Starting phenix.real_space_refine on Fri Feb 14 17:38:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xr4_33407/02_2025/7xr4_33407.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xr4_33407/02_2025/7xr4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7xr4_33407/02_2025/7xr4_33407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xr4_33407/02_2025/7xr4_33407.map" model { file = "/net/cci-nas-00/data/ceres_data/7xr4_33407/02_2025/7xr4_33407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xr4_33407/02_2025/7xr4_33407.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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-2': 8, 'PC1:plan-1': 8} Unresolved non-hydrogen planarities: 48 Restraints were copied for chains: C, B Time building chain proxies: 6.34, per 1000 atoms: 0.63 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: 2.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.92 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: 3.23 Time building geometry restraints manager: 3.13 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 1.310 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.300 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- 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= 0.429 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.003 0.001 TRP A 286 HIS 0.003 0.002 HIS B 495 PHE 0.042 0.002 PHE A 372 TYR 0.007 0.002 TYR C 287 ARG 0.002 0.000 ARG B 384 *********************** 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 : 0.965 Fit side-chains REVERT: A 387 ARG cc_start: 0.8277 (mmm-85) cc_final: 0.8073 (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: 0.8202 (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: 0.1852 time to fit residues: 48.1795 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 : 1.021 ------------------------------------------------------------------------------- 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 106 optimal weight: 0.0470 chunk 95 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.121476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.100068 restraints weight = 12213.463| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.43 r_work: 0.2869 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2746 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10155 Z= 0.183 Angle : 0.532 5.704 13653 Z= 0.272 Chirality : 0.039 0.124 1701 Planarity : 0.004 0.041 1611 Dihedral : 9.923 70.201 1809 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 0.10 % Allowed : 9.24 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.25), residues: 1257 helix: 2.20 (0.16), residues: 1047 sheet: -0.47 (0.66), residues: 60 loop : -1.04 (0.61), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 355 HIS 0.003 0.001 HIS B 143 PHE 0.024 0.002 PHE B 372 TYR 0.020 0.002 TYR A 287 ARG 0.002 0.000 ARG A 119 *********************** 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: 1 poor density : 167 time to evaluate : 1.088 Fit side-chains REVERT: A 315 MET cc_start: 0.8067 (tpp) cc_final: 0.7845 (mmt) REVERT: A 377 GLU cc_start: 0.8563 (mt-10) cc_final: 0.8211 (mt-10) REVERT: C 368 LEU cc_start: 0.8484 (tp) cc_final: 0.8270 (tp) outliers start: 1 outliers final: 1 residues processed: 167 average time/residue: 0.1788 time to fit residues: 45.6496 Evaluate side-chains 152 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 7.9990 chunk 15 optimal weight: 0.0370 chunk 33 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 312 GLN C 378 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.119652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.096340 restraints weight = 12427.544| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.44 r_work: 0.2813 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.004 0.032 10155 Z= 0.241 Angle : 0.524 5.675 13653 Z= 0.272 Chirality : 0.040 0.129 1701 Planarity : 0.004 0.036 1611 Dihedral : 9.092 66.358 1803 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.86 % Allowed : 11.43 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.25), residues: 1257 helix: 2.22 (0.16), residues: 1047 sheet: -0.28 (0.66), residues: 60 loop : -0.75 (0.62), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 286 HIS 0.002 0.001 HIS B 143 PHE 0.017 0.002 PHE B 388 TYR 0.022 0.002 TYR B 287 ARG 0.002 0.000 ARG C 387 *********************** 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 166 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 1.064 Fit side-chains REVERT: B 334 LEU cc_start: 0.8364 (tp) cc_final: 0.8021 (tp) REVERT: B 368 LEU cc_start: 0.8491 (tp) cc_final: 0.8274 (tp) REVERT: C 