 180 " --> pdb=" O GLU C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 226 through 248 Processing helix chain 'C' and resid 279 through 298 Processing helix chain 'C' and resid 311 through 319 Processing helix chain 'C' and resid 320 through 326 Processing helix chain 'C' and resid 358 through 368 Processing helix chain 'C' and resid 369 through 378 Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.871A pdb=" N GLN C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 419 Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 441 Processing helix chain 'C' and resid 452 through 472 Processing helix chain 'C' and resid 473 through 489 removed outlier: 3.766A pdb=" N ILE C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N SER C 479 " --> pdb=" O PRO C 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 117 Processing helix chain 'D' and resid 120 through 125 removed outlier: 4.254A pdb=" N ASP D 125 " --> pdb=" O THR D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 129 Processing helix chain 'D' and resid 148 through 159 removed outlier: 3.555A pdb=" N ILE D 152 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 169 through 181 Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 189 through 194 removed outlier: 4.240A pdb=" N GLU D 192 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU D 194 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 248 Processing helix chain 'D' and resid 279 through 298 Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 320 through 326 Processing helix chain 'D' and resid 358 through 368 Processing helix chain 'D' and resid 369 through 377 removed outlier: 3.535A pdb=" N LEU D 375 " --> pdb=" O ILE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 392 removed outlier: 3.690A pdb=" N GLN D 383 " --> pdb=" O SER D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 419 Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 441 Processing helix chain 'D' and resid 452 through 472 Processing helix chain 'D' and resid 473 through 488 removed outlier: 4.247A pdb=" N ILE D 477 " --> pdb=" O PRO D 473 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N SER D 479 " --> pdb=" O PRO D 475 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 111 Processing sheet with id=AA2, first strand: chain 'B' and resid 106 through 111 removed outlier: 3.657A pdb=" N GLU B 139 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 106 through 111 Processing sheet with id=AA4, first strand: chain 'D' and resid 106 through 111 removed outlier: 3.670A pdb=" N GLU D 139 " --> pdb=" O ASP D 134 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1758 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: 1.43 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1577 1.31 - 1.44: 3030 1.44 - 1.56: 6085 1.56 - 1.68: 81 1.68 - 1.81: 48 Bond restraints: 10821 Sorted by residual: bond pdb=" C31 POV A 701 " pdb=" O31 POV A 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.32e+01 bond pdb=" C31 POV C 701 " pdb=" O31 POV C 701 " ideal model delta sigma weight residual 1.327 1.442 -0.115 2.00e-02 2.50e+03 3.31e+01 bond pdb=" C31 POV D 703 " pdb=" O31 POV D 703 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C31 POV D 704 " pdb=" O31 POV D 704 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.27e+01 bond pdb=" C31 POV B 705 " pdb=" O31 POV B 705 " ideal model delta sigma weight residual 1.327 1.441 -0.114 2.00e-02 2.50e+03 3.25e+01 ... (remaining 10816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 14004 1.93 - 3.87: 347 3.87 - 5.80: 170 5.80 - 7.73: 24 7.73 - 9.66: 17 Bond angle restraints: 14562 Sorted by residual: angle pdb=" N GLU A 218 " pdb=" CA GLU A 218 " pdb=" C GLU A 218 " ideal model delta sigma weight residual 113.16 108.52 4.64 1.24e+00 6.50e-01 1.40e+01 angle pdb=" N VAL D 311 " pdb=" CA VAL D 311 " pdb=" C VAL D 311 " ideal model delta sigma weight residual 112.96 109.32 3.64 1.00e+00 1.00e+00 1.33e+01 angle pdb=" CA SER B 222 " pdb=" C SER B 222 " pdb=" O SER B 222 " ideal model delta sigma weight residual 122.13 118.04 4.09 1.13e+00 