Starting phenix.real_space_refine on Wed Aug 5 06:42:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uv3_64522/08_2026/9uv3_64522.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uv3_64522/08_2026/9uv3_64522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9uv3_64522/08_2026/9uv3_64522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uv3_64522/08_2026/9uv3_64522.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9uv3_64522/08_2026/9uv3_64522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uv3_64522/08_2026/9uv3_64522.map" } resolution = 2.88 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 56 5.16 5 C 5583 2.51 5 N 1412 2.21 5 O 1546 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8604 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "C" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3423 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 445} Chain: "D" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "A" Number of atoms: 3423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3423 Classifications: {'peptide': 462} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 445} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'COA:plan-2': 1, 'COA:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'PC1': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'COA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'COA:plan-2': 1, 'COA:plan-4': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.64, per 1000 atoms: 0.19 Number of scatterers: 8604 At special positions: 0 Unit cell: (69.7, 95.94, 97.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 7 15.00 O 1546 8.00 N 1412 7.00 C 5583 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 325.6 milliseconds 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2056 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 2 sheets defined 74.6% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 405 through 418 removed outlier: 3.706A pdb=" N ALA B 409 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 443 Processing helix chain 'B' and resid 444 through 445 No H-bonds generated for 'chain 'B' and resid 444 through 445' Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 449 through 461 Processing helix chain 'B' and resid 464 through 473 removed outlier: 3.892A pdb=" N ALA B 468 " --> pdb=" O ILE B 464 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLY B 473 " --> pdb=" O LEU B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 508 removed outlier: 3.671A pdb=" N ARG B 508 " --> pdb=" O LEU B 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 23 Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 29 through 50 Processing helix chain 'C' and resid 56 through 78 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 82 through 108 Processing helix chain 'C' and resid 114 through 148 Processing helix chain 'C' and resid 159 through 181 Processing helix chain 'C' and resid 183 through 208 Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 213 through 236 Processing helix chain 'C' and resid 238 through 264 Processing helix chain 'C' and resid 266 through 272 Processing helix chain 'C' and resid 273 through 278 removed outlier: 4.183A pdb=" N THR C 277 " --> pdb=" O GLY C 273 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASP C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 273 through 278' Processing helix chain 'C' and resid 295 through 306 Processing helix chain 'C' and resid 314 through 320 removed outlier: 3.884A pdb=" N ALA C 318 " --> pdb=" O GLY C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.809A pdb=" N VAL C 357 " --> pdb=" O GLY C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 377 removed outlier: 4.606A pdb=" N ASP C 377 " --> pdb=" O ASP C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 381 Processing helix chain 'C' and resid 395 through 399 Processing helix chain 'C' and resid 413 through 417 Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.664A pdb=" N PHE C 440 " --> pdb=" O PRO C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 450 through 462 Processing helix chain 'D' and resid 407 through 418 Processing helix chain 'D' and resid 421 through 443 Processing helix chain 'D' and resid 444 through 445 No H-bonds generated for 'chain 'D' and resid 444 