Starting phenix.real_space_refine on Thu Jul 2 21:45:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xr4_33407/07_2026/7xr4_33407.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xr4_33407/07_2026/7xr4_33407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xr4_33407/07_2026/7xr4_33407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xr4_33407/07_2026/7xr4_33407.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xr4_33407/07_2026/7xr4_33407.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xr4_33407/07_2026/7xr4_33407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xr4_33407/07_2026/7xr4_33407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xr4_33407/07_2026/7xr4_33407.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 6717 2.51 5 N 1539 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3185 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 14, 'TRANS': 410} Chain breaks: 2 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 147 Unusual residues: {'PC1': 8, 'Y01': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 392 Unresolved non-hydrogen dihedrals: 224 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PC1:plan-1': 8, 'PC1:plan-2': 8} Unresolved non-hydrogen planarities: 48 Restraints were copied for chains: B, C Time building chain proxies: 2.10, per 1000 atoms: 0.21 Number of scatterers: 10026 At special positions: 0 Unit cell: (111.28, 114.4, 85.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 75 16.00 O 1695 8.00 N 1539 7.00 C 6717 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: 1.14 Conformation dependent library (CDL) restraints added in 393.9 milliseconds 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2316 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 87.2% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 37 through 44 removed outlier: 4.328A pdb=" N ASN A 44 " --> pdb=" O LYS A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 65 Processing helix chain 'A' and resid 71 through 92 Proline residue: A 81 - end of helix removed outlier: 3.757A pdb=" N LEU A 92 " --> pdb=" O MET A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 107 Processing helix chain 'A' and resid 109 through 114 Processing helix chain 'A' and resid 114 through 143 Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.825A pdb=" N GLY A 260 " --> pdb=" O MET A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 303 removed outlier: 3.604A pdb=" N TYR A 287 " --> pdb=" O MET A 283 " (cutoff:3.500A) Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 305 through 330 Processing helix chain 'A' and resid 330 through 341 Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.536A pdb=" N ALA A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 367 through 379 Processing helix chain 'A' and resid 382 through 394 Proline residue: A 391 - end of helix Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.577A pdb=" N ASN A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 439 Processing helix chain 'A' and resid 445 through 458 removed outlier: 4.117A pdb=" N LEU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU A 452 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 470 removed outlier: 4.159A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 497 removed outlier: 3.912A pdb=" N LEU A 474 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET A 477 " --> pdb=" O LEU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'B' and resid 38 through 44 removed outlier: 4.329A pdb=" N ASN B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 65 Processing helix chain 'B' and resid 71 through 92 Proline residue: B 81 - end of helix removed outlier: 3.758A pdb=" N LEU B 92 " --> pdb=" O MET B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 107 Processing helix chain 'B' and resid 109 through 114 Processing helix chain 'B' and resid 114 through 143 Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 241 through 260 removed outlier: 3.825A pdb=" N GLY B 260 " --> pdb=" O MET B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 303 removed outlier: 3.604A pdb=" N TYR B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 305 through 330 Processing helix chain 'B' and resid 330 through 341 Processing helix chain 'B' and resid 343 through 351 removed outlier: 3.536A pdb=" N ALA B 349 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B 350 " --> pdb=" O SER B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 