Starting phenix.real_space_refine on Wed Mar 4 03:24:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xr4_33407/03_2026/7xr4_33407.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xr4_33407/03_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_33407/03_2026/7xr4_33407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xr4_33407/03_2026/7xr4_33407.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xr4_33407/03_2026/7xr4_33407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xr4_33407/03_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-5986/lib/python3.9/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: 296 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: 2.65, per 1000 atoms: 0.26 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: 0.93 Conformation dependent library (CDL) restraints added in 582.5 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: 0.28 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: 1.72 Time building geometry restraints manager: 1.23 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: 5922 25.07 - 50.14: 276 50.14 - 75.21: 57 75.21 - 100.28: 15 100.28 - 125.35: 3 Dihedral angle restraints: 6273 sinusoidal: 2670 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 6270 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: 0.02 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: 1.590 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 15.583 125.349 3957 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 covalent geometry : bond 0.00660 (10155) covalent geometry : angle 0.94436 (13653) hydrogen bonds : bond 0.11721 ( 793) hydrogen bonds : angle 5.76168 ( 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 : 0.355 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: 0.0859 time to fit residues: 22.6921 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 : 0.360 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 312 GLN B 397 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.119199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.096101 restraints weight = 12345.244| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.43 r_work: 0.2819 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10155 Z= 0.151 Angle : 0.561 5.778 13653 Z= 0.284 Chirality : 0.040 0.130 1701 Planarity : 0.004 0.042 1611 Dihedral : 10.369 68.042 1809 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 0.19 % Allowed : 9.52 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.38 (0.25), residues: 1257 helix: 2.06 (0.16), residues: 1047 sheet: -0.56 (0.65), residues: 60 loop : -0.90 (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 covalent geometry : bond 0.00353 (10155) covalent geometry : angle 0.56094 (13653) hydrogen bonds : bond 0.04038 ( 793) hydrogen bonds : angle 4.68832 ( 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 165 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.353 Fit side-chains REVERT: A 377 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8225 (mt-10) REVERT: B 334 LEU cc_start: 0.8321 (tp) cc_final: 0.7985 (tp) outliers start: 2 outliers final: 2 residues processed: 163 average time/residue: 0.0762 time to fit residues: 19.2929 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 : 0.357 ------------------------------------------------------------------------------- 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: 0.7980 chunk 95 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 42 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 312 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.116200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.091729 restraints weight = 12543.872| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.49 r_work: 0.2753 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2622 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10155 Z= 0.246 Angle : 0.609 6.100 13653 Z= 0.314 Chirality : 0.043 0.149 1701 Planarity : 0.004 0.040 1611 Dihedral : 9.860 63.315 1803 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.33 % Allowed : 12.29 % Favored : 86.38 % 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: 2.09 (0.24), residues: 1257 helix: 1.80 (0.16), residues: 1050 sheet: -0.43 (0.66), residues: 60 loop : -0.66 (0.63), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 373 TYR 0.023 0.002 TYR B 287 PHE 0.024 0.002 PHE B 249 TRP 0.006 0.001 TRP C 286 HIS 0.003 0.002 HIS C 495 Details of bonding type rmsd covalent geometry : bond 0.00609 (10155) covalent geometry : angle 0.60898 (13653) hydrogen bonds : bond 0.04456 ( 793) hydrogen bonds : angle 4.74492 ( 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 168 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 0.356 Fit