7.83e-01 1.31e+01 angle pdb=" N ALA B 226 " pdb=" CA ALA B 226 " pdb=" C ALA B 226 " ideal model delta sigma weight residual 113.16 108.76 4.40 1.24e+00 6.50e-01 1.26e+01 angle pdb=" N PHE A 217 " pdb=" CA PHE A 217 " pdb=" C PHE A 217 " ideal model delta sigma weight residual 111.90 107.31 4.59 1.32e+00 5.74e-01 1.21e+01 ... (remaining 14557 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 6190 35.84 - 71.67: 160 71.67 - 107.50: 9 107.50 - 143.34: 4 143.34 - 179.17: 1 Dihedral angle restraints: 6364 sinusoidal: 2652 harmonic: 3712 Sorted by residual: dihedral pdb=" CH3 ACE I 1 " pdb=" C ACE I 1 " pdb=" N ALA I 2 " pdb=" CA ALA I 2 " ideal model delta sinusoidal sigma weight residual 180.00 0.83 179.17 1 5.00e+00 4.00e-02 7.68e+02 dihedral pdb=" CA PRO D 475 " pdb=" C PRO D 475 " pdb=" N VAL D 476 " pdb=" CA VAL D 476 " ideal model delta harmonic sigma weight residual 180.00 159.59 20.41 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA PRO A 475 " pdb=" C PRO A 475 " pdb=" N VAL A 476 " pdb=" CA VAL A 476 " ideal model delta harmonic sigma weight residual 180.00 160.42 19.58 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 6361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1225 0.044 - 0.088: 332 0.088 - 0.132: 82 0.132 - 0.176: 5 0.176 - 0.220: 3 Chirality restraints: 1647 Sorted by residual: chirality pdb=" CA TYR I 8 " pdb=" N TYR I 8 " pdb=" C TYR I 8 " pdb=" CB TYR I 8 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLU D 218 " pdb=" N GLU D 218 " pdb=" C GLU D 218 " pdb=" CB GLU D 218 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA GLU A 218 " pdb=" N GLU A 218 " pdb=" C GLU A 218 " pdb=" CB GLU A 218 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1644 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 164 " 0.042 5.00e-02 4.00e+02 6.28e-02 6.31e+00 pdb=" N PRO D 165 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D 165 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 165 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 224 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C GLN A 224 " -0.042 2.00e-02 2.50e+03 pdb=" O GLN A 224 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA A 225 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 474 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO B 475 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 475 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 475 " -0.030 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.79: 2511 2.79 - 3.38: 12151 3.38 - 3.96: 19385 3.96 - 4.55: 27366 4.55 - 5.14: 39840 Nonbonded interactions: 101253 Sorted by model distance: nonbonded pdb=" NE ARG C 297 " pdb=" NH1 ARG C 377 " model vdw 2.202 3.200 nonbonded pdb=" NH2 ARG A 164 " pdb=" O VAL A 168 " model vdw 2.216 3.120 nonbonded pdb=" O SER B 104 " pdb=" NH2 ARG B 146 " model vdw 2.222 3.120 nonbonded pdb=" OD2 ASP B 316 " pdb=" NH2 ARG B 377 " model vdw 2.247 3.120 nonbonded pdb=" OE2 GLU D 418 " pdb=" N GLY D 452 " model vdw 2.252 3.120 ... (remaining 101248 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 83 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 112 through 162 or (resid 163 and (name N o \ r name CA or name C or name O or name CB )) or resid 164 through 488 or (resid 7 \ 03 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39)) or (resid 704 and (name C31 or name C32 or name C33 or name C34 or na \ me C35 or name C36 or name C37)) or (resid 707 and (name C32 or name C33 or name \ C34 or name C35 or name C36)))) selection = (chain 'B' and (resid 83 through 162 or (resid 163 and (name N or name CA or nam \ e C or name O or name CB )) or resid 164 through 488 or (resid 703 and (name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or re \ sid 704 or (resid 707 and (name C32 or name C33 or name C34 or name C35 or name \ C36)))) selection = (chain 'C' and (resid 83 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 112 through 488 or (resid 703 and (name C33 \ or name C34 or name C35 or name C36 or name C37 or name C38 or name C39)) or (r \ esid 704 and (name C31 or name C32 or name C33 or name C34 or name C35 or name C \ 36 or name C37)) or (resid 707 and (name C32 or name C33 or name C34 or name C35 \ or name C36)))) selection = (chain 'D' and (resid 83 through 110 or (resid 111 and (name N or name CA or nam \ e C or name O or name CB )) or resid 112 through 162 or (resid 163 and (name N o \ r name CA or name C or name O or name CB )) or resid 164 through 488 or (resid 7 \ 01 and (name C33 or name C34 or name C35 or name C36 or name C37 or name C38 or \ name C39)) or resid 702 or (resid 705 and (name C32 or name C33 or name C34 or n \ ame C35 or name C36)))) } ncs_group { reference = (chain 'I' and (resid 1 through 9 or (resid 10 and (name N or name CA or name C \ or name O or name CB )) or resid 11)) selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.880 Find NCS groups from input model: 0.290 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 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 : 0.008 0.115 10821 Z= 0.397 Angle : 0.881 9.664 14562 Z= 0.401 Chirality : 0.042 0.220 1647 Planarity : 0.005 0.063 1788 Dihedral : 15.890 179.174 3952 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % 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: 1.47 (0.25), residues: 1224 helix: 2.33 (0.20), residues: 747 sheet: 1.12 (0.76), residues: 40 loop : -1.58 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 377 TYR 0.011 0.001 TYR I 8 PHE 0.013 0.001 PHE B 179 TRP 0.005 0.001 TRP C 434 HIS 0.003 0.001 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.40 (10821) covalent geometry : angle 0.88057 / 0.40 (14562) hydrogen bonds : bond 0.14155 / 9.31 ( 615) hydrogen bonds : angle 5.26644 / 3.65 ( 1758) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7727 (p90) cc_final: 0.7486 (p90) REVERT: A 134 ASP cc_start: 0.7570 (t70) cc_final: 0.7025 (t0) REVERT: A 189 LYS cc_start: 0.9157 (ptpp) cc_final: 0.8915 (ptpp) REVERT: B 134 ASP cc_start: 0.8146 (t0) cc_final: 0.7634 (t0) REVERT: B 362 ARG cc_start: 0.7623 (mtp180) cc_final: 0.7100 (ttp-170) REVERT: C 134 ASP cc_start: 0.8066 (t0) cc_final: 0.7709 (t0) REVERT: D 178 LYS cc_start: 0.8798 (mmpt) cc_final: 0.8535 (mmmt) REVERT: D 362 ARG cc_start: 0.7480 (mtt180) cc_final: 0.7000 (ttt180) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1023 time to fit residues: 28.2558 Evaluate side-chains 143 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 138 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.138695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096041 restraints weight = 19504.548| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.76 r_work: 0.3167 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10821 Z= 0.159 Angle : 0.578 7.527 14562 Z= 0.298 Chirality : 0.042 0.150 1647 Planarity : 0.005 0.058 1788 Dihedral : 12.858 177.654 1623 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.18 % Allowed : 8.53 % Favored : 90.29 % 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: 1.64 (0.25), residues: 1224 helix: 2.46 (0.19), residues: 746 sheet: 1.72 (0.81), residues: 40 loop : -1.56 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 191 TYR 0.015 0.001 TYR D 483 PHE 0.021 0.001 PHE C 292 TRP 0.005 0.001 TRP C 454 HIS 0.003 0.001 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (10821) covalent geometry : angle 0.57769 / 0.30 (14562) hydrogen bonds : bond 0.04459 / 3.00 ( 615) hydrogen bonds : angle 4.23253 / 2.89 ( 1758) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 165 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7749 (p90) cc_final: 0.7502 (p90) REVERT: A 134 ASP cc_start: 0.7178 (t70) cc_final: 0.6629 (t0) REVERT: B 178 LYS cc_start: 0.9011 (mppt) cc_final: 0.8539 (mmtt) REVERT: B 293 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 362 ARG cc_start: 0.7539 (mtp180) cc_final: 0.6627 (ttt180) REVERT: C 134 ASP cc_start: 0.8143 (t0) cc_final: 0.7706 (t0) REVERT: C 247 GLU cc_start: 0.8690 (pt0) cc_final: 0.8345 (pt0) REVERT: C 293 GLU cc_start: 0.8704 (tt0) cc_final: 0.8490 (tm-30) REVERT: C 427 LYS cc_start: 0.9253 (mmtt) cc_final: 0.9047 (mmtt) REVERT: D 178 LYS cc_start: 0.8697 (mmpt) cc_final: 0.8476 (mmmt) REVERT: D 362 ARG cc_start: 0.7634 (mtt180) cc_final: 0.6770 (ttp-170) outliers start: 13 outliers final: 10 residues processed: 172 average time/residue: 0.0968 time to fit residues: 23.7757 Evaluate side-chains 156 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 146 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 124 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 73 optimal weight: 0.0040 chunk 58 optimal weight: 0.0030 chunk 37 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.6008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 GLN C 138 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.137530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.094629 restraints weight = 19623.824| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.78 r_work: 0.3146 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10821 Z= 0.157 Angle : 0.550 7.068 14562 Z= 0.284 Chirality : 0.042 0.144 1647 Planarity : 0.005 0.057 1788 Dihedral : 11.151 179.189 1623 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.81 % Allowed : 11.25 % Favored : 86.93 % 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: 1.66 (0.25), residues: 1224 helix: 2.41 (0.19), residues: 755 sheet: 1.64 (0.84), residues: 40 loop : -1.48 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 146 TYR 0.012 0.001 TYR D 483 PHE 0.016 0.001 PHE D 244 TRP 0.005 0.001 TRP C 454 HIS 0.006 0.001 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (10821) covalent geometry : angle 0.55020 / 0.28 (14562) hydrogen bonds : bond 0.04269 / 2.84 ( 615) hydrogen bonds : angle 4.04363 / 2.75 ( 1758) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.7788 (p90) cc_final: 0.7552 (p90) REVERT: A 134 ASP cc_start: 0.7181 (t70) cc_final: 0.6599 (t0) REVERT: B 176 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8703 (mm-30) REVERT: B 178 LYS cc_start: 0.9027 (mppt) cc_final: 0.8759 (mmmm) REVERT: B 293 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8078 (tm-30) REVERT: B 362 ARG cc_start: 0.7576 (mtp180) cc_final: 0.6664 (ttp-170) REVERT: C 134 ASP cc_start: 0.8103 (t0) cc_final: 0.7628 (t0) REVERT: C 189 LYS cc_start: 0.9363 (tptm) cc_final: 0.9097 (tppt) REVERT: C 293 GLU cc_start: 0.8734 (tt0) cc_final: 0.8465 (tm-30) REVERT: D 178 LYS cc_start: 0.8700 (mmpt) cc_final: 0.8478 (mmmt) REVERT: D 362 ARG cc_start: 0.7707 (mtt180) cc_final: 0.6829 (ttp-170) outliers start: 20 outliers final: 17 residues processed: 167 average time/residue: 0.0909 time to fit residues: 21.9103 Evaluate side-chains 149 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 49 optimal weight: 7.9990 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 83 optimal weight: 6.9990 chunk 91 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 40 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN B 157 GLN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.134757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.091350 restraints weight = 19900.313| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.74 r_work: 0.3091 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 10821 Z= 0.282 Angle : 0.647 8.180 14562 Z= 0.334 Chirality : 0.045 0.153 1647 Planarity : 0.005 0.057 1788 Dihedral : 10.660 178.782 1623 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.17 % Favored : 95.67 % Rotamer: Outliers : 2.36 % Allowed : 13.43 % Favored : 84.21 % 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: 1.49 (0.24), residues: 1224 helix: 2.20 (0.19), residues: 762 sheet: 1.51 (0.84), residues: 40 loop : -1.44 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 146 TYR 0.010 0.002 TYR C 156 PHE 0.021 0.002 PHE C 244 TRP 0.007 0.001 TRP C 454 HIS 0.003 0.001 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.28 (10821) covalent geometry : angle 0.64732 / 0.33 (14562) hydrogen bonds : bond 0.04970 / 3.31 ( 615) hydrogen bonds : angle 4.21684 / 2.87 ( 1758) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.421 Fit side-chains REVERT: A 86 PHE