367 through 379 Processing helix chain 'B' and resid 382 through 394 Proline residue: B 391 - end of helix Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.577A pdb=" N ASN B 416 " --> pdb=" O ILE B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 439 Processing helix chain 'B' and resid 445 through 458 removed outlier: 4.117A pdb=" N LEU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 452 " --> pdb=" O VAL B 448 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 462 No H-bonds generated for 'chain 'B' and resid 460 through 462' Processing helix chain 'B' and resid 463 through 470 removed outlier: 4.158A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 470 " --> pdb=" O LEU B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 497 removed outlier: 3.911A pdb=" N LEU B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET B 477 " --> pdb=" O LEU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 507 Processing helix chain 'C' and resid 38 through 44 removed outlier: 4.329A pdb=" N ASN C 44 " --> pdb=" O LYS C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 65 Processing helix chain 'C' and resid 71 through 92 Proline residue: C 81 - end of helix removed outlier: 3.758A pdb=" N LEU C 92 " --> pdb=" O MET C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 114 through 143 Processing helix chain 'C' and resid 163 through 176 Processing helix chain 'C' and resid 179 through 184 Processing helix chain 'C' and resid 241 through 260 removed outlier: 3.825A pdb=" N GLY C 260 " --> pdb=" O MET C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 303 removed outlier: 3.603A pdb=" N TYR C 287 " --> pdb=" O MET C 283 " (cutoff:3.500A) Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 305 through 330 Processing helix chain 'C' and resid 330 through 341 Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.537A pdb=" N ALA C 349 " --> pdb=" O PHE C 345 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 367 through 379 Processing helix chain 'C' and resid 382 through 394 Proline residue: C 391 - end of helix Processing helix chain 'C' and resid 398 through 416 removed outlier: 3.577A pdb=" N ASN C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 439 Processing helix chain 'C' and resid 445 through 458 removed outlier: 4.118A pdb=" N LEU C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 452 " --> pdb=" O VAL C 448 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 470 removed outlier: 4.159A pdb=" N LEU C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N VAL C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 497 removed outlier: 3.912A pdb=" N LEU C 474 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET C 477 " --> pdb=" O LEU C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 507 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 193 removed outlier: 3.854A pdb=" N LYS A 231 " --> pdb=" O LYS A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 193 removed outlier: 3.854A pdb=" N LYS B 231 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 186 through 193 removed outlier: 3.854A pdb=" N LYS C 231 " --> pdb=" O LYS C 193 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2379 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: 1.29 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1807 1.33 - 1.45: 2021 1.45 - 1.57: 6195 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 10155 Sorted by residual: bond pdb=" CAX Y01 A 602 " pdb=" OAH Y01 A 602 " ideal model delta sigma weight residual 1.248 1.343 -0.095 2.00e-02 2.50e+03 2.24e+01 bond pdb=" CAX Y01 C 602 " pdb=" OAH Y01 C 602 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" CAX Y01 B 602 " pdb=" OAH Y01 B 602 " ideal model delta sigma weight residual 1.248 1.341 -0.093 2.00e-02 2.50e+03 2.18e+01 bond pdb=" CAX Y01 C 602 " pdb=" OAF Y01 C 602 " ideal model delta sigma weight residual 1.247 1.207 0.040 2.00e-02 2.50e+03 3.92e+00 bond pdb=" CAX Y01 A 602 " pdb=" OAF Y01 A 602 " ideal model delta sigma weight residual 1.247 1.208 0.039 2.00e-02 2.50e+03 3.89e+00 ... (remaining 10150 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 12938 1.81 - 3.62: 432 3.62 - 5.43: 253 5.43 - 7.24: 24 7.24 - 9.05: 6 Bond angle restraints: 13653 Sorted by residual: angle pdb=" CAM Y01 C 602 " pdb=" CAY Y01 C 602 " pdb=" OAW Y01 C 602 " ideal model delta sigma weight residual 111.19 120.24 -9.05 3.00e+00 1.11e-01 9.09e+00 angle pdb=" CAM Y01 B 602 " pdb=" CAY Y01 B 602 " pdb=" OAW Y01 B 602 " ideal model delta sigma weight residual 111.19 120.21 -9.02 3.00e+00 1.11e-01 9.04e+00 angle pdb=" CAM Y01 A 602 " pdb=" CAY Y01 A 602 " pdb=" OAW Y01 A 602 " ideal model delta sigma weight residual 111.19 120.18 -8.99 3.00e+00 1.11e-01 8.98e+00 angle pdb=" CBB Y01 C 602 " pdb=" CBE Y01 C 602 " pdb=" CBI Y01 C 602 " ideal model delta sigma weight residual 119.27 111.67 7.60 3.00e+00 1.11e-01 6.42e+00 angle pdb=" CBB Y01 A 602 " pdb=" CBE Y01 A 602 " pdb=" CBI Y01 A 602 " ideal model delta sigma weight residual 119.27 111.67 7.60 3.00e+00 1.11e-01 6.42e+00 ... (remaining 13648 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 5793 25.07 - 50.14: 267 50.14 - 75.21: 36 75.21 - 100.28: 0 100.28 - 125.35: 3 Dihedral angle restraints: 6099 sinusoidal: 2496 harmonic: 3603 Sorted by residual: dihedral pdb=" CBC Y01 A 602 " pdb=" CAR Y01 A 602 " pdb=" CAT Y01 A 602 " pdb=" CBH Y01 A 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.22 -125.35 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CBC Y01 C 602 " pdb=" CAR Y01 C 602 " pdb=" CAT Y01 C 602 " pdb=" CBH Y01 C 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.19 -125.32 1 3.00e+01 1.11e-03 1.68e+01 dihedral pdb=" CBC Y01 B 602 " pdb=" CAR Y01 B 602 " pdb=" CAT Y01 B 602 " pdb=" CBH Y01 B 602 " ideal model delta sinusoidal sigma weight residual -57.13 68.19 -125.32 1 3.00e+01 1.11e-03 1.68e+01 ... (remaining 6096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 1599 0.093 - 0.187: 90 0.187 - 0.280: 6 0.280 - 0.373: 3 0.373 - 0.466: 3 Chirality restraints: 1701 Sorted by residual: chirality pdb=" CBG Y01 C 602 " pdb=" CAQ Y01 C 602 " pdb=" CBD Y01 C 602 " pdb=" CBI Y01 C 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CBG Y01 B 602 " pdb=" CAQ Y01 B 602 " pdb=" CBD Y01 B 602 " pdb=" CBI Y01 B 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.46 2.00e-01 2.50e+01 5.37e+00 chirality pdb=" CBG Y01 A 602 " pdb=" CAQ Y01 A 602 " pdb=" CBD Y01 A 602 " pdb=" CBI Y01 A 602 " both_signs ideal model delta sigma weight residual False -2.33 -2.80 0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 1698 not shown) Planarity restraints: 1611 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 372 " -0.018 2.00e-02 2.50e+03 1.80e-02 5.70e+00 pdb=" CG PHE C 372 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 372 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 372 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 372 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 372 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 372 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 372 " -0.018 2.00e-02 2.50e+03 1.80e-02 5.69e+00 pdb=" CG PHE A 372 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE A 372 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 372 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 372 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 372 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE A 372 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 372 " -0.018 2.00e-02 2.50e+03 1.80e-02 5.69e+00 pdb=" CG PHE B 372 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 372 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 372 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 372 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 372 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 372 " -0.001 2.00e-02 2.50e+03 ... (remaining 1608 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2868 2.82 - 3.34: 10651 3.34 - 3.86: 16733 3.86 - 4.38: 19300 4.38 - 4.90: 33588 Nonbonded interactions: 83140 Sorted by model distance: nonbonded pdb=" O THR A 503 " pdb=" NE2 GLN A 507 " model vdw 2.304 3.120 nonbonded pdb=" O THR C 503 " pdb=" NE2 GLN C 507 " model vdw 2.305 3.120 nonbonded pdb=" O THR B 503 " pdb=" NE2 GLN B 507 " model vdw 2.305 3.120 nonbonded pdb=" O LEU C 430 " pdb=" OG1 THR C 433 " model vdw 2.321 3.040 nonbonded pdb=" O LEU B 430 " pdb=" OG1 THR B 433 " model vdw 2.321 3.040 ... (remaining 83135 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 'B' selection = chain 'C' } 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: 1.490 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 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 0.095 10155 Z= 0.282 Angle : 0.944 9.047 13653 Z= 0.420 Chirality : 0.052 0.466 1701 Planarity : 0.004 0.042 1611 Dihedral : 14.226 125.349 3783 