Starting phenix.real_space_refine on Wed Mar 4 00:14:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i7m_52657/03_2026/9i7m_52657.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i7m_52657/03_2026/9i7m_52657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i7m_52657/03_2026/9i7m_52657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i7m_52657/03_2026/9i7m_52657.map" model { file = "/net/cci-nas-00/data/ceres_data/9i7m_52657/03_2026/9i7m_52657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i7m_52657/03_2026/9i7m_52657.cif" } resolution = 3.12 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= 0.049 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 S 54 5.16 5 Na 9 4.78 5 C 6171 2.51 5 N 1479 2.21 5 O 1629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9342 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3068 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 15, 'TRANS': 394} Chain breaks: 2 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {' NA': 3, '6Z6': 1} Inner-chain residues flagged as termini: ['pdbres="ASP A1002 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: C, E Time building chain proxies: 2.38, per 1000 atoms: 0.25 Number of scatterers: 9342 At special positions: 0 Unit cell: (105.739, 102.583, 72.5972, 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) S 54 16.00 Na 9 11.00 O 1629 8.00 N 1479 7.00 C 6171 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: 0.79 Conformation dependent library (CDL) restraints added in 358.9 milliseconds 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2256 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 3 sheets defined 81.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 48 through 68 removed outlier: 3.561A pdb=" N VAL A 58 " --> pdb=" O THR A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 82 Processing helix chain 'A' and resid 82 through 94 Processing helix chain 'A' and resid 95 through 110 removed outlier: 3.509A pdb=" N LEU A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 146 Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 189 through 192 Processing helix chain 'A' and resid 222 through 241 Processing helix chain 'A' and resid 242 through 244 No H-bonds generated for 'chain 'A' and resid 242 through 244' Processing helix chain 'A' and resid 246 through 283 removed outlier: 3.595A pdb=" N PHE A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 263 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) Proline residue: A 270 - end of helix removed outlier: 3.937A pdb=" N GLU A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 311 Processing helix chain 'A' and resid 311 through 322 Processing helix chain 'A' and resid 324 through 332 removed outlier: 3.982A pdb=" N PHE A 328 " --> pdb=" O ASN A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 343 Processing helix chain 'A' and resid 348 through 359 removed outlier: 3.801A pdb=" N GLU A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 375 removed outlier: 3.897A pdb=" N PHE A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) Proline residue: A 372 - end of helix Processing helix chain 'A' and resid 379 through 397 removed outlier: 3.668A pdb=" N ALA A 383 " --> pdb=" O MET A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 419 removed outlier: 3.645A pdb=" N THR A 414 " --> pdb=" O SER A 410 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.546A pdb=" N ALA A 437 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 433 through 438' Processing helix chain 'A' and resid 445 through 478 removed outlier: 4.192A pdb=" N ALA A 450 " --> pdb=" O THR A 446 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP A 453 " --> pdb=" O ILE A 449 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU A 454 " --> pdb=" O ALA A 450 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG A 457 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE A 458 " --> pdb=" O LEU A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 484 removed outlier: 3.504A pdb=" N GLU A 483 " --> pdb=" O ARG A 479 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 484 " --> pdb=" O LYS A 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 479 through 484' Processing helix chain 'C' and resid 48 through 68 removed outlier: 3.561A pdb=" N VAL C 58 " --> pdb=" O THR C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 82 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 95 through 110 removed outlier: 3.509A pdb=" N LEU C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 146 Processing helix chain 'C' and resid 171 through 184 Processing helix chain 'C' and resid 189 through 192 Processing helix chain 'C' and resid 222 through 241 Processing helix chain 'C' and resid 242 through 244 No H-bonds generated for 'chain 'C' and resid 242 through 244' Processing helix chain 'C' and resid 246 through 283 