cc_start: 0.7789 (p90) cc_final: 0.7545 (p90) REVERT: B 116 ASN cc_start: 0.8601 (m-40) cc_final: 0.8149 (m110) REVERT: B 178 LYS cc_start: 0.9055 (mppt) cc_final: 0.8742 (mmmm) REVERT: B 362 ARG cc_start: 0.7766 (mtp180) cc_final: 0.6698 (ttp-170) REVERT: C 102 ASN cc_start: 0.6451 (t0) cc_final: 0.6225 (t0) REVERT: C 188 ASN cc_start: 0.9161 (t0) cc_final: 0.8690 (t0) REVERT: C 189 LYS cc_start: 0.9336 (tptm) cc_final: 0.9045 (tppt) REVERT: D 178 LYS cc_start: 0.8792 (mmpt) cc_final: 0.8530 (mmmt) REVERT: D 181 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7207 (pp20) REVERT: D 380 LYS cc_start: 0.8483 (mptt) cc_final: 0.8029 (mppt) outliers start: 26 outliers final: 23 residues processed: 153 average time/residue: 0.0924 time to fit residues: 20.1078 Evaluate side-chains 147 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 372 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 33 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 125 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 0.9990 chunk 115 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 GLN C 116 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.137035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.094547 restraints weight = 19475.330| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.74 r_work: 0.3144 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10821 Z= 0.125 Angle : 0.544 8.255 14562 Z= 0.281 Chirality : 0.041 0.147 1647 Planarity : 0.004 0.057 1788 Dihedral : 9.762 179.070 1623 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.36 % Allowed : 14.25 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.25), residues: 1224 helix: 2.38 (0.19), residues: 772 sheet: 1.82 (0.86), residues: 40 loop : -1.38 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.010 0.001 TYR B 415 PHE 0.025 0.001 PHE C 292 TRP 0.007 0.001 TRP A 289 HIS 0.002 0.000 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10821) covalent geometry : angle 0.54443 / 0.28 (14562) hydrogen bonds : bond 0.04153 / 2.76 ( 615) hydrogen bonds : angle 3.96600 / 2.69 ( 1758) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.462 Fit side-chains REVERT: A 86 PHE cc_start: 0.7761 (p90) cc_final: 0.7506 (p90) REVERT: A 134 ASP cc_start: 0.6934 (t70) cc_final: 0.6356 (t70) REVERT: A 143 ASP cc_start: 0.9268 (t0) cc_final: 0.8933 (t0) REVERT: A 155 TYR cc_start: 0.7183 (t80) cc_final: 0.6898 (t80) REVERT: A 188 ASN cc_start: 0.9429 (m-40) cc_final: 0.9042 (p0) REVERT: A 366 LEU cc_start: 0.9221 (tp) cc_final: 0.8987 (tt) REVERT: B 362 ARG cc_start: 0.7586 (mtp180) cc_final: 0.6511 (ttp-170) REVERT: C 189 LYS cc_start: 0.9321 (tptm) cc_final: 0.9109 (tppt) REVERT: C 293 GLU cc_start: 0.8734 (tt0) cc_final: 0.8487 (tm-30) REVERT: D 178 LYS cc_start: 0.8737 (mmpt) cc_final: 0.8536 (mmmt) REVERT: D 181 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7366 (pp20) outliers start: 26 outliers final: 22 residues processed: 155 average time/residue: 0.0894 time to fit residues: 20.1201 Evaluate side-chains 148 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 126 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 42 optimal weight: 0.0270 chunk 22 optimal weight: 0.5980 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 35 optimal weight: 10.0000 overall best weight: 1.3042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 157 GLN B 480 ASN C 116 ASN D 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.136454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.092105 restraints weight = 19777.912| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.92 r_work: 0.3127 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10821 Z= 0.141 Angle : 0.548 8.142 14562 Z= 0.280 Chirality : 0.041 0.140 1647 Planarity : 0.004 0.056 1788 Dihedral : 9.202 179.224 1623 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.45 % Allowed : 14.52 % Favored : 83.03 % 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: 1.84 (0.25), residues: 1224 helix: 2.42 (0.19), residues: 772 sheet: 1.84 (0.85), residues: 40 loop : -1.31 