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.29 % Allowed : 0.86 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.24), residues: 1257 helix: 1.68 (0.16), residues: 1029 sheet: -0.79 (0.64), residues: 60 loop : -1.58 (0.51), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 384 TYR 0.007 0.002 TYR C 287 PHE 0.042 0.002 PHE A 372 TRP 0.003 0.001 TRP A 286 HIS 0.003 0.002 HIS B 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00660 / 0.28 (10155) covalent geometry : angle 0.94436 / 0.42 (13653) hydrogen bonds : bond 0.11721 / 7.83 ( 793) hydrogen bonds : angle 5.76168 / 4.14 ( 2379) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 176 time to evaluate : 0.263 Fit side-chains REVERT: A 387 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.8074 (mmm160) REVERT: B 287 TYR cc_start: 0.9199 (t80) cc_final: 0.8902 (t80) REVERT: C 285 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8203 (mmt) REVERT: C 368 LEU cc_start: 0.8402 (tp) cc_final: 0.8156 (tp) outliers start: 3 outliers final: 1 residues processed: 176 average time/residue: 0.0829 time to fit residues: 21.9918 Evaluate side-chains 153 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 MET Chi-restraints excluded: chain C residue 285 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.096902 restraints weight = 12366.310| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.37 r_work: 0.2815 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10155 Z= 0.150 Angle : 0.540 5.820 13653 Z= 0.280 Chirality : 0.040 0.129 1701 Planarity : 0.004 0.042 1611 Dihedral : 10.940 118.618 1635 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.29 % Allowed : 9.62 % Favored : 90.10 % 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: 2.35 (0.25), residues: 1257 helix: 2.04 (0.16), residues: 1047 sheet: -0.57 (0.65), residues: 60 loop : -0.93 (0.60), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 119 TYR 0.019 0.002 TYR A 287 PHE 0.026 0.002 PHE B 372 TRP 0.005 0.001 TRP C 286 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (10155) covalent geometry : angle 0.54018 / 0.28 (13653) hydrogen bonds : bond 0.04101 / 2.87 ( 793) hydrogen bonds : angle 4.70984 / 3.42 ( 2379) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 165 time to evaluate : 0.364 Fit side-chains REVERT: A 377 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8393 (mt-10) REVERT: B 334 LEU cc_start: 0.8355 (tp) cc_final: 0.8038 (tp) REVERT: C 368 LEU cc_start: 0.8507 (tp) cc_final: 0.8280 (tp) outliers start: 3 outliers final: 2 residues processed: 165 average time/residue: 0.0767 time to fit residues: 19.4345 Evaluate side-chains 150 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 148 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 76 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 52 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 312 GLN B 44 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.121055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.099528 restraints weight = 12219.973| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.29 r_work: 0.2858 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10155 Z= 0.137 Angle : 0.513 5.826 13653 Z= 0.266 Chirality : 0.040 0.123 1701 Planarity : 0.004 0.038 1611 Dihedral : 10.075 117.341 1629 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.67 % Allowed : 11.05 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.25), residues: 1257 helix: 2.21 (0.16), residues: 1050 sheet: -0.24 (0.66), residues: 60 loop : -0.78 (0.64), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 387 TYR 0.022 0.002 TYR B 287 PHE 0.017 0.001 PHE B 388 TRP 0.006 0.001 TRP C 286 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (10155) covalent geometry : angle 0.51324 / 0.27 (13653) hydrogen bonds : bond 0.03791 / 2.65 ( 793) hydrogen bonds : angle 4.46298 / 3.24 ( 2379) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 155 time to evaluate : 0.329 Fit side-chains REVERT: B 287 TYR cc_start: 0.9242 (t80) cc_final: 0.8927 (t80) REVERT: B 322 ILE cc_start: 0.8835 (mm) cc_final: 0.8633 (mm) REVERT: B 334 LEU cc_start: 0.8332 (tp) cc_final: 0.7989 (tp) REVERT: C 334 LEU cc_start: 0.8335 (tp) cc_final: 0.8048 (tp) outliers start: 7 outliers final: 5 residues processed: 161 average time/residue: 0.0603 time to fit residues: 15.3321 Evaluate side-chains 154 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 149 