removed outlier: 3.594A pdb=" N PHE C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA C 263 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE C 264 " --> pdb=" O LYS C 260 " (cutoff:3.500A) Proline residue: C 270 - end of helix removed outlier: 3.937A pdb=" N GLU C 283 " --> pdb=" O GLY C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 311 Processing helix chain 'C' and resid 311 through 322 Processing helix chain 'C' and resid 324 through 332 removed outlier: 3.983A pdb=" N PHE C 328 " --> pdb=" O ASN C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 343 Processing helix chain 'C' and resid 348 through 359 removed outlier: 3.801A pdb=" N GLU C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 375 removed outlier: 3.897A pdb=" N PHE C 369 " --> pdb=" O ARG C 365 " (cutoff:3.500A) Proline residue: C 372 - end of helix Processing helix chain 'C' and resid 379 through 397 removed outlier: 3.668A pdb=" N ALA C 383 " --> pdb=" O MET C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 419 removed outlier: 3.645A pdb=" N THR C 414 " --> pdb=" O SER C 410 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 418 " --> pdb=" O THR C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 432 No H-bonds generated for 'chain 'C' and resid 430 through 432' Processing helix chain 'C' and resid 433 through 438 removed outlier: 3.547A pdb=" N ALA C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 438 " --> pdb=" O VAL C 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 433 through 438' Processing helix chain 'C' and resid 445 through 478 removed outlier: 4.192A pdb=" N ALA C 450 " --> pdb=" O THR C 446 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP C 453 " --> pdb=" O ILE C 449 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU C 454 " --> pdb=" O ALA C 450 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG C 457 " --> pdb=" O TRP C 453 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE C 458 " --> pdb=" O LEU C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 484 removed outlier: 3.504A pdb=" N GLU C 483 " --> pdb=" O ARG C 479 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS C 484 " --> pdb=" O LYS C 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 479 through 484' Processing helix chain 'E' and resid 48 through 68 removed outlier: 3.561A pdb=" N VAL E 58 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 82 Processing helix chain 'E' and resid 82 through 94 Processing helix chain 'E' and resid 95 through 110 removed outlier: 3.510A pdb=" N LEU E 99 " --> pdb=" O LEU E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 146 Processing helix chain 'E' and resid 171 through 184 Processing helix chain 'E' and resid 189 through 192 Processing helix chain 'E' and resid 222 through 241 Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 246 through 283 removed outlier: 3.595A pdb=" N PHE E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA E 263 " --> pdb=" O MET E 259 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE E 264 " --> pdb=" O LYS E 260 " (cutoff:3.500A) Proline residue: E 270 - end of helix removed outlier: 3.937A pdb=" N GLU E 283 " --> pdb=" O GLY E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 311 Processing helix chain 'E' and resid 311 through 322 Processing helix chain 'E' and resid 324 through 332 removed outlier: 3.982A pdb=" N PHE E 328 " --> pdb=" O ASN E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 343 Processing helix chain 'E' and resid 348 through 359 removed outlier: 3.800A pdb=" N GLU E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 375 removed outlier: 3.897A pdb=" N PHE E 369 " --> pdb=" O ARG E 365 " (cutoff:3.500A) Proline residue: E 372 - end of helix Processing helix chain 'E' and resid 379 through 397 removed outlier: 3.668A pdb=" N ALA E 383 " --> pdb=" O MET E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 419 removed outlier: 3.646A pdb=" N THR E 414 " --> pdb=" O SER E 410 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE E 418 " --> pdb=" O THR E 414 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 432 No H-bonds generated for 'chain 'E' and resid 430 through 432' Processing helix chain 'E' and resid 433 through 438 removed outlier: 3.547A pdb=" N ALA E 437 " --> pdb=" O ILE E 433 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL E 438 " --> pdb=" O VAL E 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 433 through 438' Processing helix chain 'E' and resid 445 through 478 removed outlier: 4.192A pdb=" N ALA E 450 " --> pdb=" O THR E 446 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL E 451 " --> pdb=" O LEU E 447 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N TRP E 453 " --> pdb=" O ILE E 449 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU E 454 " --> pdb=" O ALA E 450 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ARG