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 146 TYR 0.008 0.001 TYR B 415 PHE 0.015 0.001 PHE D 244 TRP 0.005 0.001 TRP C 289 HIS 0.001 0.000 HIS D 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (10821) covalent geometry : angle 0.54837 / 0.28 (14562) hydrogen bonds : bond 0.04102 / 2.73 ( 615) hydrogen bonds : angle 3.87085 / 2.63 ( 1758) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.414 Fit side-chains REVERT: A 86 PHE cc_start: 0.7790 (p90) cc_final: 0.7527 (p90) REVERT: A 134 ASP cc_start: 0.6945 (t70) cc_final: 0.6397 (t70) REVERT: A 143 ASP cc_start: 0.9299 (t0) cc_final: 0.8980 (t0) REVERT: A 155 TYR cc_start: 0.7215 (t80) cc_final: 0.6928 (t80) REVERT: B 116 ASN cc_start: 0.8597 (m-40) cc_final: 0.8194 (m110) REVERT: B 178 LYS cc_start: 0.9015 (mmtm) cc_final: 0.8603 (mmmm) REVERT: B 362 ARG cc_start: 0.7598 (mtp180) cc_final: 0.6514 (ttp-170) REVERT: C 189 LYS cc_start: 0.9326 (tptm) cc_final: 0.9105 (tppt) REVERT: C 293 GLU cc_start: 0.8737 (tt0) cc_final: 0.8468 (tm-30) REVERT: D 178 LYS cc_start: 0.8754 (mmpt) cc_final: 0.8546 (mmmt) REVERT: D 181 GLU cc_start: 0.7779 (tm-30) cc_final: 0.7443 (pp20) outliers start: 27 outliers final: 24 residues processed: 156 average time/residue: 0.0977 time to fit residues: 22.0114 Evaluate side-chains 153 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 0.0980 chunk 97 optimal weight: 9.9990 chunk 25 optimal weight: 0.5980 chunk 6 optimal weight: 8.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN B 157 GLN C 116 ASN D 85 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.136055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.093445 restraints weight = 19447.295| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.77 r_work: 0.3127 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10821 Z= 0.164 Angle : 0.569 8.154 14562 Z= 0.290 Chirality : 0.042 0.148 1647 Planarity : 0.004 0.056 1788 Dihedral : 9.149 179.051 1623 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.36 % Allowed : 15.06 % Favored : 82.58 % 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: 1.83 (0.25), residues: 1224 helix: 2.41 (0.19), residues: 772 sheet: 1.86 (0.84), residues: 40 loop : -1.30 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.008 0.001 TYR B 415 PHE 0.028 0.001 PHE C 292 TRP 0.005 0.001 TRP C 454 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (10821) covalent geometry : angle 0.56889 / 0.29 (14562) hydrogen bonds : bond 0.04214 / 2.80 ( 615) hydrogen bonds : angle 3.88759 / 2.65 ( 1758) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.401 Fit side-chains REVERT: A 86 PHE cc_start: 0.7806 (p90) cc_final: 0.7528 (p90) REVERT: A 134 ASP cc_start: 0.6941 (t70) cc_final: 0.6348 (t70) REVERT: A 143 ASP cc_start: 0.9308 (t0) cc_final: 0.8997 (t0) REVERT: A 155 TYR cc_start: 0.7227 (t80) cc_final: 0.6951 (t80) REVERT: A 188 ASN cc_start: 0.9410 (m110) cc_final: 0.9034 (p0) REVERT: B 116 ASN cc_start: 0.8599 (m-40) cc_final: 0.8199 (m110) REVERT: B 178 LYS cc_start: 0.9020 (mmtm) cc_final: 0.8686 (mmmm) REVERT: B 362 ARG cc_start: 0.7648 (mtp180) cc_final: 0.6543 (ttp-170) REVERT: C 189 LYS cc_start: 0.9337 (tptm) cc_final: 0.9114 (tppt) REVERT: C 293 GLU cc_start: 0.8783 (tt0) cc_final: 0.8503 (tm-30) REVERT: D 178 LYS cc_start: 0.8787 (mmpt) cc_final: 0.8522 (mmmt) REVERT: D 181 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7451 (pp20) outliers start: 26 outliers final: 25 residues processed: 151 average time/residue: 0.0822 time to fit residues: 18.1042 Evaluate side-chains 154 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 26 optimal weight: 0.8980 chunk 98 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 118 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 GLN C 116 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.136051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.091688 restraints weight = 19556.528| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.90 r_work: 0.3113 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10821 Z= 0.152 Angle : 0.568 7.843 14562 Z= 0.290 