Starting phenix.real_space_refine on Thu Jul 2 07:53:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jzs_36752/07_2026/8jzs_36752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jzs_36752/07_2026/8jzs_36752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8jzs_36752/07_2026/8jzs_36752.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jzs_36752/07_2026/8jzs_36752.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jzs_36752/07_2026/8jzs_36752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jzs_36752/07_2026/8jzs_36752.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jzs_36752/07_2026/8jzs_36752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jzs_36752/07_2026/8jzs_36752.map" } resolution = 2.95 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= -0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 4996 2.51 5 N 1190 2.21 5 O 1274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 7500 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3680 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 3680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3680 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 21, 'TRANS': 464} Chain breaks: 4 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 70 Unusual residues: {'CLR': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.83, per 1000 atoms: 0.24 Number of scatterers: 7500 At special positions: 0 Unit cell: (119.671, 88.9299, 91.1257, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1274 8.00 N 1190 7.00 C 4996 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 436 " " NAG B 601 " - " ASN B 436 " Time building additional restraints: 0.66 Conformation dependent library (CDL) restraints added in 487.0 milliseconds 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1776 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 2 sheets defined 78.3% alpha, 2.7% 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 18 through 28 Processing helix chain 'B' and resid 34 through 57 removed outlier: 3.502A pdb=" N GLY B 38 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL B 40 " --> pdb=" O ALA B 36 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 70 through 98 removed outlier: 4.255A pdb=" N SER B 89 " --> pdb=" O THR B 85 " (cutoff:3.500A) Proline residue: B 90 - end of helix Processing helix chain 'B' and resid 101 through 118 Processing helix chain 'B' and resid 118 through 125 removed outlier: 3.866A pdb=" N LEU B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 134 removed outlier: 4.452A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 132 " --> pdb=" O THR B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 184 removed outlier: 3.503A pdb=" N ASN B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR B 176 " --> pdb=" O LYS B 172 " (cutoff:3.500A) Proline residue: B 177 - end of helix removed outlier: 4.035A pdb=" N GLN B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 183 " --> pdb=" O GLY B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 212 removed outlier: 3.572A pdb=" N ASN B 196 " --> pdb=" O ARG B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.631A pdb=" N GLN B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 243 removed outlier: 3.502A pdb=" N ILE B 228 " --> pdb=" O THR B 224 " (cutoff:3.500A) Proline residue: B 229 - end of helix removed outlier: 3.847A pdb=" N PHE B 240 " --> pdb=" O ALA B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 262 Processing helix chain 'B' and resid 310 through 327 removed outlier: 3.756A pdb=" N ASP B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Proline residue: B 323 - end of helix Processing helix chain 'B' and resid 328 through 348 removed outlier: 3.828A pdb=" N VAL B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 389 removed outlier: 4.133A pdb=" N THR B 370 " --> pdb=" O ALA B 366 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 372 " --> pdb=" O TRP B 368 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA B 374 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU B 379 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Proline residue: B 382 - end of helix Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.866A