E 457 " --> pdb=" O TRP E 453 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N PHE E 458 " --> pdb=" O LEU E 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 479 through 484 removed outlier: 3.504A pdb=" N GLU E 483 " --> pdb=" O ARG E 479 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS E 484 " --> pdb=" O LYS E 480 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 479 through 484' Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199 removed outlier: 3.756A pdb=" N GLN A 216 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 194 through 199 removed outlier: 3.756A pdb=" N GLN C 216 " --> pdb=" O SER C 197 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 194 through 199 removed outlier: 3.756A pdb=" N GLN E 216 " --> pdb=" O SER E 197 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 2034 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: 1.30 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1458 1.29 - 1.42: 2187 1.42 - 1.55: 5739 1.55 - 1.68: 0 1.68 - 1.82: 102 Bond restraints: 9486 Sorted by residual: bond pdb=" C ALA C 269 " pdb=" N PRO C 270 " ideal model delta sigma weight residual 1.334 1.383 -0.049 1.51e-02 4.39e+03 1.05e+01 bond pdb=" C ALA A 269 " pdb=" N PRO A 270 " ideal model delta sigma weight residual 1.334 1.383 -0.049 1.51e-02 4.39e+03 1.03e+01 bond pdb=" C ALA E 269 " pdb=" N PRO E 270 " ideal model delta sigma weight residual 1.334 1.382 -0.048 1.51e-02 4.39e+03 1.02e+01 bond pdb=" C LEU E 97 " pdb=" N PRO E 98 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.36e-02 5.41e+03 9.47e+00 bond pdb=" C LEU C 97 " pdb=" N PRO C 98 " ideal model delta sigma weight residual 1.335 1.377 -0.042 1.36e-02 5.41e+03 9.45e+00 ... (remaining 9481 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 12361 2.22 - 4.44: 485 4.44 - 6.65: 69 6.65 - 8.87: 0 8.87 - 11.09: 6 Bond angle restraints: 12921 Sorted by residual: angle pdb=" N ILE A 433 " pdb=" CA ILE A 433 " pdb=" C ILE A 433 " ideal model delta sigma weight residual 110.62 121.71 -11.09 1.02e+00 9.61e-01 1.18e+02 angle pdb=" N ILE C 433 " pdb=" CA ILE C 433 " pdb=" C ILE C 433 " ideal model delta sigma weight residual 110.62 121.70 -11.08 1.02e+00 9.61e-01 1.18e+02 angle pdb=" N ILE E 433 " pdb=" CA ILE E 433 " pdb=" C ILE E 433 " ideal model delta sigma weight residual 110.62 121.69 -11.07 1.02e+00 9.61e-01 1.18e+02 angle pdb=" N VAL E 432 " pdb=" CA VAL E 432 " pdb=" C VAL E 432 " ideal model delta sigma weight residual 112.04 121.88 -9.84 1.40e+00 5.10e-01 4.94e+01 angle pdb=" N VAL C 432 " pdb=" CA VAL C 432 " pdb=" C VAL C 432 " ideal model delta sigma weight residual 112.04 121.87 -9.83 1.40e+00 5.10e-01 4.93e+01 ... (remaining 12916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.59: 4801 11.59 - 23.17: 563 23.17 - 34.75: 210 34.75 - 46.34: 57 46.34 - 57.92: 27 Dihedral angle restraints: 5658 sinusoidal: 2148 harmonic: 3510 Sorted by residual: dihedral pdb=" C VAL E 432 " pdb=" N VAL E 432 " pdb=" CA VAL E 432 " pdb=" CB VAL E 432 " ideal model delta harmonic sigma weight residual -122.00 -141.79 19.79 0 2.50e+00 1.60e-01 6.27e+01 dihedral pdb=" C VAL C 432 " pdb=" N VAL C 432 " pdb=" CA VAL C 432 " pdb=" CB VAL C 432 " ideal model delta harmonic sigma weight residual -122.00 -141.78 19.78 0 2.50e+00 1.60e-01 6.26e+01 dihedral pdb=" C VAL A 432 " pdb=" N VAL A 432 " pdb=" CA VAL A 432 " pdb=" CB VAL A 432 " ideal model delta harmonic sigma weight residual -122.00 -141.75 19.75 0 2.50e+00 1.60e-01 6.24e+01 ... (remaining 5655 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 1575 0.147 - 0.294: 63 0.294 - 0.441: 3 0.441 - 0.589: 0 0.589 - 0.736: 3 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA VAL C 432 " pdb=" N VAL C 432 " pdb=" C VAL C 432 " pdb=" CB VAL C 432 " both_signs ideal model delta sigma weight residual False 2.44 1.71 0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA VAL E 432 " pdb=" N VAL E 432 " pdb=" C VAL E 432 " pdb=" CB VAL E 432 " both_signs ideal model delta sigma weight residual False 2.44 1.71 0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CA VAL A 432 " pdb=" N VAL A 432 " pdb=" C VAL A 432 " pdb=" CB VAL A 432 " both_signs ideal model delta sigma weight residual False 2.44 1.71 0.73 2.00e-01 2.50e+01 1.35e+01 ... (remaining 1641 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 90 " 0.230 9.50e-02 1.11e+02 1.04e-01 8.02e+00 pdb=" NE ARG E 90 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG E 90 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG E 90 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG E 90 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 90 " -0.229 9.50e-02 1.11e+02 1.03e-01 7.99e+00 pdb=" NE ARG A 90 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 90 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG A 90 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 