through 445' Processing helix chain 'D' and resid 446 through 448 No H-bonds generated for 'chain 'D' and resid 446 through 448' Processing helix chain 'D' and resid 449 through 462 Processing helix chain 'D' and resid 464 through 472 removed outlier: 3.958A pdb=" N ALA D 468 " --> pdb=" O ILE D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 508 removed outlier: 3.663A pdb=" N ARG D 508 " --> pdb=" O LEU D 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 24 Processing helix chain 'A' and resid 26 through 50 removed outlier: 4.517A pdb=" N ARG A 31 " --> pdb=" O HIS A 27 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLN A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 78 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 82 through 108 Processing helix chain 'A' and resid 114 through 148 Processing helix chain 'A' and resid 159 through 181 Processing helix chain 'A' and resid 183 through 208 Processing helix chain 'A' and resid 210 through 212 No H-bonds generated for 'chain 'A' and resid 210 through 212' Processing helix chain 'A' and resid 213 through 237 Processing helix chain 'A' and resid 238 through 264 Processing helix chain 'A' and resid 266 through 272 Processing helix chain 'A' and resid 295 through 306 Processing helix chain 'A' and resid 322 through 337 Processing helix chain 'A' and resid 353 through 362 Processing helix chain 'A' and resid 372 through 377 removed outlier: 4.485A pdb=" N ASP A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 380 No H-bonds generated for 'chain 'A' and resid 378 through 380' Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 436 through 441 Processing helix chain 'A' and resid 450 through 462 Processing sheet with id=AA1, first strand: chain 'C' and resid 369 through 371 removed outlier: 8.477A pdb=" N LEU C 370 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N PHE C 342 " --> pdb=" O LEU C 370 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL C 309 " --> pdb=" O ARG C 341 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N GLY C 343 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE C 311 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL C 420 " --> pdb=" O HIS C 445 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 371 removed outlier: 8.328A pdb=" N LEU A 370 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N PHE A 342 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR A 384 " --> pdb=" O SER A 308 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 385 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N PHE A 423 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 387 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL A 420 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LEU A 447 " --> pdb=" O VAL A 420 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 422 " --> pdb=" O LEU A 447 " (cutoff:3.500A) 636 hydrogen bonds defined for protein. 1863 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: 1.51 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1469 1.32 - 1.45: 2185 1.45 - 1.57: 5009 1.57 - 1.70: 12 1.70 - 1.82: 106 Bond restraints: 8781 Sorted by residual: bond pdb=" O3B COA C 601 " pdb=" P3B COA C 601 " ideal model delta sigma weight residual 1.683 1.615 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" O3B COA A 501 " pdb=" P3B COA A 501 " ideal model delta sigma weight residual 1.683 1.617 0.066 2.00e-02 2.50e+03 1.09e+01 bond pdb=" C11 PC1 D 601 " pdb=" O13 PC1 D 601 " ideal model delta sigma weight residual 1.407 1.454 -0.047 2.00e-02 2.50e+03 5.56e+00 bond pdb=" O13 PC1 D 601 " pdb=" P PC1 D 601 " ideal model delta sigma weight residual 1.652 1.606 0.046 2.00e-02 2.50e+03 5.25e+00 bond pdb=" C1 PC1 D 601 " pdb=" O11 PC1 D 601 " ideal model delta sigma weight residual 1.411 1.454 -0.043 2.00e-02 2.50e+03 4.63e+00 ... (remaining 8776 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11748 2.30 - 4.61: 167 4.61 - 6.91: 23 6.91 - 9.21: 4 9.21 - 11.52: 6 Bond angle restraints: 11948 Sorted by residual: angle pdb=" C TYR C 431 " pdb=" CA TYR C 431 " pdb=" CB TYR C 431 " ideal model delta sigma weight residual 116.54 110.65 5.89 1.15e+00 7.56e-01 2.62e+01 angle pdb=" CB MET A 355 " pdb=" CG MET A 355 " pdb=" SD MET A 355 " ideal model delta sigma weight residual 112.70 