pdb=" N HIS B 395 " --> pdb=" O ILE B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 431 removed outlier: 3.951A pdb=" N LYS B 431 " --> pdb=" O LEU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 479 removed outlier: 3.590A pdb=" N TYR B 458 " --> pdb=" O GLN B 454 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 460 " --> pdb=" O PRO B 456 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B 469 " --> pdb=" O GLU B 465 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 473 " --> pdb=" O SER B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 510 Processing helix chain 'B' and resid 531 through 558 removed outlier: 3.544A pdb=" N TYR B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 28 Processing helix chain 'A' and resid 34 through 57 removed outlier: 3.503A pdb=" N GLY A 38 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N VAL A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN A 57 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 70 through 98 removed outlier: 4.255A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 125 removed outlier: 3.866A pdb=" N LEU A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 134 removed outlier: 4.452A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ALA A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 184 removed outlier: 3.503A pdb=" N ASN A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 4.035A pdb=" N GLN A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 212 removed outlier: 3.572A pdb=" N ASN A 196 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.631A pdb=" N GLN A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 243 removed outlier: 3.502A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix removed outlier: 3.847A pdb=" N PHE A 240 " --> pdb=" O ALA A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 262 Processing helix chain 'A' and resid 310 through 327 removed outlier: 3.756A pdb=" N ASP A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 328 through 348 removed outlier: 3.828A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 389 removed outlier: 4.133A pdb=" N THR A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 372 " --> pdb=" O TRP A 368 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 390 through 395 removed outlier: 3.865A pdb=" N HIS A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 431 removed outlier: 3.951A pdb=" N LYS A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.590A pdb=" N TYR A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU A 473 " --> pdb=" O SER A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 510 Processing helix chain 'A' and resid 531 through 558 removed outlier: 3.544A pdb=" N TYR A 535 " --> pdb=" O TYR A 531 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 349 through 350 removed outlier: 3.655A pdb=" N VAL B 442 " --> pdb=" O ILE B 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 349 through 350 removed outlier: 3.655A pdb=" N VAL A 442 " --> pdb=" O ILE A 439 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1551 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: 1.14 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1126 1.30 - 1.43: 2046 1.43 - 1.55: 4456 1.55 - 1.68: 2 1.68 - 1.81: 62 Bond restraints: 7692 Sorted by residual: bond pdb=" CA ALA B 35 " pdb=" C ALA B 35 " ideal model delta sigma weight residual 1.524 1.438 0.085 1.32e-02 5.74e+03 4.19e+01 bond pdb=" CA ALA A 35 " pdb=" C ALA A 35 " ideal model delta sigma weight residual 1.524 1.439 0.085 1.32e-02 5.74e+03 4.13e+01 bond pdb=" CA GLU A 189 " pdb=" C GLU A 189 " ideal model delta sigma weight residual 1.520 1.439 0.081 1.39e-02 5.18e+03 3.37e+01 bond pdb=" CA GLU B 189 " pdb=" C GLU B 189 " ideal model delta sigma weight residual 1.520 1.440 0.080 1.39e-02 5.18e+03 3.31e+01 bond pdb=" CA PRO A 188 " pdb=" CB PRO A 188 " ideal model delta sigma weight residual 1.533 1.452 0.081 1.42e-02 4.96e+03 3.28e+01 ... (remaining 7687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 10081 2.06 - 4.12: 276 4.12 - 6.19: 93 6.19 - 8.25: 22 8.25 - 10.31: 12 Bond angle restraints: 10484 Sorted by residual: angle pdb=" N