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain C residue 139 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 123 optimal weight: 0.0970 chunk 23 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN C 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.098005 restraints weight = 12355.518| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.49 r_work: 0.2909 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10155 Z= 0.122 Angle : 0.499 5.680 13653 Z= 0.258 Chirality : 0.039 0.120 1701 Planarity : 0.004 0.042 1611 Dihedral : 9.571 117.450 1629 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.81 % Allowed : 11.62 % Favored : 86.57 % 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: 2.89 (0.25), residues: 1257 helix: 2.37 (0.16), residues: 1047 sheet: 0.10 (0.68), residues: 60 loop : -0.71 (0.64), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 387 TYR 0.011 0.002 TYR B 287 PHE 0.019 0.001 PHE B 388 TRP 0.005 0.001 TRP C 286 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (10155) covalent geometry : angle 0.49916 / 0.26 (13653) hydrogen bonds : bond 0.03601 / 2.52 ( 793) hydrogen bonds : angle 4.33784 / 3.15 ( 2379) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.283 Fit side-chains REVERT: B 231 LYS cc_start: 0.6667 (ttpt) cc_final: 0.6089 (ttpt) REVERT: B 322 ILE cc_start: 0.8901 (mm) cc_final: 0.8672 (mm) REVERT: C 334 LEU cc_start: 0.8395 (tp) cc_final: 0.8105 (tp) outliers start: 19 outliers final: 13 residues processed: 162 average time/residue: 0.0707 time to fit residues: 17.6756 Evaluate side-chains 161 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 0.0020 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.123491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.100749 restraints weight = 12307.033| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.52 r_work: 0.2881 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10155 Z= 0.115 Angle : 0.490 6.188 13653 Z= 0.253 Chirality : 0.039 0.143 1701 Planarity : 0.004 0.043 1611 Dihedral : 9.233 117.398 1629 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.81 % Allowed : 12.48 % Favored : 85.71 % 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: 3.04 (0.25), residues: 1257 helix: 2.46 (0.16), residues: 1047 sheet: 0.29 (0.70), residues: 60 loop : -0.63 (0.63), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 478 TYR 0.027 0.002 TYR B 287 PHE 0.018 0.001 PHE B 411 TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10155) covalent geometry : angle 0.49018 / 0.25 (13653) hydrogen bonds : bond 0.03470 / 2.43 ( 793) hydrogen bonds : angle 4.23507 / 3.07 ( 2379) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 0.332 Fit side-chains REVERT: B 231 LYS cc_start: 0.6669 (ttpt) cc_final: 0.6078 (ttpt) REVERT: B 322 ILE cc_start: 0.8882 (mm) cc_final: 0.8643 (mm) REVERT: C 334 LEU cc_start: 0.8365 (tp) cc_final: 0.8085 (tp) outliers start: 19 outliers final: 14 residues processed: 167 average time/residue: 0.0681 time to fit residues: 17.4074 Evaluate side-chains 166 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 90 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3257 r_free = 0.3257 target = 0.120559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.098100 restraints weight = 12486.206| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 1.56 r_work: 0.2844 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10155 Z= 0.161 Angle : 0.539 6.355 13653 Z= 0.275 Chirality : 0.041 0.144 1701 Planarity : 0.004 0.043 1611 Dihedral : 9.328 116.529 1629 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.90 % Allowed : 14.48 % Favored : 83.62 % 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: 2.88 (0.25), residues: 1257 helix: 2.40 (0.16), residues: 1032 sheet: 0.25 (0.70), residues: 60 loop : -0.74 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 373 TYR 0.031 0.002 TYR B 287 PHE 0.019 0.002 PHE C 388 TRP 0.008 0.001 TRP C 286 HIS 0.002 0.001 HIS C 495 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (10155) covalent geometry : angle 0.53877 / 0.28 (13653) hydrogen bonds : bond 0.03803 / 2.67 ( 793) hydrogen bonds : angle 4.33402 / 3.15 ( 2379) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.309 Fit side-chains REVERT: A 40 LYS cc_start: 0.6251 (mtpp) cc_final: 0.5865 (mptt) REVERT: B 231 LYS cc_start: 0.6671 (ttpt) cc_final: 0.6295 (tmmt) REVERT: B 259 MET cc_start: 0.8699 (mtp) cc_final: 0.8496 (mtp) REVERT: B 322 ILE cc_start: 0.8905 (mm) cc_final: 0.8649 (mm) REVERT: B 334 LEU cc_start: 0.8395 (tp) cc_final: 0.8074 (tp) REVERT: C 231 LYS cc_start: 0.6451 (tttm) cc_final: 0.6064 (tmmt) REVERT: C 275 GLU cc_start: 0.8448 (tt0) cc_final: 0.8140 (tt0) REVERT: C 334 LEU cc_start: 0.8344 (tp) cc_final: 0.8055 (tp) outliers start: 20 outliers final: 20 residues processed: 168 average time/residue: 0.0801 time to fit residues: 20.5325 Evaluate side-chains 177 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.4980 chunk 85 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.126707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.101836 restraints weight = 12254.586| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 1.67 r_work: 0.2912 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10155 Z= 0.126 Angle : 0.509 7.321 13653 Z= 0.261 Chirality : 0.040 0.148 1701 Planarity : 0.004 0.044 1611 Dihedral : 9.106 116.810 1629 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.81 % Allowed : 15.43 % Favored : 82.76 % 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: 2.99 (0.25), residues: 1257 helix: 2.48 (0.16), residues: 1035 sheet: 0.32 (0.70), residues: 60 loop : -0.78 (0.58), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 119 TYR 0.032 0.002 TYR B 287 PHE 0.017 0.001 PHE B 388 TRP 0.005 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (10155) covalent geometry : angle 0.50871 / 0.26 (13653) hydrogen bonds : bond 0.03554 / 2.49 ( 793) hydrogen bonds : angle 4.24672 / 3.08 ( 2379) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 0.326 Fit side-chains REVERT: B 231 LYS cc_start: 0.6687 (ttpt) cc_final: 0.6338 (tmmt) REVERT: B 287 TYR cc_start: 0.9242 (t80) cc_final: 0.8971 (t80) REVERT: B 322 ILE cc_start: 0.8922 (mm) cc_final: 0.8658 (mm) REVERT: B 334 LEU cc_start: 0.8349 (tp) cc_final: 0.8023 (tp) REVERT: C 231 LYS cc_start: 0.6456 (tttm) cc_final: 0.6076 (tmmt) REVERT: C 334 LEU cc_start: 0.8311 (tp) cc_final: 0.8012 (tp) outliers start: 19 outliers final: 16 residues processed: 169 average time/residue: 0.0723 time to fit residues: 18.6519 Evaluate side-chains 173 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 415 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 444 SER Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 0.0050 chunk 111 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 115 optimal weight: 0.0970 chunk 70 optimal weight: 0.1980 chunk 10 optimal weight: 0.8980 chunk 97 optimal weight: 0.0020 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.2400 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.127755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.106332 restraints weight = 12168.962| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.44 r_work: 0.2953 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10155 Z= 0.102 Angle : 0.481 7.197 13653 Z= 0.248 Chirality : 0.039 0.152 1701 Planarity : 0.004 0.045 1611 Dihedral : 8.572 117.048 1629 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.14 % Allowed : 16.10 % Favored : 82.76 % 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: 3.25 (0.25), residues: 1257 helix: 2.66 (0.16), residues: 1038 sheet: 0.42 (0.72), residues: 60 loop : -0.79 (0.57), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 478 TYR 0.028 0.002 TYR B 287 PHE 0.017 0.001 PHE B 388 TRP 0.004 0.001 TRP B 355 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (10155) covalent geometry : angle 0.48111 / 0.25 (13653) hydrogen bonds : bond 0.03210 / 2.22 ( 793) hydrogen bonds : angle 4.06799 / 2.95 ( 2379) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 0.348 Fit side-chains REVERT: B 287 TYR cc_start: 0.9071 (t80) cc_final: 0.8851 (t80) REVERT: B 322 ILE cc_start: 0.8857 (mm) cc_final: 0.8595 (mm) REVERT: C 231 LYS cc_start: 0.6235 (tttm) cc_final: 0.5854 (tmmt) outliers start: 12 outliers final: 8 residues processed: 173 average time/residue: 0.0673 time to fit residues: 18.1953 Evaluate side-chains 167 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 0.0870 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 3 optimal weight: 0.0570 chunk 29 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN C 274 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.126621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.104773 restraints weight = 12079.205| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.49 r_work: 0.3081 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10155 Z= 