334 LEU cc_start: 0.8361 (tp) cc_final: 0.8058 (tp) outliers start: 9 outliers final: 7 residues processed: 163 average time/residue: 0.1712 time to fit residues: 42.9569 Evaluate side-chains 153 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain B residue 139 VAL 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 444 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 37 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 44 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 116 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3287 r_free = 0.3287 target = 0.122025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.099578 restraints weight = 12196.315| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.48 r_work: 0.2862 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10155 Z= 0.187 Angle : 0.498 5.697 13653 Z= 0.259 Chirality : 0.039 0.121 1701 Planarity : 0.004 0.041 1611 Dihedral : 8.374 68.523 1803 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.43 % Allowed : 12.10 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.25), residues: 1257 helix: 2.35 (0.16), residues: 1047 sheet: -0.04 (0.67), residues: 60 loop : -0.74 (0.63), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 286 HIS 0.002 0.001 HIS B 143 PHE 0.018 0.001 PHE B 388 TYR 0.026 0.002 TYR B 287 ARG 0.001 0.000 ARG B 478 *********************** 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 174 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 1.024 Fit side-chains REVERT: B 231 LYS cc_start: 0.6689 (ttpt) cc_final: 0.6105 (ttpt) REVERT: B 287 TYR cc_start: 0.9186 (t80) cc_final: 0.8946 (t80) REVERT: B 334 LEU cc_start: 0.8367 (tp) cc_final: 0.8048 (tp) REVERT: C 334 LEU cc_start: 0.8354 (tp) cc_final: 0.8074 (tp) outliers start: 15 outliers final: 10 residues processed: 168 average time/residue: 0.1781 time to fit residues: 45.2041 Evaluate side-chains 164 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE 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 421 ASP Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 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 20 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 11 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 123 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.123321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.100519 restraints weight = 12219.230| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.55 r_work: 0.2871 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1963 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= 0.174 Angle : 0.495 6.920 13653 Z= 0.255 Chirality : 0.039 0.154 1701 Planarity : 0.004 0.042 1611 Dihedral : 8.078 66.717 1803 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.33 % Allowed : 12.76 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.95 (0.25), residues: 1257 helix: 2.41 (0.16), residues: 1047 sheet: 0.17 (0.68), residues: 60 loop : -0.63 (0.63), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS B 143 PHE 0.020 0.001 PHE C 388 TYR 0.016 0.002 TYR B 287 ARG 0.001 0.000 ARG A 373 *********************** 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 176 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.998 Fit side-chains REVERT: B 231 LYS cc_start: 0.6675 (ttpt) cc_final: 0.6094 (ttpt) REVERT: B 334 LEU cc_start: 0.8390 (tp) cc_final: 0.8097 (tp) REVERT: C 334 LEU cc_start: 0.8361 (tp) cc_final: 0.8085 (tp) outliers start: 14 outliers final: 13 residues processed: 169 average time/residue: 0.1843 time to fit residues: 46.8156 Evaluate side-chains 166 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 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 110 optimal weight: 3.9990 chunk 11 optimal weight: 0.0570 chunk 34 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 0.0980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.124054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.102135 restraints weight = 12138.254| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.44 r_work: 0.2898 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2061 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= 0.176 Angle : 0.500 7.365 13653 Z= 0.257 Chirality : 0.039 0.138 1701 Planarity : 0.004 0.044 1611 Dihedral : 7.927 65.296 1803 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.71 % Allowed : 14.76 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.25), residues: 1257 helix: 2.51 (0.16), residues: 1035 sheet: 0.33 (0.70), residues: 60 loop : -0.75 (0.58), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 PHE 0.016 0.001 PHE C 388 TYR 0.035 0.002 TYR B 287 ARG 