Chirality : 0.041 0.138 1647 Planarity : 0.004 0.056 1788 Dihedral : 8.962 179.146 1623 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.36 % Allowed : 15.34 % Favored : 82.30 % 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: 1.85 (0.25), residues: 1224 helix: 2.43 (0.19), residues: 772 sheet: 1.85 (0.83), residues: 40 loop : -1.30 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 146 TYR 0.008 0.001 TYR B 415 PHE 0.029 0.001 PHE C 118 TRP 0.006 0.001 TRP C 454 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (10821) covalent geometry : angle 0.56813 / 0.29 (14562) hydrogen bonds : bond 0.04148 / 2.76 ( 615) hydrogen bonds : angle 3.85519 / 2.63 ( 1758) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.392 Fit side-chains REVERT: A 86 PHE cc_start: 0.7832 (p90) cc_final: 0.7559 (p90) REVERT: A 134 ASP cc_start: 0.6874 (t70) cc_final: 0.6296 (t70) REVERT: A 143 ASP cc_start: 0.9295 (t0) cc_final: 0.9003 (t0) REVERT: A 155 TYR cc_start: 0.7212 (t80) cc_final: 0.6941 (t80) REVERT: B 116 ASN cc_start: 0.8571 (m-40) cc_final: 0.8174 (m110) REVERT: B 178 LYS cc_start: 0.9026 (mmtm) cc_final: 0.8690 (mmmm) REVERT: B 362 ARG cc_start: 0.7640 (mtp180) cc_final: 0.6550 (ttp-170) REVERT: C 189 LYS cc_start: 0.9332 (tptm) cc_final: 0.9115 (tppt) REVERT: C 293 GLU cc_start: 0.8783 (tt0) cc_final: 0.8497 (tm-30) REVERT: D 178 LYS cc_start: 0.8786 (mmpt) cc_final: 0.8525 (mmmt) REVERT: D 181 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7558 (tm-30) outliers start: 26 outliers final: 24 residues processed: 156 average time/residue: 0.0847 time to fit residues: 19.3599 Evaluate side-chains 153 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 27 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 111 optimal weight: 0.6980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 157 GLN C 116 ASN D 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.135276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090804 restraints weight = 19766.869| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.91 r_work: 0.3100 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10821 Z= 0.178 Angle : 0.593 8.744 14562 Z= 0.303 Chirality : 0.042 0.157 1647 Planarity : 0.005 0.056 1788 Dihedral : 8.975 179.045 1623 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.36 % Allowed : 15.61 % Favored : 82.03 % 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: 1.80 (0.25), residues: 1224 helix: 2.39 (0.19), residues: 772 sheet: 1.74 (0.82), residues: 40 loop : -1.30 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 191 TYR 0.008 0.001 TYR B 415 PHE 0.017 0.001 PHE C 118 TRP 0.005 0.001 TRP C 454 HIS 0.002 0.001 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (10821) covalent geometry : angle 0.59321 / 0.30 (14562) hydrogen bonds : bond 0.04317 / 2.87 ( 615) hydrogen bonds : angle 3.89029 / 2.66 ( 1758) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.296 Fit side-chains REVERT: A 86 PHE cc_start: 0.7821 (p90) cc_final: 0.7537 (p90) REVERT: A 134 ASP cc_start: 0.6831 (t70) cc_final: 0.6253 (t70) REVERT: A 143 ASP cc_start: 0.9303 (t0) cc_final: 0.9033 (t0) REVERT: A 155 TYR cc_start: 0.7223 (t80) cc_final: 0.6962 (t80) REVERT: A 247 GLU cc_start: 0.8708 (pp20) cc_final: 0.8401 (pt0) REVERT: B 116 ASN cc_start: 0.8552 (m-40) cc_final: 0.8158 (m110) REVERT: B 178 LYS cc_start: 0.9014 (mmtm) cc_final: 0.8662 (mmmm) REVERT: B 362 ARG cc_start: 0.7675 (mtp180) cc_final: 0.6552 (ttp-170) REVERT: C 170 LEU cc_start: 0.9324 (pp) cc_final: 0.9088 (mp) REVERT: C 189 LYS cc_start: 0.9328 (tptm) cc_final: 0.9111 (tppt) REVERT: D 181 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7596 (tm-30) REVERT: D 380 LYS cc_start: 0.8459 (mptt) cc_final: 0.7985 (mppt) outliers start: 26 outliers final: 23 residues processed: 152 average time/residue: 0.0899 time to fit residues: 19.5499 Evaluate side-chains 153 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 5 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 71 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 78 optimal weight: 0.0170 chunk 93 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 overall best weight: 1.