124.22 -11.52 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CA TYR C 431 " pdb=" C TYR C 431 " pdb=" N ALA C 432 " ideal model delta sigma weight residual 119.52 116.81 2.71 7.90e-01 1.60e+00 1.17e+01 angle pdb=" CB MET A 194 " pdb=" CG MET A 194 " pdb=" SD MET A 194 " ideal model delta sigma weight residual 112.70 122.94 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" CB MET C 41 " pdb=" CG MET C 41 " pdb=" SD MET C 41 " ideal model delta sigma weight residual 112.70 122.82 -10.12 3.00e+00 1.11e-01 1.14e+01 ... (remaining 11943 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.27: 4459 19.27 - 38.54: 531 38.54 - 57.80: 136 57.80 - 77.07: 34 77.07 - 96.34: 10 Dihedral angle restraints: 5170 sinusoidal: 1956 harmonic: 3214 Sorted by residual: dihedral pdb=" CA VAL C 434 " pdb=" C VAL C 434 " pdb=" N GLN C 435 " pdb=" CA GLN C 435 " ideal model delta harmonic sigma weight residual 180.00 158.29 21.71 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA MET C 409 " pdb=" C MET C 409 " pdb=" N PRO C 410 " pdb=" CA PRO C 410 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" N9A COA C 601 " pdb=" C1B COA C 601 " pdb=" C2B COA C 601 " pdb=" O2B COA C 601 " ideal model delta sinusoidal sigma weight residual -74.37 -170.71 96.34 1 3.00e+01 1.11e-03 1.18e+01 ... (remaining 5167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1240 0.060 - 0.120: 176 0.120 - 0.181: 7 0.181 - 0.241: 2 0.241 - 0.301: 2 Chirality restraints: 1427 Sorted by residual: chirality pdb=" C2B COA C 601 " pdb=" C1B COA C 601 " pdb=" C3B COA C 601 " pdb=" O2B COA C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.70 0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C3B COA A 501 " pdb=" C2B COA A 501 " pdb=" C4B COA A 501 " pdb=" O3B COA A 501 " both_signs ideal model delta sigma weight residual False -2.73 -2.46 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C2B COA A 501 " pdb=" C1B COA A 501 " pdb=" C3B COA A 501 " pdb=" O2B COA A 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 1424 not shown) Planarity restraints: 1480 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 415 " 0.009 2.00e-02 2.50e+03 1.26e-02 3.95e+00 pdb=" CG TRP B 415 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP B 415 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP B 415 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 415 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 415 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 415 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 415 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 415 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 415 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 214 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 215 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 345 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.71e+00 pdb=" N PRO A 346 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " -0.023 5.00e-02 4.00e+02 ... (remaining 1477 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 584 2.73 - 3.28: 9371 3.28 - 3.82: 16014 3.82 - 4.36: 17673 4.36 - 4.90: 30995 Nonbonded interactions: 74637 Sorted by model distance: nonbonded pdb=" N GLU A 374 " pdb=" OE1 GLU A 374 " model vdw 2.192 3.120 nonbonded pdb=" OG SER C 266 " pdb=" OG SER C 269 " model vdw 2.268 3.040 nonbonded pdb=" O LEU C 100 " pdb=" ND2 ASN C 104 " model vdw 2.269 3.120 nonbonded pdb=" OH TYR D 439 " pdb=" O22 PC1 D 601 " model vdw 2.276 3.040 nonbonded pdb=" NH2 ARG C 292 " pdb=" O LYS C 441 " model vdw 2.298 3.120 ... (remaining 74632 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 403 through 510) } 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: 2.940 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.690 Find NCS groups from input model: 0.290 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 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 : 0.004 0.068 8782 Z= 0.163 Angle : 0.660 11.517 11948 Z= 0.319 Chirality : 0.042 0.301 1427 Planarity : 0.004 0.045 1480 Dihedral : 18.477 96.338 3114 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.98 % Favored : 95.85 % Rotamer: Outliers : 3.03 % Allowed : 33.63 % Favored : 63.34 % 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: 2.40 (0.26), residues: 