GLU A 189 " pdb=" CA GLU A 189 " pdb=" C GLU A 189 " ideal model delta sigma weight residual 114.31 104.00 10.31 1.29e+00 6.01e-01 6.39e+01 angle pdb=" N GLU B 189 " pdb=" CA GLU B 189 " pdb=" C GLU B 189 " ideal model delta sigma weight residual 114.31 104.02 10.29 1.29e+00 6.01e-01 6.36e+01 angle pdb=" C GLY B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta sigma weight residual 121.86 131.16 -9.30 1.65e+00 3.67e-01 3.17e+01 angle pdb=" C GLY A 28 " pdb=" N ALA A 29 " pdb=" CA ALA A 29 " ideal model delta sigma weight residual 121.86 131.13 -9.27 1.65e+00 3.67e-01 3.16e+01 angle pdb=" C PRO B 188 " pdb=" CA PRO B 188 " pdb=" CB PRO B 188 " ideal model delta sigma weight residual 111.56 102.73 8.83 1.65e+00 3.67e-01 2.86e+01 ... (remaining 10479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 3889 14.98 - 29.96: 387 29.96 - 44.93: 98 44.93 - 59.91: 18 59.91 - 74.89: 4 Dihedral angle restraints: 4396 sinusoidal: 1626 harmonic: 2770 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 153 " pdb=" CB CYS B 153 " ideal model delta sinusoidal sigma weight residual 93.00 57.08 35.92 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 153 " pdb=" CB CYS A 153 " ideal model delta sinusoidal sigma weight residual 93.00 57.08 35.92 1 1.00e+01 1.00e-02 1.83e+01 dihedral pdb=" CA PRO A 390 " pdb=" C PRO A 390 " pdb=" N ILE A 391 " pdb=" CA ILE A 391 " ideal model delta harmonic sigma weight residual -180.00 -159.71 -20.29 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1129 0.082 - 0.163: 83 0.163 - 0.245: 18 0.245 - 0.327: 10 0.327 - 0.408: 4 Chirality restraints: 1244 Sorted by residual: chirality pdb=" C13 CLR B 603 " pdb=" C12 CLR B 603 " pdb=" C14 CLR B 603 " pdb=" C17 CLR B 603 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" C13 CLR A 602 " pdb=" C12 CLR A 602 " pdb=" C14 CLR A 602 " pdb=" C17 CLR A 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.53 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" C14 CLR A 602 " pdb=" C13 CLR A 602 " pdb=" C15 CLR A 602 " pdb=" C8 CLR A 602 " both_signs ideal model delta sigma weight residual False -2.32 -2.67 0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 1241 not shown) Planarity restraints: 1268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 389 " 0.051 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO B 390 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO B 390 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 390 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 389 " 0.051 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO A 390 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 187 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.45e+00 pdb=" C GLY A 187 " -0.047 2.00e-02 2.50e+03 pdb=" O GLY A 187 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO A 188 " 0.015 2.00e-02 2.50e+03 ... (remaining 1265 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2245 2.82 - 3.34: 7525 3.34 - 3.86: 12346 3.86 - 4.38: 14366 4.38 - 4.90: 24720 Nonbonded interactions: 61202 Sorted by model distance: nonbonded pdb=" C21 CLR B 602 " pdb=" C23 CLR B 602 " model vdw 2.299 3.088 nonbonded pdb=" C21 CLR A 603 " pdb=" C23 CLR A 603 " model vdw 2.300 3.088 nonbonded pdb=" OE2 GLU A 309 " pdb=" NZ LYS A 311 " model vdw 2.364 3.120 nonbonded pdb=" OE2 GLU B 309 " pdb=" NZ LYS B 311 " model vdw 2.364 3.120 nonbonded pdb=" OD1 ASP A 253 " pdb=" OG SER A 255 " model vdw 2.373 3.040 ... (remaining 61197 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 0.085 7696 Z= 0.498 Angle : 0.959 14.925 10494 Z= 0.511 Chirality : 0.059 0.408 1244 Planarity : 0.006 0.078 1266 Dihedral : 12.858 74.890 2614 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.41 % Favored : 95.17 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 0.71 (0.29), residues: 952 helix: 1.17 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -1.50 (0.41), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 34 TYR 0.015 0.001 TYR B 335 PHE 0.021 0.001 PHE A 237 TRP 0.007 0.001 TRP B 452 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00754 / 0.50 ( 7692) covalent geometry : angle 0.93070 / 0.51 (10484) SS BOND : bond 0.00292 / 0.15 ( 2) SS BOND : angle 0.40998 / 0.20 ( 4) hydrogen bonds : bond 0.16320 / 11.13 ( 519) hydrogen bonds : angle 6.48046 / 4.77 ( 1551) link_NAG-ASN : bond 0.00249 / 0.12 ( 2) link_NAG-ASN : angle 9.73488 / 5.31 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 413 MET cc_start: 0.8525 (ttp) cc_final: 0.8273 (ttp) REVERT: A 413 MET cc_start: 0.8507 (ttp) cc_final: 0.8245 (ttp) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.3348 time to fit residues: 54.7292 Evaluate side-chains 90 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.0570 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.0570 chunk 74 optimal weight: 0.8980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 57 ASN B 63 ASN B 196 ASN B 457 GLN A 57 ASN A 63 ASN A 196 ASN A 457 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.143940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111382 restraints weight = 9456.087| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.71 r_work: 0.3135 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 7696 Z= 0.139 Angle : 0.635 8.044 10494 Z= 0.311 Chirality : 0.039 0.154 1244 Planarity : 0.005 0.059 1266 Dihedral : 5.160 37.621 1062 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.94 % Favored : 96.85 % Rotamer: Outliers : 1.60 % Allowed : 9.04 % Favored : 89.36 % 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: 1.18 (0.28), residues: 952 helix: 1.63 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -1.91 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 393 TYR 0.007 0.001 TYR B 458 PHE 0.017 0.001 PHE A 240 TRP 0.011 0.001 TRP B 453 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 7692) covalent geometry : angle 0.63127 / 0.31 (10484) SS BOND : bond 0.00177 / 0.09 ( 2) SS BOND : angle 0.35328 / 0.17 ( 4) hydrogen bonds : bond 0.04605 / 3.18 ( 519) hydrogen bonds : angle 4.45464 / 3.33 ( 1551) link_NAG-ASN : bond 0.00027 / 0.01 ( 2) link_NAG-ASN : angle 2.90594 / 1.53 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 THR cc_start: 0.8968 (m) cc_final: 0.8699 (m) REVERT: B 413 MET cc_start: 0.9094 (ttp) cc_final: 0.8736 (ttp) REVERT: A 222 PHE cc_start: 0.8408 (m-80) cc_final: 0.8181 (m-80) REVERT: A 340 THR cc_start: 0.8964 (m) cc_final: 0.8698 (m) REVERT: A 413 MET cc_start: 0.9077 (ttp) cc_final: 0.8708 (ttp) outliers start: 12 outliers final: 2 residues processed: 106 average time/residue: 0.4113 time to fit residues: 47.1270 Evaluate side-chains 96 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain A residue 84 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 ASN A 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.128965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.094544 restraints weight = 9446.887| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 1.76 r_work: 0.2897 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7696 Z= 0.220 Angle : 0.698 7.040 10494 Z= 0.344 Chirality : 0.044 0.234 1244 Planarity : 0.005 0.059 1266 Dihedral : 5.249 38.854 1062 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.20 % Favored : 95.59 % Rotamer: Outliers : 4.12 % Allowed : 11.04 % Favored : 84.84 % 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: 1.31 (0.28), residues: 952 helix: 1.72 (0.19), residues: 704 sheet: None (None), residues: 0 loop : -1.67 (0.42), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 393 TYR 0.029 0.002 TYR A 113 PHE 0.015 0.002 PHE A 194 TRP 0.009 0.002 TRP B 453 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.22 ( 7692) covalent geometry : angle 0.69758 / 0.34 (10484) SS BOND : bond 0.00176 / 0.09 ( 2) SS BOND : angle 0.21159 / 0.11 ( 4) hydrogen bonds : bond 0.06018 / 4.18 ( 519) hydrogen bonds : angle 4.50792 / 3.38 ( 1551) link_NAG-ASN : bond 0.00116 / 0.06 ( 2) link_NAG-ASN : angle 1.46312 / 0.