90 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 90 " 0.228 9.50e-02 1.11e+02 1.03e-01 7.96e+00 pdb=" NE ARG C 90 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG C 90 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG C 90 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG C 90 " 0.001 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 21 2.51 - 3.11: 6600 3.11 - 3.71: 14893 3.71 - 4.30: 21716 4.30 - 4.90: 35409 Nonbonded interactions: 78639 Sorted by model distance: nonbonded pdb=" OG1 THR C 131 " pdb="NA NA C1005 " model vdw 1.913 2.470 nonbonded pdb=" OG1 THR A 131 " pdb="NA NA A1005 " model vdw 1.913 2.470 nonbonded pdb=" OG1 THR E 131 " pdb="NA NA E1005 " model vdw 1.913 2.470 nonbonded pdb=" O VAL C 432 " pdb=" OG1 THR C 436 " model vdw 2.087 3.040 nonbonded pdb=" O VAL E 432 " pdb=" OG1 THR E 436 " model vdw 2.087 3.040 ... (remaining 78634 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 'A' selection = chain 'C' selection = chain 'E' } 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: 0.010 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.070 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 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 : 0.007 0.049 9486 Z= 0.410 Angle : 1.047 11.089 12921 Z= 0.635 Chirality : 0.073 0.736 1644 Planarity : 0.008 0.104 1566 Dihedral : 12.804 57.923 3402 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.27 % 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: -3.02 (0.19), residues: 1212 helix: -1.58 (0.14), residues: 951 sheet: None (None), residues: 0 loop : -2.92 (0.30), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.002 ARG C 90 TYR 0.020 0.004 TYR C 80 PHE 0.019 0.004 PHE C 233 TRP 0.014 0.004 TRP C 267 HIS 0.002 0.001 HIS E 308 Details of bonding type rmsd covalent geometry : bond 0.00706 ( 9486) covalent geometry : angle 1.04704 (12921) hydrogen bonds : bond 0.16719 ( 684) hydrogen bonds : angle 7.21547 ( 2034) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 286 time to evaluate : 0.263 Fit side-chains REVERT: A 267 TRP cc_start: 0.7610 (m100) cc_final: 0.7278 (m-10) REVERT: E 267 TRP cc_start: 0.7560 (m100) cc_final: 0.7267 (m-10) outliers start: 0 outliers final: 0 residues processed: 286 average time/residue: 0.0835 time to fit residues: 34.6758 Evaluate side-chains 210 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 146 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 = 0.168613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137204 restraints weight = 9018.672| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.45 r_work: 0.3342 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9486 Z= 0.138 Angle : 0.622 6.592 12921 Z= 0.310 Chirality : 0.039 0.133 1644 Planarity : 0.005 0.041 1566 Dihedral : 5.913 44.123 1395 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.13 % Allowed : 11.89 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.59 (0.22), residues: 1212 helix: 0.16 (0.16), residues: 990 sheet: -2.51 (0.74), residues: 27 loop : -2.42 (0.36), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 457 TYR 0.015 0.002 TYR C 80 PHE 0.012 0.002 PHE C 81 TRP 0.009 0.001 TRP E 267 HIS 0.004 0.001 HIS E 146 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9486) covalent geometry : angle 0.62242 (12921) hydrogen bonds : bond 0.04787 ( 684) hydrogen bonds : angle 4.84002 ( 2034) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 228 time to evaluate : 0.313 Fit side-chains REVERT: A 242 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7168 (tp30) REVERT: E 242 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7257 (tp30) outliers start: 21 outliers final: 10 residues processed: 236 average time/residue: 0.0756 time to fit residues: 26.2197 Evaluate side-chains 207 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** 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 = 0.3835 r_free = 0.3835 target = 0.165434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.133725 restraints weight = 9051.791| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.40 r_work: 0.3305 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9486 Z= 0.148 Angle : 0.608 5.776 12921 Z= 0.302 Chirality : 0.040 0.134 1644 Planarity : 0.004 0.044 1566 Dihedral : 5.675 43.474 1395 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.85 % Allowed : 13.41 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.19 (0.23), residues: 1212 helix: 0.73 (0.16), residues: 990 sheet: -1.96 (0.89), residues: 27 loop : -2.38 (0.38), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 90 TYR 0.023 0.002 TYR E 297 PHE 0.012 0.002 PHE C 229 TRP 0.003 0.001 TRP A 453 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9486) covalent geometry : angle 0.60812 (12921) hydrogen bonds : bond 0.04695 ( 684) hydrogen bonds : angle 4.64960 ( 2034) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.303 Fit side-chains REVERT: A 242 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7208 (tp30) REVERT: A 456 ASP cc_start: 0.8055 (t0) cc_final: 0.7838 (t0) REVERT: C 435 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8242 (mp) REVERT: E 242 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: E 283 GLU cc_start: 0.8443 (pt0) cc_final: 0.8242 (pt0) outliers start: 28 outliers final: 16 residues processed: 219 average time/residue: 0.0742 time to fit residues: 24.6754 Evaluate side-chains 212 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 81 optimal weight: 0.4980 chunk 114 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 98 optimal weight: 4.