1132 helix: 2.51 (0.18), residues: 784 sheet: -0.69 (0.67), residues: 60 loop : -0.54 (0.42), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 425 TYR 0.014 0.001 TYR D 440 PHE 0.008 0.001 PHE C 234 TRP 0.034 0.001 TRP B 415 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 ( 8781) covalent geometry : angle 0.65967 / 0.32 (11948) hydrogen bonds : bond 0.09721 / 6.19 ( 636) hydrogen bonds : angle 4.50716 / 3.36 ( 1863) Misc. bond : bond 0.00191 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.266 Fit side-chains outliers start: 27 outliers final: 23 residues processed: 164 average time/residue: 0.3738 time to fit residues: 66.9504 Evaluate side-chains 158 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain C residue 250 SER Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 330 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 431 TYR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 405 LEU Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 404 SER Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 222 ASN D 458 ASN A 238 ASN A 428 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.103681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.075157 restraints weight = 14425.011| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.74 r_work: 0.2897 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8782 Z= 0.136 Angle : 0.534 7.137 11948 Z= 0.270 Chirality : 0.040 0.164 1427 Planarity : 0.004 0.044 1480 Dihedral : 11.417 73.805 1333 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.80 % Favored : 96.02 % Rotamer: Outliers : 4.26 % Allowed : 26.91 % Favored : 68.83 % 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: 2.56 (0.26), residues: 1132 helix: 2.59 (0.18), residues: 788 sheet: -0.44 (0.66), residues: 60 loop : -0.42 (0.42), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 425 TYR 0.011 0.001 TYR C 106 PHE 0.009 0.001 PHE B 480 TRP 0.014 0.001 TRP B 415 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8781) covalent geometry : angle 0.53447 / 0.27 (11948) hydrogen bonds : bond 0.03532 / 2.30 ( 636) hydrogen bonds : angle 3.83216 / 2.86 ( 1863) Misc. bond : bond 0.00143 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.334 Fit side-chains REVERT: B 412 LEU cc_start: 0.9124 (mm) cc_final: 0.8845 (mm) REVERT: C 381 ASP cc_start: 0.8460 (t0) cc_final: 0.8247 (t0) REVERT: C 418 GLN cc_start: 0.9063 (tt0) cc_final: 0.8472 (tm-30) REVERT: D 408 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7974 (tm) REVERT: A 194 MET cc_start: 0.8815 (tmm) cc_final: 0.8599 (tmm) outliers start: 38 outliers final: 12 residues processed: 162 average time/residue: 0.3837 time to fit residues: 67.7698 Evaluate side-chains 144 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 373 ASP Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 450 HIS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 42 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 94 optimal weight: 0.0570 chunk 111 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 overall best weight: 1.1502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.101685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.072790 restraints weight = 14366.238| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.72 r_work: 0.2843 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8782 Z= 0.175 Angle : 0.537 6.730 11948 Z= 0.274 Chirality : 0.041 0.168 1427 Planarity : 0.004 0.048 1480 Dihedral : 10.313 67.224 1309 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 4.26 % Allowed : 26.01 % Favored : 69.73 % 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: 2.45 (0.26), residues: 1132 helix: 2.50 (0.18), residues: 786 sheet: -0.50 (0.66), residues: 60 loop : -0.39 (0.41), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.012 0.001 TYR D 440 PHE 0.010 0.001 PHE A 178 TRP 0.009 0.001 TRP B 415 HIS 0.003 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 ( 8781) covalent geometry : angle 0.53655 / 0.27 (11948) hydrogen bonds : bond 0.03604 / 2.35 ( 636) hydrogen bonds : angle 3.85780 / 2.88 ( 1863) Misc. bond : bond 0.00153 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 131 time to evaluate : 0.235 Fit side-chains REVERT: B 403 TYR cc_start: 0.4046 (OUTLIER) cc_final: 0.2990 (t80) REVERT: B 412 