Starting phenix.real_space_refine on Thu Jul 2 17:23:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i7m_52657/07_2026/9i7m_52657.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i7m_52657/07_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_52657/07_2026/9i7m_52657.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i7m_52657/07_2026/9i7m_52657.map" model { file = "/net/cci-nas-00/data/ceres_data/9i7m_52657/07_2026/9i7m_52657.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i7m_52657/07_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-6108/lib/python3.11/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, 41 Ad-hoc single atom residues: {' NA': 3} Unusual residues: {'6Z6': 1} Inner-chain residues flagged as termini: ['pdbres="ASP A1002 "'] Classifications: {'peptide': 1, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {None: 1} Chain breaks: 3 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: 2.53, per 1000 atoms: 0.27 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: 1.09 Conformation dependent library (CDL) restraints added in 348.9 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: 0.24 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: 1.52 Time building geometry restraints manager: 1.12 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 3.210 nonbonded pdb=" OG1 THR A 131 " pdb="NA NA A1005 " model vdw 1.913 3.210 nonbonded pdb=" OG1 THR E 131 " pdb="NA NA E1005 " model vdw 1.913 3.210 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: 0.03 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: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 10.250 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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/Z covalent geometry : bond 0.00706 / 0.41 ( 9486) covalent geometry : angle 1.04704 / 0.64 (12921) hydrogen bonds : bond 0.16719 / 11.15 ( 684) hydrogen bonds : angle 7.21547 / 5.08 ( 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 : 0.327 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: 0.0845 time to fit residues: 35.1282 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 : 0.242 ------------------------------------------------------------------------------- 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: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.169054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137582 restraints weight = 8994.400| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.48 r_work: 0.3348 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.1724 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= 0.142 Angle : 0.636 6.911 12921 Z= 0.316 Chirality : 0.039 0.136 1644 Planarity : 0.005 0.041 1566 Dihedral : 5.959 43.254 1395 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.24 % Allowed : 12.09 % Favored : 85.67 % 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: -0.59 (0.23), residues: 1212 helix: 0.19 (0.16), residues: 987 sheet: -2.51 (0.75), residues: 27 loop : -2.53 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 457 TYR 0.016 0.002 TYR C 80 PHE 0.012 0.002 PHE C 81 TRP 0.008 0.001 TRP E 267 HIS 0.004 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9486) covalent geometry : angle 0.63607 / 0.32 (12921) hydrogen bonds : bond 0.04888 / 3.37 ( 684) hydrogen bonds : angle 4.85221 / 3.40 ( 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 251 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 229 time to evaluate : 0.323 Fit side-chains REVERT: A 242 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7254 (tp30) REVERT: E 242 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7167 (tp30) outliers start: 22 outliers final: 10 residues processed: 237 average time/residue: 0.0737 time to fit residues: 25.9416 Evaluate side-chains 209 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.212 ------------------------------------------------------------------------------- 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 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 453 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3797 r_free = 0.3797 target = 0.161636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.129661 restraints weight = 9076.061| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.40 r_work: 0.3261 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9486 Z= 0.192 Angle : 0.650 6.287 12921 Z= 0.326 Chirality : 0.042 0.138 1644 Planarity : 0.004 0.046 1566 Dihedral : 5.823 45.274 1395 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.74 % Allowed : 14.33 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.23), residues: 1212 helix: 0.63 (0.16), residues: 969 sheet: -2.06 (0.88), residues: 27 loop : -2.28 (0.34), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 90 TYR 0.021 0.002 TYR E 297 PHE 0.017 0.002 PHE C 81 TRP 0.003 0.001 TRP A 267 HIS 0.002 0.001 HIS E 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 ( 9486) covalent geometry : angle 0.65040 / 0.33 (12921) hydrogen bonds : bond 0.05183 / 3.59 ( 684) hydrogen bonds : angle 4.80536 / 3.37 ( 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 228 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.392 Fit side-chains REVERT: A 242 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7248 (tp30) REVERT: A 256 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7195 (mt-10) REVERT: A 448 ILE cc_start: 0.7707 (OUTLIER) cc_final: 0.7295 (mt) REVERT: C 448 ILE cc_start: 0.7807 (mm) cc_final: 0.7398 (mt) REVERT: E 242 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7195 (tp30) REVERT: E 256 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6998 (mt-10) REVERT: E 283 GLU cc_start: 0.8419 (pt0) cc_final: 0.8166 (pt0) outliers start: 27 outliers final: 17 residues processed: 213 average time/residue: 0.0754 time to fit residues: 24.3509 Evaluate side-chains 209 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 256 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 A residue 448 ILE 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 247 LEU 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 256 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 114 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3826 r_free = 0.3826 target = 0.164458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.132819 restraints weight = 9191.841| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.39 r_work: 0.3303 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9486 Z= 0.137 Angle : 0.596 5.700 12921 Z= 0.298 Chirality : 0.039 0.135 1644 Planarity : 0.004 0.044 1566 Dihedral : 5.433 43.964 1395 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.54 % Allowed : 15.14 % 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: 0.39 (0.24), residues: 1212 helix: 0.84 (0.16), residues: 999 sheet: -1.83 (0.98), residues: 27 loop : -2.28 (0.39), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 122 TYR 0.021 0.002 TYR A 297 PHE 0.011 0.002 PHE C 81 TRP 0.003 0.001 TRP E 453 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 9486) covalent geometry : angle 0.59567 / 0.30 (12921) hydrogen bonds : bond 0.04487 / 3.12 ( 684) hydrogen bonds : angle 4.62949 / 3.24 ( 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 230 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.367 Fit side-chains REVERT: A 242 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7236 (tp30) REVERT: A 456 ASP cc_start: 0.8027 (t0) cc_final: 0.7789 (t0) REVERT: C 448 ILE cc_start: 0.7909 (mm) cc_final: 0.7447 (mt) REVERT: E 242 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7212 (tp30) REVERT: E 448 ILE cc_start: 0.7928 (mm) cc_final: 0.7491 (mt) outliers start: 25 outliers final: 19 residues processed: 216 average time/residue: 0.0686 time to fit residues: 22.8332 Evaluate side-chains 210 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET 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 353 PHE 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 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: 1.9990 chunk 73 optimal weight: 1.9990 chunk 81 optimal weight: 0.0370 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 119 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.166230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.134656 restraints weight = 9038.745| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.38 r_work: 0.3319 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9486 Z= 0.126 Angle : 0.588 5.308 12921 Z= 0.293 Chirality : 0.039 0.140 1644 Planarity : 0.004 0.048 1566 Dihedral : 5.305 42.864 1395 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.56 % Allowed : 14.53 % 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: 0.60 (0.24), residues: 1212 helix: 1.00 (0.16), residues: 996 sheet: -1.75 (0.98), residues: 27 loop : -2.25 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 122 TYR 0.020 0.002 TYR E 297 PHE 0.013 0.001 PHE C 81 TRP 0.003 0.001 TRP E 453 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 9486) covalent geometry : angle 0.58796 / 0.29 (12921) hydrogen bonds : bond 0.04332 / 3.01 ( 684) hydrogen bonds : angle 4.56062 / 3.19 ( 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 239 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 204 time to evaluate : 0.365 Fit side-chains REVERT: A 242 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7279 (tp30) REVERT: A 456 ASP cc_start: 0.7978 (t0) cc_final: 0.7758 (t0) REVERT: C 448 ILE cc_start: 0.7892 (mm) cc_final: 0.7422 (mt) REVERT: E 242 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: E 448 ILE cc_start: 0.7897 (mm) cc_final: 0.7434 (mt) outliers start: 35 outliers final: 23 residues processed: 221 average time/residue: 0.0759 time to fit residues: 25.2126 Evaluate side-chains 216 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET 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 108 LEU 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 283 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 353 PHE 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 353 PHE 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: 0.9990 chunk 89 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3838 r_free = 0.3838 target = 0.165551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.134055 restraints weight = 9040.590| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 1.44 r_work: 0.3318 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9486 Z= 0.126 Angle : 0.587 5.305 12921 Z= 0.293 Chirality : 0.039 0.139 1644 Planarity : 0.004 0.048 1566 Dihedral : 5.341 42.863 1395 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.54 % Allowed : 16.87 % 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: 0.60 (0.24), residues: 1212 helix: 1.00 (0.16), residues: 996 sheet: -1.75 (0.98), residues: 27 loop : -2.25 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 122 TYR 0.019 0.002 TYR E 297 PHE 0.013 0.001 PHE C 81 TRP 0.003 0.001 TRP E 453 HIS 0.002 