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** 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 = 0.3848 r_free = 0.3848 target = 0.166754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.136750 restraints weight = 9163.948| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.46 r_work: 0.3322 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9486 Z= 0.126 Angle : 0.580 5.502 12921 Z= 0.289 Chirality : 0.039 0.135 1644 Planarity : 0.004 0.043 1566 Dihedral : 5.432 42.953 1395 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.15 % Allowed : 14.53 % Favored : 82.32 % 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: 0.54 (0.24), residues: 1212 helix: 0.95 (0.16), residues: 996 sheet: -1.95 (0.94), residues: 27 loop : -2.25 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 122 TYR 0.020 0.002 TYR A 297 PHE 0.013 0.002 PHE E 81 TRP 0.003 0.001 TRP E 453 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9486) covalent geometry : angle 0.58005 (12921) hydrogen bonds : bond 0.04352 ( 684) hydrogen bonds : angle 4.55911 ( 2034) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.239 Fit side-chains REVERT: A 242 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: A 456 ASP cc_start: 0.7983 (t0) cc_final: 0.7767 (t0) REVERT: C 435 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8247 (mp) REVERT: E 242 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7171 (tp30) REVERT: E 283 GLU cc_start: 0.8456 (pt0) cc_final: 0.8231 (pt0) outliers start: 31 outliers final: 17 residues processed: 217 average time/residue: 0.0705 time to fit residues: 23.3438 Evaluate side-chains 211 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.3980 chunk 101 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 119 optimal weight: 4.9990 chunk 61 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** 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 = 0.3844 r_free = 0.3844 target = 0.166542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135054 restraints weight = 9065.648| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.40 r_work: 0.3326 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9486 Z= 0.127 Angle : 0.580 5.502 12921 Z= 0.289 Chirality : 0.039 0.135 1644 Planarity : 0.004 0.043 1566 Dihedral : 5.433 42.953 1395 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.03 % Allowed : 17.28 % Favored : 80.69 % 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: 0.54 (0.24), residues: 1212 helix: 0.95 (0.16), residues: 996 sheet: -1.95 (0.94), residues: 27 loop : -2.25 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 122 TYR 0.020 0.002 TYR A 297 PHE 0.013 0.002 PHE E 81 TRP 0.003 0.001 TRP E 453 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9486) covalent geometry : angle 0.57975 (12921) hydrogen bonds : bond 0.04352 ( 684) hydrogen bonds : angle 4.55911 ( 2034) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.289 Fit side-chains REVERT: A 242 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: A 448 ILE cc_start: 0.7256 (mm) cc_final: 0.6904 (mt) REVERT: A 456 ASP cc_start: 0.8031 (t0) cc_final: 0.7796 (t0) REVERT: C 435 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8246 (mp) REVERT: E 242 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7188 (tp30) REVERT: E 283 GLU cc_start: 0.8460 (pt0) cc_final: 0.8239 (pt0) outliers start: 20 outliers final: 17 residues processed: 198 average time/residue: 0.0696 time to fit residues: 21.1618 Evaluate side-chains 211 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 82 optimal weight: 10.0000 chunk 92 optimal weight: 0.0570 chunk 89 optimal weight: 0.5980 chunk 107 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** 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 = 0.3844 r_free = 0.3844 target = 0.166516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135006 restraints weight = 9039.007| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.39 r_work: 0.3322 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9486 Z= 0.127 Angle : 0.580 5.502 12921 Z= 0.289 Chirality : 0.039 0.135 1644 Planarity : 0.004 0.043 1566 Dihedral : 5.431 42.953 1395 