LEU cc_start: 0.9209 (mm) cc_final: 0.8908 (mm) REVERT: C 381 ASP cc_start: 0.8534 (t0) cc_final: 0.8252 (t0) REVERT: C 409 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8935 (ttm) REVERT: C 418 GLN cc_start: 0.8971 (tt0) cc_final: 0.8430 (tm-30) REVERT: D 408 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7966 (tm) REVERT: D 505 LYS cc_start: 0.8267 (ttmm) cc_final: 0.7940 (ttmm) REVERT: A 194 MET cc_start: 0.8858 (tmm) cc_final: 0.8651 (tmm) REVERT: A 374 GLU cc_start: 0.8402 (mp0) cc_final: 0.8161 (mp0) outliers start: 38 outliers final: 10 residues processed: 155 average time/residue: 0.4779 time to fit residues: 79.8587 Evaluate side-chains 138 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 403 TYR Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.0270 chunk 4 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.6040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 108 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.074353 restraints weight = 14140.566| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.85 r_work: 0.2885 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8782 Z= 0.126 Angle : 0.524 7.580 11948 Z= 0.261 Chirality : 0.040 0.172 1427 Planarity : 0.004 0.048 1480 Dihedral : 9.616 67.909 1305 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.15 % Favored : 95.58 % Rotamer: Outliers : 4.04 % Allowed : 26.57 % Favored : 69.39 % 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: 2.53 (0.26), residues: 1132 helix: 2.57 (0.18), residues: 788 sheet: -0.50 (0.66), residues: 60 loop : -0.43 (0.41), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 425 TYR 0.018 0.001 TYR B 439 PHE 0.007 0.001 PHE B 480 TRP 0.008 0.001 TRP B 415 HIS 0.004 0.000 HIS C 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8781) covalent geometry : angle 0.52359 / 0.26 (11948) hydrogen bonds : bond 0.03348 / 2.18 ( 636) hydrogen bonds : angle 3.76362 / 2.81 ( 1863) Misc. bond : bond 0.00170 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 0.337 Fit side-chains REVERT: B 412 LEU cc_start: 0.9191 (mm) cc_final: 0.8916 (mm) REVERT: B 415 TRP cc_start: 0.8051 (t-100) cc_final: 0.7801 (t-100) REVERT: C 381 ASP cc_start: 0.8559 (t0) cc_final: 0.8266 (t0) REVERT: C 409 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.9072 (ttm) REVERT: C 418 GLN cc_start: 0.8956 (tt0) cc_final: 0.8447 (tm-30) REVERT: D 408 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7995 (tm) REVERT: D 505 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7894 (ttmm) REVERT: D 507 PHE cc_start: 0.8539 (OUTLIER) cc_final: 0.7476 (t80) outliers start: 36 outliers final: 13 residues processed: 152 average time/residue: 0.4310 time to fit residues: 71.2156 Evaluate side-chains 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 410 ILE Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 381 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 3 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 25 optimal weight: 0.0050 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.100917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.071464 restraints weight = 14224.751| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 2.84 r_work: 0.2833 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8782 Z= 0.180 Angle : 0.559 7.920 11948 Z= 0.281 Chirality : 0.041 0.182 1427 Planarity : 0.004 0.049 1480 Dihedral : 9.159 67.269 1301 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.98 % Favored : 95.76 % Rotamer: Outliers : 4.48 % Allowed : 26.23 % Favored : 69.28 % 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: 2.43 (0.26), residues: 1132 helix: 2.48 (0.18), residues: 786 sheet: -0.49 (0.66), residues: 60 loop : -0.38 (0.41), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 425 TYR 0.012 0.001 TYR C 106 PHE 0.010 0.001 PHE B 424 TRP 0.006 0.001 TRP B 415 HIS 0.002 0.001 HIS C 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.18 ( 8781) covalent geometry : angle 0.55901 / 0.28 (11948) hydrogen bonds : bond 0.03616 / 2.36 ( 636) hydrogen bonds : angle 3.86263 / 2.88 ( 1863) Misc. bond : bond 0.00162 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 130 time to evaluate : 0.346 Fit side-chains REVERT: B 412 LEU cc_start: 0.9218 (mm) cc_final: 0.8914 (mm) REVERT: B 415 TRP cc_start: 