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 ( 9486) covalent geometry : angle 0.58746 / 0.29 (12921) hydrogen bonds : bond 0.04333 / 3.01 ( 684) hydrogen bonds : angle 4.56062 / 3.19 ( 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 216 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.338 Fit side-chains REVERT: A 242 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7269 (tp30) REVERT: A 448 ILE cc_start: 0.7543 (mm) cc_final: 0.7113 (mt) REVERT: A 456 ASP cc_start: 0.8024 (t0) cc_final: 0.7775 (t0) REVERT: C 448 ILE cc_start: 0.7885 (mm) cc_final: 0.7419 (mt) REVERT: E 242 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7227 (tp30) REVERT: E 448 ILE cc_start: 0.7906 (mm) cc_final: 0.7440 (mt) outliers start: 25 outliers final: 23 residues processed: 201 average time/residue: 0.0715 time to fit residues: 22.0344 Evaluate side-chains 216 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET 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 108 LEU 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 283 GLU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 353 PHE 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 353 PHE 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: 1.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3827 r_free = 0.3827 target = 0.164287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133744 restraints weight = 9085.205| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 1.52 r_work: 0.3301 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9486 Z= 0.151 Angle : 0.614 5.712 12921 Z= 0.306 Chirality : 0.041 0.198 1644 Planarity : 0.005 0.074 1566 Dihedral : 5.332 42.814 1395 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.64 % Allowed : 16.87 % 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: 0.61 (0.24), residues: 1212 helix: 0.99 (0.16), residues: 996 sheet: -1.71 (0.96), residues: 27 loop : -2.21 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 122 TYR 0.036 0.002 TYR A 297 PHE 0.016 0.002 PHE A 81 TRP 0.003 0.001 TRP E 453 HIS 0.001 0.001 HIS C 476 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 ( 9486) covalent geometry : angle 0.61427 / 0.31 (12921) hydrogen bonds : bond 0.04514 / 3.14 ( 684) hydrogen bonds : angle 4.58433 / 3.20 ( 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 226 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.254 Fit side-chains REVERT: A 242 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7335 (tp30) REVERT: A 456 ASP cc_start: 0.8071 (t0) cc_final: 0.7828 (t0) REVERT: C 448 ILE cc_start: 0.7932 (mm) cc_final: 0.7485 (mt) REVERT: E 242 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7284 (tp30) REVERT: E 448 ILE cc_start: 0.7911 (mm) cc_final: 0.7464 (mt) outliers start: 26 outliers final: 23 residues processed: 210 average time/residue: 0.0665 time to fit residues: 21.5037 Evaluate side-chains 219 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET 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 435 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain C residue 108 LEU 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 283 GLU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 353 PHE 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 353 PHE Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 111 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.4980 chunk 107 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3834 r_free = 0.3834 target = 0.165266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133761 restraints weight = 9050.089| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.39 r_work: 0.3319 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3183 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9486 Z= 0.136 Angle : 0.614 6.634 12921 Z= 0.303 Chirality : 0.040 0.153 1644 Planarity : 0.004 0.056 1566 Dihedral : 5.282 42.753 1395 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.64 % Allowed : 17.17 % Favored : 80.18 % 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: 0.69 (0.24), residues: 1212 helix: 1.06 (0.16), residues: 996 sheet: -1.66 (0.97), residues: 27 loop : -2.21 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.039 0.002 TYR A 297 PHE 0.014 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/Z covalent geometry : bond 0.00301 / 0.14 ( 9486) covalent geometry : angle 0.61355 / 0.30 (12921) hydrogen bonds : bond 0.04375 / 3.04 ( 684) hydrogen bonds : angle 4.59155 / 3.20 ( 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 226 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.305 Fit side-chains REVERT: A 242 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: A 448 ILE cc_start: 0.7424 (mm) cc_final: 0.7141 (mm) REVERT: C 448 ILE cc_start: 0.7888 (mm) cc_final: 0.7456 (mt) REVERT: E 242 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: E 448 ILE cc_start: 0.7887 (mm) cc_final: 0.7424 (mt) outliers start: 26 outliers final: 22 residues processed: 209 average time/residue: 0.0680 time to fit residues: 22.0057 Evaluate side-chains 217 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET 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 108 LEU 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 353 PHE 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 212 VAL Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 35 optimal weight: 0.0970 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 0.0010 chunk 99 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 57 optimal