side-chains REVERT: B 231 LYS cc_start: 0.6658 (ttpt) cc_final: 0.6026 (ttpt) REVERT: B 334 LEU cc_start: 0.8396 (tp) cc_final: 0.8011 (tp) outliers start: 14 outliers final: 13 residues processed: 162 average time/residue: 0.0739 time to fit residues: 18.7747 Evaluate side-chains 162 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 74 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 B residue 468 VAL 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 93 optimal weight: 0.9990 chunk 70 optimal weight: 0.3980 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 123 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 118 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.120375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.096259 restraints weight = 12429.975| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.48 r_work: 0.2823 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1717 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= 0.132 Angle : 0.515 5.929 13653 Z= 0.267 Chirality : 0.039 0.120 1701 Planarity : 0.004 0.040 1611 Dihedral : 8.577 69.492 1803 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.52 % Allowed : 13.52 % Favored : 84.95 % 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: 2.55 (0.25), residues: 1257 helix: 2.14 (0.16), residues: 1050 sheet: -0.16 (0.66), residues: 60 loop : -0.84 (0.64), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 387 TYR 0.024 0.002 TYR B 287 PHE 0.021 0.001 PHE B 388 TRP 0.005 0.001 TRP C 286 HIS 0.003 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00305 (10155) covalent geometry : angle 0.51502 (13653) hydrogen bonds : bond 0.03733 ( 793) hydrogen bonds : angle 4.45128 ( 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: 16 poor density : 157 time to evaluate : 0.306 Fit side-chains REVERT: B 231 LYS cc_start: 0.6712 (ttpt) cc_final: 0.6265 (tmmt) REVERT: B 334 LEU cc_start: 0.8326 (tp) cc_final: 0.7982 (tp) REVERT: C 334 LEU cc_start: 0.8323 (tp) cc_final: 0.8014 (tp) outliers start: 16 outliers final: 12 residues processed: 166 average time/residue: 0.0697 time to fit residues: 18.6790 Evaluate side-chains 162 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL 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 386 THR 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 139 VAL Chi-restraints excluded: chain C residue 434 LEU 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: 0.5980 chunk 50 optimal weight: 0.6980 chunk 67 optimal weight: 0.0980 chunk 30 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.121673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.099312 restraints weight = 12394.836| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.37 r_work: 0.2861 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1851 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= 0.129 Angle : 0.510 6.568 13653 Z= 0.263 Chirality : 0.039 0.134 1701 Planarity : 0.004 0.041 1611 Dihedral : 8.327 68.512 1803 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.71 % Allowed : 13.90 % Favored : 84.38 % 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: 2.74 (0.25), residues: 1257 helix: 2.27 (0.16), residues: 1050 sheet: 0.11 (0.68), residues: 60 loop : -0.82 (0.64), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 384 TYR 0.011 0.001 TYR C 404 PHE 0.020 0.001 PHE B 388 TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS B 143 Details of bonding type rmsd covalent geometry : bond 0.00300 (10155) covalent geometry : angle 0.50990 (13653) hydrogen bonds : bond 0.03641 ( 793) hydrogen bonds : angle 4.36088 ( 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 180 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.374 Fit side-chains REVERT: B 231 LYS cc_start: 0.6635 (ttpt) cc_final: 0.6215 (tmmt) REVERT: B 287 TYR cc_start: 0.9293 (t80) cc_final: 0.8908 (t80) REVERT: B 334 LEU cc_start: 0.8364 (tp) cc_final: 0.8058 (tp) REVERT: C 334 LEU cc_start: 0.8345 (tp) cc_final: 0.8059 (tp) outliers start: 18 outliers final: 15 residues processed: 171 average time/residue: 0.0768 time to fit residues: 20.6115 Evaluate side-chains 171 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 180 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 118 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 overall best weight: 0.