0.001 0.000 ARG B 87 *********************** 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 178 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 160 time to evaluate : 1.021 Fit side-chains REVERT: A 256 MET cc_start: 0.9314 (ttm) cc_final: 0.9114 (ttm) REVERT: B 231 LYS cc_start: 0.6486 (ttpt) cc_final: 0.5932 (ttpt) REVERT: B 287 TYR cc_start: 0.9141 (t80) cc_final: 0.8919 (t80) REVERT: C 231 LYS cc_start: 0.6258 (tttm) cc_final: 0.5857 (tmmt) REVERT: C 334 LEU cc_start: 0.8345 (tp) cc_final: 0.8069 (tp) outliers start: 18 outliers final: 17 residues processed: 167 average time/residue: 0.1849 time to fit residues: 46.2142 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 : 1.091 ------------------------------------------------------------------------------- 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 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 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 38 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 90 optimal weight: 0.5980 chunk 82 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 54 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.123289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.095753 restraints weight = 12644.083| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 1.88 r_work: 0.2794 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10155 Z= 0.178 Angle : 0.495 7.918 13653 Z= 0.254 Chirality : 0.039 0.146 1701 Planarity : 0.004 0.044 1611 Dihedral : 7.779 63.672 1803 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.71 % Allowed : 15.05 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.25), residues: 1257 helix: 2.54 (0.16), residues: 1035 sheet: 0.36 (0.71), residues: 60 loop : -0.73 (0.57), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 PHE 0.016 0.001 PHE A 388 TYR 0.028 0.002 TYR B 287 ARG 0.001 0.000 ARG A 387 *********************** 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 183 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 1.057 Fit side-chains REVERT: A 40 LYS cc_start: 0.6042 (mtpp) cc_final: 0.4821 (tptt) REVERT: A 256 MET cc_start: 0.9369 (ttm) cc_final: 0.9089 (ttm) REVERT: B 231 LYS cc_start: 0.6474 (ttpt) cc_final: 0.5973 (ttpt) REVERT: B 287 TYR cc_start: 0.9104 (t80) cc_final: 0.8895 (t80) REVERT: B 334 LEU cc_start: 0.8340 (tp) cc_final: 0.8014 (tp) REVERT: C 231 LYS cc_start: 0.6243 (tttm) cc_final: 0.5836 (tmmt) REVERT: C 317 MET cc_start: 0.8297 (tpp) cc_final: 0.7950 (mtt) REVERT: C 334 LEU cc_start: 0.8340 (tp) cc_final: 0.8071 (tp) outliers start: 18 outliers final: 15 residues processed: 173 average time/residue: 0.1825 time to fit residues: 46.8797 Evaluate side-chains 173 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 468 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.121163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.094867 restraints weight = 12366.127| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.76 r_work: 0.2799 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2102 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= 0.208 Angle : 0.512 8.382 13653 Z= 0.262 Chirality : 0.040 0.150 1701 Planarity : 0.004 0.044 1611 Dihedral : 7.878 63.032 1803 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.62 % Allowed : 15.52 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.24), residues: 1257 helix: 2.46 (0.16), residues: 1038 sheet: 0.29 (0.70), residues: 60 loop : -0.60 (0.57), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 PHE 0.014 0.001 PHE B 388 TYR 0.024 0.002 TYR B 287 ARG 0.001 0.000 ARG C 384 *********************** 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: 17 poor density : 158 time to evaluate : 1.096 Fit side-chains REVERT: A 40 LYS cc_start: 0.5978 (mtpp) cc_final: 0.4803 (tptt) REVERT: A 256 MET cc_start: 0.9354 (ttm) cc_final: 0.9047 (ttm) REVERT: B 231 LYS cc_start: 0.6406 (ttpt) cc_final: 0.6157 (tmmt) REVERT: B 287 TYR cc_start: 0.9108 (t80) cc_final: 0.8889 (t80) REVERT: B 334 LEU cc_start: 0.8339 (tp) cc_final: 0.8014 (tp) REVERT: C 231 LYS cc_start: 0.6429 (tttm) cc_final: 0.6051 (tmmt) REVERT: C 334 LEU cc_start: 0.8286 (tp) cc_final: 0.7992 (tp) outliers start: 17 outliers final: 16 residues processed: 166 average time/residue: 0.1894 time to fit residues: 47.0716 Evaluate side-chains 174 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.026 ------------------------------------------------------------------------------- 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 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 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 122 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.123063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.095400 restraints weight = 12412.319| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.87 r_work: 0.2790 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2173 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= 0.186 Angle : 0.505 8.745 13653 Z= 0.257 Chirality : 0.039 0.159 1701 Planarity : 0.004 0.043 1611 Dihedral : 7.782 63.860 1803 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.62 % Allowed : 15.