weight: 0.3980 chunk 3 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.165433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.133709 restraints weight = 8978.578| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.41 r_work: 0.3309 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9486 Z= 0.136 Angle : 0.613 6.634 12921 Z= 0.303 Chirality : 0.040 0.153 1644 Planarity : 0.004 0.056 1566 Dihedral : 5.282 42.753 1395 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.44 % Allowed : 17.38 % Favored : 80.18 % 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: 0.69 (0.24), residues: 1212 helix: 1.06 (0.16), residues: 996 sheet: -1.66 (0.97), residues: 27 loop : -2.21 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.039 0.002 TYR A 297 PHE 0.014 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/Z covalent geometry : bond 0.00301 / 0.14 ( 9486) covalent geometry : angle 0.61332 / 0.30 (12921) hydrogen bonds : bond 0.04375 / 3.04 ( 684) hydrogen bonds : angle 4.59155 / 3.20 ( 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 217 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.215 Fit side-chains REVERT: A 242 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7331 (tp30) REVERT: C 448 ILE cc_start: 0.7881 (mm) cc_final: 0.7450 (mt) REVERT: E 242 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: E 448 ILE cc_start: 0.7844 (mm) cc_final: 0.7412 (mt) outliers start: 24 outliers final: 22 residues processed: 202 average time/residue: 0.0599 time to fit residues: 18.5200 Evaluate side-chains 217 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET 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 108 LEU 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 353 PHE 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 212 VAL Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 120 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3839 r_free = 0.3839 target = 0.165908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133516 restraints weight = 9082.145| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.51 r_work: 0.3319 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3180 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9486 Z= 0.137 Angle : 0.619 8.042 12921 Z= 0.305 Chirality : 0.040 0.160 1644 Planarity : 0.004 0.048 1566 Dihedral : 5.211 41.963 1395 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.34 % Allowed : 17.58 % 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: 0.78 (0.24), residues: 1212 helix: 1.11 (0.17), residues: 996 sheet: -1.39 (1.03), residues: 27 loop : -2.17 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.042 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/Z covalent geometry : bond 0.00310 / 0.14 ( 9486) covalent geometry : angle 0.61881 / 0.30 (12921) hydrogen bonds : bond 0.04394 / 3.05 ( 684) hydrogen bonds : angle 4.58999 / 3.20 ( 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 227 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.256 Fit side-chains REVERT: A 242 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: A 444 ASP cc_start: 0.7101 (m-30) cc_final: 0.6751 (t0) REVERT: C 448 ILE cc_start: 0.7824 (mm) cc_final: 0.7376 (mt) REVERT: E 242 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7343 (tp30) REVERT: E 448 ILE cc_start: 0.7919 (mm) cc_final: 0.7517 (mt) outliers start: 23 outliers final: 20 residues processed: 213 average time/residue: 0.0652 time to fit residues: 21.3123 Evaluate side-chains 216 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 194 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 MET 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 108 LEU 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 353 PHE 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 141 LEU Chi-restraints excluded: chain E residue 242 GLU Chi-restraints excluded: chain E residue 340 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain E residue 417 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 447 LEU 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: 0.4980 chunk 85 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 114 optimal weight: 0.0040 chunk 79 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 = 0.3846 r_free = 0.3846 target = 0.166622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134158 restraints weight = 8894.621| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 1.55 r_work: 0.3312 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3172 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2649 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= 0.133 Angle : 0.636 9.831 12921 Z= 0.309 Chirality : 0.040 0.211 1644 Planarity : 0.004 0.046 1566 Dihedral : 5.192 41.536 1395 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.24 % Allowed : 19.00 % Favored : 78.76 % 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: 0.83 (0.24), residues: 1212 helix: 1.14 (0.17), residues: 996 sheet: -1.28 (1.05), residues: 27 loop : -2.15 (0.39), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 457 TYR 0.038 0.002 TYR A 297 PHE 0.020 0.002 PHE E 81 TRP 0.003 0.001 TRP A 453 HIS 0.001 0.001 HIS A 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 ( 9486) covalent geometry : angle 0.63600 / 0.31 (12921) hydrogen bonds : bond 0.04293 / 2.99 ( 684) hydrogen bonds : angle 4.59530 / 3.21 ( 2034) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2240.42 seconds wall clock time: 39 minutes 3.33 seconds (2343.33 seconds total)