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.119940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097656 restraints weight = 12503.090| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.52 r_work: 0.2826 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10155 Z= 0.161 Angle : 0.540 6.799 13653 Z= 0.276 Chirality : 0.041 0.165 1701 Planarity : 0.004 0.042 1611 Dihedral : 8.417 66.643 1803 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.81 % Allowed : 15.62 % Favored : 82.57 % 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: 2.64 (0.24), residues: 1257 helix: 2.25 (0.16), residues: 1032 sheet: 0.13 (0.69), residues: 60 loop : -0.89 (0.57), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 387 TYR 0.025 0.002 TYR C 287 PHE 0.018 0.002 PHE B 388 TRP 0.005 0.001 TRP C 286 HIS 0.002 0.001 HIS C 495 Details of bonding type rmsd covalent geometry : bond 0.00388 (10155) covalent geometry : angle 0.54018 (13653) hydrogen bonds : bond 0.03836 ( 793) hydrogen bonds : angle 4.41394 ( 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: 19 poor density : 162 time to evaluate : 0.359 Fit side-chains REVERT: A 40 LYS cc_start: 0.6167 (mtpp) cc_final: 0.5749 (mptt) REVERT: B 231 LYS cc_start: 0.6623 (ttpt) cc_final: 0.6225 (tmmt) REVERT: B 334 LEU cc_start: 0.8390 (tp) cc_final: 0.8066 (tp) REVERT: C 334 LEU cc_start: 0.8322 (tp) cc_final: 0.8016 (tp) outliers start: 19 outliers final: 18 residues processed: 171 average time/residue: 0.0781 time to fit residues: 20.8404 Evaluate side-chains 176 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 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 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: 0.5980 chunk 85 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.125356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.100258 restraints weight = 12328.569| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.68 r_work: 0.2791 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1971 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= 0.129 Angle : 0.513 7.284 13653 Z= 0.262 Chirality : 0.040 0.155 1701 Planarity : 0.004 0.043 1611 Dihedral : 8.102 68.261 1803 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.62 % Allowed : 16.29 % Favored : 82.10 % 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: 2.84 (0.25), residues: 1257 helix: 2.37 (0.16), residues: 1035 sheet: 0.25 (0.69), residues: 60 loop : -0.76 (0.59), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 387 TYR 0.019 0.002 TYR C 287 PHE 0.019 0.001 PHE C 388 TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00303 (10155) covalent geometry : angle 0.51333 (13653) hydrogen bonds : bond 0.03584 ( 793) hydrogen bonds : angle 4.31616 ( 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 178 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.377 Fit side-chains REVERT: B 231 LYS cc_start: 0.6473 (ttpt) cc_final: 0.6192 (tmmt) REVERT: B 334 LEU cc_start: 0.8294 (tp) cc_final: 0.7973 (tp) REVERT: C 334 LEU cc_start: 0.8213 (tp) cc_final: 0.7928 (tp) outliers start: 17 outliers final: 17 residues processed: 168 average time/residue: 0.0745 time to fit residues: 19.7284 Evaluate side-chains 173 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 507 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.123536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.097913 restraints weight = 12501.143| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.70 r_work: 0.2896 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10155 Z= 0.142 Angle : 0.523 7.947 13653 Z= 0.267 Chirality : 0.040 0.173 1701 Planarity : 0.004 0.043 1611 Dihedral : 8.252 74.610 1803 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.81 % Allowed : 16.86 % Favored : 81.33 % 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: 2.85 (0.25), residues: 1257 helix: 2.37 (0.16), residues: 1035 sheet: 0.27 (0.70), residues: 60 loop : -0.74 (0.58), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 478 TYR 0.028 0.002 TYR C 287 PHE 0.018 0.001 PHE C 388 TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00339 (10155) covalent geometry : angle 0.52252 (13653) hydrogen bonds : bond 0.03665 ( 793) hydrogen bonds : angle 4.33039 ( 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 175 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.371 Fit side-chains REVERT: B 231 LYS cc_start: 0.6585 (ttpt) cc_final: 0.6265 (tmmt) REVERT: B 334 LEU cc_start: 0.8367 (tp) cc_final: 0.8051 (tp) REVERT: C 334 LEU cc_start: 0.8329 (tp) cc_final: 0.8050 (tp) outliers start: 19 outliers final: 19 residues processed: 163 average time/residue: 0.0728 time to fit residues: 18.7659 Evaluate side-chains 175 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 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 421 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 41 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 46 optimal weight: 0.4980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.120799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094338 restraints weight = 12543.767| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.77 