0.110 Angle : 0.500 7.793 13653 Z= 0.256 Chirality : 0.040 0.179 1701 Planarity : 0.004 0.045 1611 Dihedral : 8.541 116.733 1629 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.33 % Allowed : 17.05 % Favored : 81.62 % 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: 3.23 (0.25), residues: 1257 helix: 2.65 (0.16), residues: 1038 sheet: 0.43 (0.73), residues: 60 loop : -0.81 (0.57), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 478 TYR 0.026 0.002 TYR B 287 PHE 0.015 0.001 PHE C 411 TRP 0.004 0.001 TRP C 355 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (10155) covalent geometry : angle 0.49959 / 0.26 (13653) hydrogen bonds : bond 0.03302 / 2.30 ( 793) hydrogen bonds : angle 4.07759 / 2.95 ( 2379) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.371 Fit side-chains REVERT: A 287 TYR cc_start: 0.9177 (t80) cc_final: 0.8901 (t80) REVERT: B 322 ILE cc_start: 0.8925 (mm) cc_final: 0.8704 (mm) REVERT: C 231 LYS cc_start: 0.6336 (tttm) cc_final: 0.5909 (tmmt) REVERT: C 373 ARG cc_start: 0.8032 (ptt180) cc_final: 0.7755 (ptt-90) outliers start: 14 outliers final: 12 residues processed: 165 average time/residue: 0.0770 time to fit residues: 19.5898 Evaluate side-chains 169 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 157 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 70 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN C 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.123837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.095920 restraints weight = 12305.527| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.89 r_work: 0.2793 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10155 Z= 0.130 Angle : 0.518 9.011 13653 Z= 0.264 Chirality : 0.040 0.170 1701 Planarity : 0.004 0.045 1611 Dihedral : 8.823 116.196 1629 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.14 % Allowed : 17.24 % Favored : 81.62 % 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: 3.13 (0.25), residues: 1257 helix: 2.56 (0.16), residues: 1038 sheet: 0.46 (0.73), residues: 60 loop : -0.70 (0.58), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 478 TYR 0.019 0.002 TYR C 287 PHE 0.014 0.001 PHE C 388 TRP 0.004 0.001 TRP B 286 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 (10155) covalent geometry : angle 0.51790 / 0.26 (13653) hydrogen bonds : bond 0.03489 / 2.44 ( 793) hydrogen bonds : angle 4.15410 / 3.01 ( 2379) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2514 Ramachandran restraints generated. 1257 Oldfield, 0 Emsley, 1257 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.304 Fit side-chains REVERT: B 231 LYS cc_start: 0.6549 (ttpt) cc_final: 0.6277 (tmmt) REVERT: B 271 ASN cc_start: 0.8311 (m-40) cc_final: 0.7857 (m-40) REVERT: B 322 ILE cc_start: 0.8960 (mm) cc_final: 0.8739 (mm) REVERT: C 231 LYS cc_start: 0.6427 (tttm) cc_final: 0.6049 (tmmt) REVERT: C 334 LEU cc_start: 0.8313 (tp) cc_final: 0.8027 (tp) outliers start: 12 outliers final: 12 residues processed: 165 average time/residue: 0.0741 time to fit residues: 18.5604 Evaluate side-chains 171 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 421 ASP Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 447 LEU Chi-restraints excluded: chain C residue 468 VAL Chi-restraints excluded: chain C residue 507 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 87 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.124955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.102855 restraints weight = 12212.185| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.42 r_work: 0.2907 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10155 Z= 0.121 Angle : 0.511 10.351 13653 Z= 0.261 Chirality : 0.040 0.178 1701 Planarity : 0.004 0.045 1611 Dihedral : 8.794 116.340 1629 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.33 % Allowed : 17.14 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.25), residues: 1257 helix: 2.57 (0.16), residues: 1038 sheet: 0.44 (0.73), residues: 60 loop : -0.67 (0.58), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 478 TYR 0.028 0.002 TYR A 287 PHE 0.015 0.001 PHE A 388 TRP 0.005 0.001 TRP B 286 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10155) covalent geometry : angle 0.51150 / 0.26 (13653) hydrogen bonds : bond 0.03424 / 2.39 ( 793) hydrogen bonds : angle 4.13535 / 3.00 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2062.18 seconds wall clock time: 36 minutes 9.85 seconds (2169.85 seconds total)