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.284 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8602 (mmm) cc_final: 0.8071 (tpt) REVERT: B 320 LYS cc_start: 0.7756 (tttt) cc_final: 0.7410 (mtpm) REVERT: B 340 THR cc_start: 0.8905 (m) cc_final: 0.8634 (m) REVERT: B 413 MET cc_start: 0.9103 (ttp) cc_final: 0.8691 (ttp) REVERT: A 320 LYS cc_start: 0.7728 (tttt) cc_final: 0.7368 (mtpm) REVERT: A 340 THR cc_start: 0.8899 (m) cc_final: 0.8627 (m) REVERT: A 413 MET cc_start: 0.9102 (ttp) cc_final: 0.8698 (ttp) outliers start: 31 outliers final: 11 residues processed: 107 average time/residue: 0.3725 time to fit residues: 43.5221 Evaluate side-chains 92 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 5.9990 chunk 14 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 48 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 ASN A 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.135307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102664 restraints weight = 9444.416| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.62 r_work: 0.2943 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7696 Z= 0.150 Angle : 0.612 7.847 10494 Z= 0.299 Chirality : 0.040 0.200 1244 Planarity : 0.004 0.036 1266 Dihedral : 4.975 33.921 1062 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 3.46 % Allowed : 14.63 % Favored : 81.91 % 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 (0.28), residues: 952 helix: 1.98 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.68 (0.43), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.008 0.001 TYR B 335 PHE 0.013 0.001 PHE B 194 TRP 0.011 0.001 TRP A 197 HIS 0.002 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7692) covalent geometry : angle 0.61207 / 0.30 (10484) SS BOND : bond 0.00178 / 0.09 ( 2) SS BOND : angle 0.11176 / 0.06 ( 4) hydrogen bonds : bond 0.04828 / 3.35 ( 519) hydrogen bonds : angle 4.29155 / 3.22 ( 1551) link_NAG-ASN : bond 0.00040 / 0.02 ( 2) link_NAG-ASN : angle 1.17739 / 0.62 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.8611 (mmm) cc_final: 0.8202 (tpt) REVERT: B 320 LYS cc_start: 0.7833 (tttt) cc_final: 0.7495 (mtpm) REVERT: B 340 THR cc_start: 0.8914 (m) cc_final: 0.8656 (m) REVERT: B 413 MET cc_start: 0.9069 (ttp) cc_final: 0.8663 (ttp) REVERT: A 320 LYS cc_start: 0.7841 (tttt) cc_final: 0.7512 (mtpm) REVERT: A 340 THR cc_start: 0.8909 (m) cc_final: 0.8653 (m) REVERT: A 413 MET cc_start: 0.9062 (ttp) cc_final: 0.8640 (ttp) outliers start: 26 outliers final: 14 residues processed: 97 average time/residue: 0.4099 time to fit residues: 43.1442 Evaluate side-chains 99 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 240 PHE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 484 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 62 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 63 ASN A 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.134906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.101965 restraints weight = 9201.412| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.63 r_work: 0.2933 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7696 Z= 0.152 Angle : 0.606 7.280 10494 Z= 0.297 Chirality : 0.040 0.222 1244 Planarity : 0.004 0.035 1266 Dihedral : 4.894 33.263 1062 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.62 % Favored : 95.17 % Rotamer: Outliers : 2.93 % Allowed : 16.22 % Favored : 80.85 % 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: 1.71 (0.28), residues: 952 helix: 1.99 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -1.56 (0.41), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 129 TYR 0.007 0.001 TYR B 335 PHE 0.012 0.001 PHE A 194 TRP 0.012 0.001 TRP A 453 HIS 0.002 0.001 HIS B 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 ( 7692) covalent geometry : angle 0.60610 / 0.30 (10484) SS BOND : bond 0.00151 / 0.08 ( 2) SS BOND : angle 0.22664 / 0.12 ( 4) hydrogen bonds : bond 0.04912 / 3.41 ( 519) hydrogen bonds : angle 4.24603 / 3.19 ( 1551) link_NAG-ASN : bond 0.00044 / 0.02 ( 2) link_NAG-ASN : angle 1.08374 / 0.