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.135800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.091308 restraints weight = 19584.588| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.90 r_work: 0.3115 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10821 Z= 0.155 Angle : 0.587 8.864 14562 Z= 0.301 Chirality : 0.042 0.146 1647 Planarity : 0.005 0.056 1788 Dihedral : 8.799 179.139 1623 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.09 % Allowed : 15.79 % Favored : 82.12 % 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: 1.80 (0.25), residues: 1224 helix: 2.38 (0.19), residues: 772 sheet: 1.73 (0.81), residues: 40 loop : -1.28 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 144 TYR 0.017 0.001 TYR D 154 PHE 0.017 0.001 PHE C 118 TRP 0.006 0.001 TRP C 454 HIS 0.001 0.000 HIS B 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (10821) covalent geometry : angle 0.58733 / 0.30 (14562) hydrogen bonds : bond 0.04183 / 2.77 ( 615) hydrogen bonds : angle 3.85171 / 2.63 ( 1758) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2448 Ramachandran restraints generated. 1224 Oldfield, 0 Emsley, 1224 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.404 Fit side-chains REVERT: A 86 PHE cc_start: 0.7810 (p90) cc_final: 0.7504 (p90) REVERT: A 134 ASP cc_start: 0.6842 (t70) cc_final: 0.6276 (t70) REVERT: A 143 ASP cc_start: 0.9303 (t0) cc_final: 0.9052 (t0) REVERT: A 155 TYR cc_start: 0.7226 (t80) cc_final: 0.6976 (t80) REVERT: A 247 GLU cc_start: 0.8686 (pp20) cc_final: 0.8365 (pt0) REVERT: B 116 ASN cc_start: 0.8548 (m-40) cc_final: 0.8145 (m110) REVERT: B 178 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8669 (mmmm) REVERT: B 362 ARG cc_start: 0.7658 (mtp180) cc_final: 0.6533 (ttp-170) REVERT: C 189 LYS cc_start: 0.9327 (tptm) cc_final: 0.9090 (tppt) REVERT: D 181 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7574 (tm-30) outliers start: 23 outliers final: 23 residues processed: 150 average time/residue: 0.0877 time to fit residues: 19.1286 Evaluate side-chains 152 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain B residue 171 ASP Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 453 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 367 VAL Chi-restraints excluded: chain C residue 395 GLU Chi-restraints excluded: chain C residue 403 LEU Chi-restraints excluded: chain C residue 449 THR Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 369 VAL Chi-restraints excluded: chain D residue 403 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 470 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 107 optimal weight: 0.0070 chunk 52 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 18 optimal weight: 7.9990 chunk 34 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 16 optimal weight: 5.9990 overall best weight: 0.7004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.138015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.094446 restraints weight = 19348.160| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.85 r_work: 0.3160 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10821 Z= 0.120 Angle : 0.573 10.681 14562 Z= 0.289 Chirality : 0.041 0.153 1647 Planarity : 0.004 0.057 1788 Dihedral : 8.245 179.430 1623 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.00 % Allowed : 16.33 % Favored : 81.67 % 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: 1.80 (0.25), residues: 1224 helix: 2.43 (0.19), residues: 754 sheet: 1.86 (0.82), residues: 40 loop : -1.23 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 144 TYR 0.016 0.001 TYR D 154 PHE 0.017 0.001 PHE C 118 TRP 0.007 0.001 TRP C 434 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (10821) covalent geometry : angle 0.57266 / 0.29 (14562) hydrogen bonds : bond 0.03746 / 2.47 ( 615) hydrogen bonds : angle 3.74646 / 2.55 ( 1758) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2323.77 seconds wall clock time: 40 minutes 31.42 seconds (2431.42 seconds total)