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.03 % Allowed : 17.38 % Favored : 80.59 % 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: 0.54 (0.24), residues: 1212 helix: 0.95 (0.16), residues: 996 sheet: -1.95 (0.94), residues: 27 loop : -2.25 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 122 TYR 0.020 0.002 TYR A 297 PHE 0.013 0.002 PHE E 81 TRP 0.003 0.001 TRP E 453 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9486) covalent geometry : angle 0.57975 (12921) hydrogen bonds : bond 0.04352 ( 684) hydrogen bonds : angle 4.55911 ( 2034) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.441 Fit side-chains REVERT: A 242 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7258 (tp30) REVERT: A 448 ILE cc_start: 0.7247 (mm) cc_final: 0.6913 (mt) REVERT: A 456 ASP cc_start: 0.8037 (t0) cc_final: 0.7799 (t0) REVERT: C 435 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8252 (mp) REVERT: E 242 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: E 283 GLU cc_start: 0.8457 (pt0) cc_final: 0.8236 (pt0) outliers start: 20 outliers final: 17 residues processed: 198 average time/residue: 0.0718 time to fit residues: 21.7970 Evaluate side-chains 211 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 435 LEU Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 12 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.166187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134834 restraints weight = 9096.576| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.37 r_work: 0.3320 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3182 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9486 Z= 0.138 Angle : 0.599 5.983 12921 Z= 0.298 Chirality : 0.040 0.150 1644 Planarity : 0.004 0.064 1566 Dihedral : 5.377 42.855 1395 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.34 % Allowed : 17.17 % Favored : 80.49 % 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: 0.76 (0.24), residues: 1212 helix: 1.13 (0.17), residues: 975 sheet: -1.83 (0.98), residues: 27 loop : -1.96 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.034 0.002 TYR A 297 PHE 0.016 0.002 PHE C 81 TRP 0.003 0.001 TRP E 453 HIS 0.001 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9486) covalent geometry : angle 0.59857 (12921) hydrogen bonds : bond 0.04415 ( 684) hydrogen bonds : angle 4.57458 ( 2034) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 0.281 Fit side-chains REVERT: A 242 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: A 448 ILE cc_start: 0.7162 (mm) cc_final: 0.6917 (mm) REVERT: A 456 ASP cc_start: 0.8039 (t0) cc_final: 0.7835 (t0) REVERT: E 242 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7237 (tp30) outliers start: 23 outliers final: 18 residues processed: 214 average time/residue: 0.0698 time to fit residues: 22.8236 Evaluate side-chains 217 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 114 optimal weight: 0.0570 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** 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 = 0.3841 r_free = 0.3841 target = 0.166199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.134399 restraints weight = 9011.043| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.45 r_work: 0.3320 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9486 Z= 0.138 Angle : 0.598 5.982 12921 Z= 0.298 Chirality : 0.040 0.150 1644 Planarity : 0.004 0.064 1566 Dihedral : 5.385 42.856 1395 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.03 % Allowed : 17.89 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.76 (0.24), residues: 1212 helix: 1.13 (0.17), residues: 975 sheet: -1.83 (0.98), residues: 27 loop : -1.96 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.034 0.002 TYR A 297 PHE 0.016 0.002 PHE C 81 TRP 0.003 0.001 TRP E 453 HIS 0.001 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9486) covalent geometry : angle 0.59827 (12921) hydrogen bonds : bond 0.04414 ( 684) hydrogen bonds : angle 4.57460 ( 2034) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.240 Fit side-chains REVERT: A 242 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7273 (tp30) REVERT: A 448 ILE cc_start: 0.7134 (mm) cc_final: 0.6892 (mm) REVERT: A 456 ASP cc_start: 0.8025 (t0) cc_final: 0.7798 (t0) REVERT: E 242 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7233 (tp30) outliers start: 20 outliers final: 18 residues processed: 204 average time/residue: 0.0743 time to fit residues: 22.9454 Evaluate side-chains 219 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.0370 chunk 99 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** 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 = 0.3840 r_free = 0.3840 target = 0.166107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.134783 restraints weight = 8963.667| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.38 r_work: 0.3327 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9486 