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.265 Fit side-chains revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8486 (mm) REVERT: B 117 MET cc_start: 0.8583 (mmm) cc_final: 0.8293 (mmm) REVERT: B 320 LYS cc_start: 0.7720 (tttt) cc_final: 0.7379 (mtpm) REVERT: B 340 THR cc_start: 0.8869 (m) cc_final: 0.8601 (m) REVERT: B 413 MET cc_start: 0.9078 (ttp) cc_final: 0.8676 (ttp) REVERT: A 320 LYS cc_start: 0.7768 (tttt) cc_final: 0.7444 (mtpm) REVERT: A 340 THR cc_start: 0.8885 (m) cc_final: 0.8615 (m) REVERT: A 391 ILE cc_start: 0.8475 (mm) cc_final: 0.8227 (mt) REVERT: A 413 MET cc_start: 0.9099 (ttp) cc_final: 0.8695 (ttp) outliers start: 22 outliers final: 13 residues processed: 96 average time/residue: 0.3836 time to fit residues: 40.1582 Evaluate side-chains 92 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 0.0970 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 20.0000 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.132235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.099018 restraints weight = 9348.895| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.68 r_work: 0.2938 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7696 Z= 0.137 Angle : 0.580 7.159 10494 Z= 0.285 Chirality : 0.038 0.140 1244 Planarity : 0.003 0.035 1266 Dihedral : 4.789 32.293 1062 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.57 % Favored : 96.11 % Rotamer: Outliers : 2.66 % Allowed : 16.89 % Favored : 80.45 % 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: 1.78 (0.28), residues: 952 helix: 2.08 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.60 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.008 0.001 TYR B 113 PHE 0.012 0.001 PHE A 194 TRP 0.011 0.001 TRP A 197 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 7692) covalent geometry : angle 0.57984 / 0.29 (10484) SS BOND : bond 0.00140 / 0.07 ( 2) SS BOND : angle 0.23857 / 0.13 ( 4) hydrogen bonds : bond 0.04550 / 3.16 ( 519) hydrogen bonds : angle 4.14932 / 3.11 ( 1551) link_NAG-ASN : bond 0.00021 / 0.01 ( 2) link_NAG-ASN : angle 1.07348 / 0.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8494 (mm) REVERT: B 320 LYS cc_start: 0.7713 (tttt) cc_final: 0.7382 (mtpm) REVERT: B 340 THR cc_start: 0.8844 (m) cc_final: 0.8585 (m) REVERT: B 413 MET cc_start: 0.9056 (ttp) cc_final: 0.8626 (ttp) REVERT: A 117 MET cc_start: 0.8192 (mmm) cc_final: 0.7910 (tpt) REVERT: A 320 LYS cc_start: 0.7705 (tttt) cc_final: 0.7379 (mtpm) REVERT: A 340 THR cc_start: 0.8858 (m) cc_final: 0.8598 (m) REVERT: A 391 ILE cc_start: 0.8483 (mm) cc_final: 0.8181 (mt) REVERT: A 413 MET cc_start: 0.9068 (ttp) cc_final: 0.8664 (ttp) outliers start: 20 outliers final: 13 residues processed: 91 average time/residue: 0.3896 time to fit residues: 38.3629 Evaluate side-chains 91 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 483 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 94 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 73 optimal weight: 0.0870 chunk 27 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.136449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104188 restraints weight = 9194.421| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.60 r_work: 0.2942 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7696 Z= 0.140 Angle : 0.578 6.537 10494 Z= 0.284 Chirality : 0.038 0.136 1244 Planarity : 0.003 0.035 1266 Dihedral : 4.756 32.491 1062 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.20 % Favored : 95.48 % Rotamer: Outliers : 3.06 % Allowed : 17.29 % Favored : 79.65 % 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 (0.28), residues: 952 helix: 2.06 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.63 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.009 0.001 TYR A 113 PHE 0.012 0.001 PHE A 194 TRP 0.013 0.001 TRP B 453 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7692) covalent geometry : angle 0.57748 / 0.28 (10484) SS BOND : bond 0.00147 / 0.07 ( 2) SS BOND : angle 0.27135 / 0.14 ( 4) hydrogen bonds : bond 0.04626 / 3.21 ( 519) hydrogen bonds : angle 4.12786 / 3.09 ( 1551) link_NAG-ASN : bond 0.00017 / 0.01 ( 2) link_NAG-ASN : angle 1.02889 / 0.