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.24), residues: 1257 helix: 2.51 (0.16), residues: 1035 sheet: 0.34 (0.71), residues: 60 loop : -0.51 (0.56), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 286 HIS 0.002 0.001 HIS C 143 PHE 0.013 0.001 PHE B 388 TYR 0.029 0.002 TYR A 287 ARG 0.001 0.000 ARG C 387 *********************** 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 175 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 1.052 Fit side-chains REVERT: A 256 MET cc_start: 0.9343 (ttm) cc_final: 0.9015 (ttm) REVERT: B 231 LYS cc_start: 0.6414 (ttpt) cc_final: 0.6172 (tmmt) REVERT: B 334 LEU cc_start: 0.8322 (tp) cc_final: 0.8000 (tp) REVERT: B 507 GLN cc_start: 0.4075 (mp10) cc_final: 0.3834 (mp10) REVERT: C 231 LYS cc_start: 0.6400 (tttm) cc_final: 0.6018 (tmmt) REVERT: C 334 LEU cc_start: 0.8276 (tp) cc_final: 0.7982 (tp) outliers start: 17 outliers final: 16 residues processed: 165 average time/residue: 0.1788 time to fit residues: 44.5290 Evaluate side-chains 171 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 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 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 58 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 117 optimal weight: 0.0020 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.123016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.095178 restraints weight = 12636.346| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.90 r_work: 0.2782 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2177 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= 0.190 Angle : 0.508 9.021 13653 Z= 0.258 Chirality : 0.040 0.181 1701 Planarity : 0.004 0.044 1611 Dihedral : 7.795 64.075 1803 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.52 % Allowed : 16.10 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.24), residues: 1257 helix: 2.50 (0.16), residues: 1038 sheet: 0.33 (0.71), residues: 60 loop : -0.57 (0.57), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 286 HIS 0.002 0.001 HIS C 143 PHE 0.016 0.001 PHE A 388 TYR 0.020 0.002 TYR A 287 ARG 0.001 0.000 ARG A 478 ********************** 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: 16 poor density : 161 time to evaluate : 0.898 Fit side-chains REVERT: A 256 MET cc_start: 0.9345 (ttm) cc_final: 0.9004 (ttm) REVERT: B 231 LYS cc_start: 0.6392 (ttpt) cc_final: 0.6152 (tmmt) REVERT: B 334 LEU cc_start: 0.8308 (tp) cc_final: 0.7983 (tp) REVERT: B 507 GLN cc_start: 0.4276 (mp10) cc_final: 0.4058 (mp10) REVERT: C 231 LYS cc_start: 0.6381 (tttm) cc_final: 0.6011 (tmmt) REVERT: C 334 LEU cc_start: 0.8275 (tp) cc_final: 0.7980 (tp) outliers start: 16 outliers final: 16 residues processed: 168 average time/residue: 0.1797 time to fit residues: 45.1628 Evaluate side-chains 172 residues out of total 1050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 156 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 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 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 118 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 3 optimal weight: 0.0070 chunk 94 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.125701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.103648 restraints weight = 12213.382| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.55 r_work: 0.2914 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10155 Z= 0.156 Angle : 0.490 9.512 13653 Z= 0.250 Chirality : 0.039 0.183 1701 Planarity : 0.004 0.044 1611 Dihedral : 7.621 63.897 1803 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 1.43 % Allowed : 16.29 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.23 (0.25), residues: 1257 helix: 2.64 (0.16), residues: 1035 sheet: 0.36 (0.72), residues: 60 loop : -0.71 (0.57), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 286 HIS 0.002 0.001 HIS C 143 PHE 0.015 0.001 PHE C 388 TYR 0.026 0.002 TYR A 287 ARG 0.001 0.000 ARG B 478 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4614.47 seconds wall clock time: 82 minutes 50.20 seconds (4970.20 seconds total)