Z= 0.138 Angle : 0.598 5.970 12921 Z= 0.298 Chirality : 0.040 0.149 1644 Planarity : 0.004 0.064 1566 Dihedral : 5.438 42.857 1395 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.03 % Allowed : 18.09 % Favored : 79.88 % 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: 0.76 (0.24), residues: 1212 helix: 1.13 (0.17), residues: 975 sheet: -1.83 (0.98), residues: 27 loop : -1.96 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.033 0.002 TYR A 297 PHE 0.016 0.002 PHE C 81 TRP 0.003 0.001 TRP E 453 HIS 0.001 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 9486) covalent geometry : angle 0.59804 (12921) hydrogen bonds : bond 0.04413 ( 684) hydrogen bonds : angle 4.57472 ( 2034) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 199 time to evaluate : 0.319 Fit side-chains REVERT: A 242 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7286 (tp30) REVERT: A 448 ILE cc_start: 0.7148 (mm) cc_final: 0.6906 (mm) REVERT: A 456 ASP cc_start: 0.8033 (t0) cc_final: 0.7830 (t0) REVERT: E 242 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7220 (tp30) outliers start: 20 outliers final: 18 residues processed: 205 average time/residue: 0.0741 time to fit residues: 23.1064 Evaluate side-chains 216 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 43 optimal weight: 4.9990 chunk 19 optimal weight: 0.1980 chunk 75 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 48 optimal weight: 0.3980 chunk 59 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** 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 = 0.3842 r_free = 0.3842 target = 0.166202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134391 restraints weight = 9062.656| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.51 r_work: 0.3312 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9486 Z= 0.138 Angle : 0.598 5.951 12921 Z= 0.298 Chirality : 0.040 0.148 1644 Planarity : 0.004 0.064 1566 Dihedral : 5.496 42.860 1395 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.13 % Allowed : 18.19 % Favored : 79.67 % 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: 0.76 (0.24), residues: 1212 helix: 1.13 (0.17), residues: 975 sheet: -1.83 (0.98), residues: 27 loop : -1.96 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.032 0.002 TYR A 297 PHE 0.015 0.002 PHE C 81 TRP 0.003 0.001 TRP E 453 HIS 0.001 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9486) covalent geometry : angle 0.59772 (12921) hydrogen bonds : bond 0.04412 ( 684) hydrogen bonds : angle 4.57490 ( 2034) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2424 Ramachandran restraints generated. 1212 Oldfield, 0 Emsley, 1212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.333 Fit side-chains REVERT: A 242 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7263 (tp30) REVERT: A 448 ILE cc_start: 0.7119 (mm) cc_final: 0.6878 (mm) REVERT: A 456 ASP cc_start: 0.8026 (t0) cc_final: 0.7818 (t0) REVERT: E 242 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7223 (tp30) outliers start: 21 outliers final: 19 residues processed: 204 average time/residue: 0.0689 time to fit residues: 21.2508 Evaluate side-chains 217 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 196 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 340 LEU Chi-restraints excluded: chain A residue 377 ILE Chi-restraints excluded: chain A residue 417 SER Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 417 SER Chi-restraints excluded: chain C residue 438 VAL Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 453 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 49 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.0670 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** 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 = 0.3847 r_free = 0.3847 target = 0.166794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135101 restraints weight = 8906.940| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 1.45 r_work: 0.3324 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9486 Z= 0.136 Angle : 0.625 9.891 12921 Z= 0.308 Chirality : 0.041 0.165 1644 Planarity : 0.004 0.059 1566 Dihedral : 5.346 41.813 1395 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.24 % Allowed : 18.19 % Favored : 79.57 % 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: 0.82 (0.24), residues: 1212 helix: 1.17 (0.17), residues: 975 sheet: -1.84 (0.95), residues: 27 loop : -1.92 (0.37), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.047 0.002 TYR A 297 PHE 0.013 0.002 PHE C 81 TRP 0.003 0.001 TRP E 453 HIS 0.001 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 9486) covalent geometry : angle 0.62537 (12921) hydrogen bonds : bond 0.04343 ( 684) hydrogen bonds : angle 4.58114 ( 2034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2322.28 seconds wall clock time: 40 minutes 18.93 seconds (2418.93 seconds total)