r_work: 0.2796 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2080 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= 0.128 Angle : 0.517 8.249 13653 Z= 0.264 Chirality : 0.040 0.191 1701 Planarity : 0.004 0.043 1611 Dihedral : 8.102 77.019 1803 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.81 % Allowed : 17.24 % Favored : 80.95 % 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: 2.95 (0.25), residues: 1257 helix: 2.44 (0.16), residues: 1035 sheet: 0.32 (0.70), residues: 60 loop : -0.70 (0.59), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 478 TYR 0.025 0.002 TYR C 287 PHE 0.016 0.001 PHE A 388 TRP 0.003 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00298 (10155) covalent geometry : angle 0.51670 (13653) hydrogen bonds : bond 0.03546 ( 793) hydrogen bonds : angle 4.28490 ( 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 177 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.271 Fit side-chains REVERT: A 287 TYR cc_start: 0.9199 (t80) cc_final: 0.8821 (t80) REVERT: B 231 LYS cc_start: 0.6543 (ttpt) cc_final: 0.6240 (tmmt) REVERT: B 334 LEU cc_start: 0.8333 (tp) cc_final: 0.8026 (tp) REVERT: C 334 LEU cc_start: 0.8292 (tp) cc_final: 0.8009 (tp) outliers start: 19 outliers final: 16 residues processed: 165 average time/residue: 0.0803 time to fit residues: 20.7045 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 : 0.349 ------------------------------------------------------------------------------- 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 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 421 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.122844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.094945 restraints weight = 12535.700| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.88 r_work: 0.2804 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2151 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= 0.123 Angle : 0.511 8.025 13653 Z= 0.261 Chirality : 0.040 0.190 1701 Planarity : 0.004 0.044 1611 Dihedral : 7.987 76.516 1803 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.71 % Allowed : 17.52 % Favored : 80.76 % 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: 3.02 (0.25), residues: 1257 helix: 2.49 (0.16), residues: 1035 sheet: 0.35 (0.71), residues: 60 loop : -0.71 (0.58), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 478 TYR 0.024 0.002 TYR C 287 PHE 0.015 0.001 PHE A 388 TRP 0.003 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00284 (10155) covalent geometry : angle 0.51065 (13653) hydrogen bonds : bond 0.03500 ( 793) hydrogen bonds : angle 4.23666 ( 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 177 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.362 Fit side-chains REVERT: A 188 ILE cc_start: 0.9345 (OUTLIER) cc_final: 0.9017 (tt) REVERT: A 287 TYR cc_start: 0.9172 (t80) cc_final: 0.8860 (t80) REVERT: B 231 LYS cc_start: 0.6481 (ttpt) cc_final: 0.6201 (tmmt) REVERT: B 334 LEU cc_start: 0.8304 (tp) cc_final: 0.7990 (tp) REVERT: C 334 LEU cc_start: 0.8286 (tp) cc_final: 0.8005 (tp) outliers start: 18 outliers final: 16 residues processed: 166 average time/residue: 0.0720 time to fit residues: 18.7688 Evaluate side-chains 173 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 188 ILE 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 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 421 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 79 optimal weight: 0.0670 chunk 119 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.122831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.095287 restraints weight = 12656.278| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.84 r_work: 0.2781 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2160 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= 0.127 Angle : 0.515 8.417 13653 Z= 0.262 Chirality : 0.040 0.196 1701 Planarity : 0.004 0.044 1611 Dihedral : 7.979 75.464 1803 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.71 % Allowed : 17.71 % Favored : 80.57 % 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: 3.00 (0.25), residues: 1257 helix: 2.48 (0.16), residues: 1035 sheet: 0.35 (0.71), residues: 60 loop : -0.74 (0.57), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 478 TYR 0.023 0.002 TYR C 287 PHE 0.014 0.001 PHE A 388 TRP 0.003 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 Details of bonding type rmsd covalent geometry : bond 0.00296 (10155) covalent geometry : angle 0.51463 (13653) hydrogen bonds : bond 0.03499 ( 793) hydrogen bonds : angle 4.23253 ( 2379) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.75 seconds wall clock time: 39 minutes 21.66 seconds (2361.66 seconds total)