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8451 (mm) REVERT: B 320 LYS cc_start: 0.7691 (tttt) cc_final: 0.7398 (mtpm) REVERT: B 340 THR cc_start: 0.8875 (m) cc_final: 0.8603 (m) REVERT: B 413 MET cc_start: 0.9057 (ttp) cc_final: 0.8624 (ttp) REVERT: B 513 LYS cc_start: 0.7471 (pmtt) cc_final: 0.7253 (pmmt) REVERT: A 320 LYS cc_start: 0.7753 (tttt) cc_final: 0.7460 (mtpm) REVERT: A 340 THR cc_start: 0.8884 (m) cc_final: 0.8624 (m) REVERT: A 391 ILE cc_start: 0.8468 (mm) cc_final: 0.8183 (mt) REVERT: A 413 MET cc_start: 0.9079 (ttp) cc_final: 0.8659 (ttp) REVERT: A 513 LYS cc_start: 0.7481 (pmtt) cc_final: 0.7264 (pmmt) outliers start: 23 outliers final: 15 residues processed: 87 average time/residue: 0.3853 time to fit residues: 36.4150 Evaluate side-chains 91 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 464 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 7 optimal weight: 0.0030 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.098300 restraints weight = 9477.942| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.74 r_work: 0.2951 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7696 Z= 0.124 Angle : 0.556 5.673 10494 Z= 0.273 Chirality : 0.037 0.134 1244 Planarity : 0.003 0.034 1266 Dihedral : 4.639 31.443 1062 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.78 % Favored : 96.01 % Rotamer: Outliers : 3.46 % Allowed : 16.76 % Favored : 79.79 % 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: 1.70 (0.28), residues: 952 helix: 2.06 (0.20), residues: 716 sheet: None (None), residues: 0 loop : -1.93 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.010 0.001 TYR A 113 PHE 0.011 0.001 PHE A 194 TRP 0.012 0.001 TRP A 453 HIS 0.001 0.001 HIS A 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 7692) covalent geometry : angle 0.55518 / 0.27 (10484) SS BOND : bond 0.00119 / 0.06 ( 2) SS BOND : angle 0.28016 / 0.16 ( 4) hydrogen bonds : bond 0.04301 / 2.97 ( 519) hydrogen bonds : angle 4.08482 / 3.06 ( 1551) link_NAG-ASN : bond 0.00060 / 0.03 ( 2) link_NAG-ASN : angle 1.05492 / 0.59 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 54 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8361 (mm) REVERT: B 320 LYS cc_start: 0.7721 (tttt) cc_final: 0.7332 (mtpm) REVERT: B 340 THR cc_start: 0.8796 (m) cc_final: 0.8542 (m) REVERT: B 413 MET cc_start: 0.9036 (ttp) cc_final: 0.8619 (ttp) REVERT: A 320 LYS cc_start: 0.7733 (tttt) cc_final: 0.7339 (mtpm) REVERT: A 340 THR cc_start: 0.8809 (m) cc_final: 0.8554 (m) REVERT: A 391 ILE cc_start: 0.8409 (mm) cc_final: 0.8136 (mt) REVERT: A 413 MET cc_start: 0.9059 (ttp) cc_final: 0.8648 (ttp) outliers start: 26 outliers final: 16 residues processed: 90 average time/residue: 0.4211 time to fit residues: 41.0451 Evaluate side-chains 89 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 72 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain B residue 484 MET Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 464 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 14 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 64 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 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 = 0.3601 r_free = 0.3601 target = 0.137068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.104891 restraints weight = 9126.532| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.59 r_work: 0.2955 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7696 Z= 0.134 Angle : 0.567 5.800 10494 Z= 0.279 Chirality : 0.037 0.134 1244 Planarity : 0.003 0.033 1266 Dihedral : 4.605 31.671 1062 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.10 % Favored : 95.69 % Rotamer: Outliers : 2.79 % Allowed : 17.69 % Favored : 79.52 % 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 (0.28), residues: 952 helix: 2.04 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.98 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.008 0.001 TYR A 113 PHE 0.011 0.001 PHE A 194 TRP 0.012 0.001 TRP A 453 HIS 0.002 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7692) covalent geometry : angle 0.56712 / 0.28 (10484) SS BOND : bond 0.00109 / 0.05 ( 2) SS BOND : angle 0.29537 / 0.16 ( 4) hydrogen bonds : bond 0.04488 / 3.11 ( 519) hydrogen bonds : angle 4.09373 / 3.06 ( 1551) link_NAG-ASN : bond 0.00028 / 0.01 ( 2) link_NAG-ASN : angle 1.04283 / 0.58 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 95 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8302 (tp) REVERT: B 320 LYS cc_start: 0.7741 (tttt) cc_final: 0.7367 (mtpm) REVERT: B 340 THR cc_start: 0.8842 (m) cc_final: 0.8595 (m) REVERT: B 413 MET cc_start: 0.9064 (ttp) cc_final: 0.8638 (ttp) REVERT: B 513 LYS cc_start: 0.7605 (pmtt) cc_final: 0.7396 (pmmt) REVERT: A 320 LYS cc_start: 0.7754 (tttt) cc_final: 0.7376 (mtpm) REVERT: A 340 THR cc_start: 0.8858 (m) cc_final: 0.8607 (m) REVERT: A 391 ILE cc_start: 0.8455 (mm) cc_final: 0.8193 (mt) REVERT: A 413 MET cc_start: 0.9058 (ttp) cc_final: 0.8628 (ttp) REVERT: A 513 LYS cc_start: 0.7615 (pmtt) cc_final: 0.7402 (pmmt) outliers start: 21 outliers final: 16 residues processed: 89 average time/residue: 0.3870 time to fit residues: 37.4253 Evaluate side-chains 88 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 41 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 87 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 457 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 457 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 = 0.3633 r_free = 0.3633 target = 0.139248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107582 restraints weight = 9071.660| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.55 r_work: 0.2968 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7696 Z= 0.128 Angle : 0.552 5.614 10494 Z= 0.272 Chirality : 0.037 0.134 1244 Planarity : 0.003 0.033 1266 Dihedral : 4.579 31.191 1062 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.79 % Allowed : 17.69 % Favored : 79.52 % 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: 1.67 (0.28), residues: 952 helix: 2.04 (0.19), residues: 716 sheet: None (None), residues: 0 loop : -1.98 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 129 TYR 0.008 0.001 TYR B 113 PHE 0.011 0.001 PHE A 194 TRP 0.011 0.001 TRP B 453 HIS 0.002 0.001 HIS B 362 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7692) covalent geometry : angle 0.55145 / 0.27 (10484) SS BOND : bond 0.00096 / 0.05 ( 2) SS BOND : angle 0.35317 / 0.20 ( 4) hydrogen bonds : bond 0.04358 / 3.02 ( 519) hydrogen bonds : angle 4.07285 / 3.05 ( 1551) link_NAG-ASN : bond 0.00048 / 0.02 ( 2) link_NAG-ASN : angle 1.01972 / 0.57 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 320 LYS cc_start: 0.7688 (tttt) cc_final: 0.7338 (mtpm) REVERT: B 340 THR cc_start: 0.8827 (m) cc_final: 0.8583 (m) REVERT: B 377 ILE cc_start: 0.8490 (mm) cc_final: 0.8265 (mt) REVERT: B 391 ILE cc_start: 0.8435 (mm) cc_final: 0.8175 (mt) REVERT: B 413 MET cc_start: 0.9065 (ttp) cc_final: 0.8659 (ttp) REVERT: B 513 LYS cc_start: 0.7591 (pmtt) cc_final: 0.7391 (pmmt) REVERT: A 117 MET cc_start: 0.7783 (mmm) cc_final: 0.7405 (mmm) REVERT: A 320 LYS cc_start: 0.7697 (tttt) cc_final: 0.7341 (mtpm) REVERT: A 340 THR cc_start: 0.8862 (m) cc_final: 0.8602 (m) REVERT: A 391 ILE cc_start: 0.8435 (mm) cc_final: 0.8179 (mt) REVERT: A 413 MET cc_start: 0.9103 (ttp) cc_final: 0.8710 (ttp) REVERT: A 513 LYS cc_start: 0.7609 (pmtt) cc_final: 0.7406 (pmmt) outliers start: 21 outliers final: 17 residues processed: 92 average time/residue: 0.4256 time to fit residues: 42.6229 Evaluate side-chains 88 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 464 SER Chi-restraints excluded: chain A residue 75 SER Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.095106 restraints weight = 9326.846| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.73 r_work: 0.2908 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7696 Z= 0.146 Angle : 0.574 5.623 10494 Z= 0.283 Chirality : 0.038 0.136 1244 Planarity : 0.003 0.034 1266 Dihedral : 4.630 31.778 1062 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.93 % Allowed : 17.15 % Favored : 79.92 % 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: 1.71 (0.28), residues: 952 helix: 2.05 (0.19), residues: 708 sheet: None (None), residues: 0 loop : -1.71 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 129 TYR 0.009 0.001 TYR A 113 PHE 0.012 0.001 PHE A 194 TRP 0.013 0.001 TRP A 453 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 7692) covalent geometry : angle 0.57411 / 0.28 (10484) SS BOND : bond 0.00098 / 0.05 ( 2) SS BOND : angle 0.27850 / 0.15 ( 4) hydrogen bonds : bond 0.04737 / 3.28 ( 519) hydrogen bonds : angle 4.13298 / 3.09 ( 1551) link_NAG-ASN : bond 0.00025 / 0.01 ( 2) link_NAG-ASN : angle 0.99235 / 0.56 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2389.05 seconds wall clock time: 41 minutes 36.46 seconds (2496.46 seconds total)