0.8074 (t-100) cc_final: 0.7869 (t-100) REVERT: C 381 ASP cc_start: 0.8575 (t0) cc_final: 0.8269 (t0) REVERT: C 409 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9079 (ttm) REVERT: C 418 GLN cc_start: 0.8953 (tt0) cc_final: 0.8499 (tm-30) REVERT: D 408 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.7993 (tm) REVERT: D 505 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7974 (ttmm) REVERT: D 507 PHE cc_start: 0.8602 (OUTLIER) cc_final: 0.7522 (t80) REVERT: A 61 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8548 (mm) outliers start: 40 outliers final: 11 residues processed: 154 average time/residue: 0.4503 time to fit residues: 74.8502 Evaluate side-chains 142 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 409 MET Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 416 MET Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 111 optimal weight: 0.2980 chunk 35 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 96 optimal weight: 0.6980 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 0.0470 chunk 21 optimal weight: 0.4980 chunk 92 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.104559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.075591 restraints weight = 14055.809| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.85 r_work: 0.2896 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8782 Z= 0.117 Angle : 0.534 8.303 11948 Z= 0.267 Chirality : 0.040 0.173 1427 Planarity : 0.004 0.050 1480 Dihedral : 8.650 68.169 1301 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.06 % Favored : 95.67 % Rotamer: Outliers : 3.48 % Allowed : 27.35 % Favored : 69.17 % 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 (0.26), residues: 1132 helix: 2.59 (0.18), residues: 788 sheet: -0.47 (0.67), residues: 60 loop : -0.47 (0.41), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 425 TYR 0.019 0.001 TYR B 439 PHE 0.007 0.001 PHE B 483 TRP 0.008 0.001 TRP B 415 HIS 0.002 0.000 HIS A 291 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8781) covalent geometry : angle 0.53412 / 0.27 (11948) hydrogen bonds : bond 0.03296 / 2.13 ( 636) hydrogen bonds : angle 3.75417 / 2.80 ( 1863) Misc. bond : bond 0.00195 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.319 Fit side-chains REVERT: B 412 LEU cc_start: 0.9207 (mm) cc_final: 0.8911 (mm) REVERT: C 381 ASP cc_start: 0.8565 (t0) cc_final: 0.8252 (t0) REVERT: C 418 GLN cc_start: 0.8862 (tt0) cc_final: 0.8418 (tm-30) REVERT: D 505 LYS cc_start: 0.8211 (ttmm) cc_final: 0.7907 (ttmm) REVERT: D 507 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7482 (t80) outliers start: 31 outliers final: 12 residues processed: 153 average time/residue: 0.3873 time to fit residues: 64.4435 Evaluate side-chains 139 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 471 GLN ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.102003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.073061 restraints weight = 14363.770| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.82 r_work: 0.2852 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8782 Z= 0.172 Angle : 0.582 9.804 11948 Z= 0.291 Chirality : 0.041 0.176 1427 Planarity : 0.004 0.048 1480 Dihedral : 8.344 69.299 1301 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.80 % Favored : 95.94 % Rotamer: Outliers : 3.48 % Allowed : 27.47 % Favored : 69.06 % 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: 2.52 (0.26), residues: 1132 helix: 2.55 (0.18), residues: 788 sheet: -0.42 (0.67), residues: 60 loop : -0.44 (0.41), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 425 TYR 0.016 0.001 TYR A 106 PHE 0.009 0.001 PHE B 424 TRP 0.025 0.001 TRP B 415 HIS 0.002 0.001 HIS C 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 8781) covalent geometry : angle 0.58200 / 0.29 (11948) hydrogen bonds : bond 0.03500 / 2.27 ( 636) hydrogen bonds : angle 3.81939 / 2.85 ( 1863) Misc. bond : bond 0.00173 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.224 Fit side-chains REVERT: B 412 LEU cc_start: 0.9210 (mm) cc_final: 0.8899 (mm) REVERT: C 371 GLU cc_start: 0.7963 (mp0) cc_final: 0.7474 (mm-30) REVERT: C 381 ASP cc_start: 0.8580 (t0) cc_final: 0.8266 (t0) REVERT: C 418 GLN cc_start: 0.8880 (tt0) cc_final: 0.8436 (tm-30) REVERT: D 408 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8000 (tm) REVERT: D 454 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8323 (mtp) REVERT: D 505 LYS cc_start: 0.8167 (ttmm) cc_final: 0.7862 (ttmm) REVERT: D 507 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.7503 (t80) REVERT: A 61 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8569 (mm) outliers start: 31 outliers final: 12 residues processed: 151 average time/residue: 0.3997 time to fit residues: 65.2092 Evaluate side-chains 143 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 454 MET Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 371 GLU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 57 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 109 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 187 GLN ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.103211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.074396 restraints weight = 14128.738| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.83 r_work: 0.2873 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8782 Z= 0.141 Angle : 0.579 10.054 11948 Z= 0.288 Chirality : 0.041 0.166 1427 Planarity : 0.004 0.050 1480 Dihedral : 7.993 70.518 1301 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.06 % Favored : 95.67 % Rotamer: Outliers : 2.69 % Allowed : 28.36 % Favored : 68.95 % 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: 2.53 (0.26), residues: 1132 helix: 2.56 (0.18), residues: 788 sheet: -0.31 (0.68), residues: 60 loop : -0.47 (0.41), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 425 TYR 0.019 0.001 TYR B 439 PHE 0.010 0.001 PHE C 126 TRP 0.022 0.001 TRP B 415 HIS 0.013 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 8781) covalent geometry : angle 0.57948 / 0.29 (11948) hydrogen bonds : bond 0.03410 / 2.20 ( 636) hydrogen bonds : angle 3.81937 / 2.83 ( 1863) Misc. bond : bond 0.00189 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.307 Fit side-chains REVERT: B 412 LEU cc_start: 0.9223 (mm) cc_final: 0.8921 (mm) REVERT: C 371 GLU cc_start: 0.8025 (mp0) cc_final: 0.7492 (mm-30) REVERT: C 381 ASP cc_start: 0.8588 (t0) cc_final: 0.8271 (t0) REVERT: C 418 GLN cc_start: 0.8852 (tt0) cc_final: 0.8400 (tm-30) REVERT: D 408 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.7996 (tm) REVERT: D 505 LYS cc_start: 0.8154 (ttmm) cc_final: 0.7852 (ttmm) REVERT: D 507 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.7537 (t80) REVERT: A 61 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8624 (mm) outliers start: 24 outliers final: 13 residues processed: 140 average time/residue: 0.4303 time to fit residues: 65.4567 Evaluate side-chains 140 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 406 MET Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 64 MET Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 319 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 59 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 0.3980 chunk 12 optimal weight: 0.0070 chunk 107 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.103635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.075091 restraints weight = 14234.244| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.82 r_work: 0.2878 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8782 Z= 0.138 Angle : 0.589 10.075 11948 Z= 0.289 Chirality : 0.041 0.157 1427 Planarity : 0.004 0.052 1480 Dihedral : 7.725 72.115 1301 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 2.24 % Allowed : 28.25 % Favored : 69.51 % 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: 2.57 (0.26), residues: 1132 helix: 2.57 (0.18), residues: 788 sheet: -0.21 (0.69), residues: 60 loop : -0.41 (0.41), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 425 TYR 0.021 0.001 TYR A 106 PHE 0.007 0.001 PHE B 424 TRP 0.020 0.001 TRP B 415 HIS 0.012 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8781) covalent geometry : angle 0.58949 / 0.29 (11948) hydrogen bonds : bond 0.03392 / 2.19 ( 636) hydrogen bonds : angle 3.79818 / 2.82 ( 1863) Misc. bond : bond 0.00197 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.322 Fit side-chains REVERT: B 412 LEU cc_start: 0.9225 (mm) cc_final: 0.8915 (mm) REVERT: C 371 GLU cc_start: 0.8072 (mp0) cc_final: 0.7541 (mm-30) REVERT: C 381 ASP cc_start: 0.8580 (t0) cc_final: 0.8265 (t0) REVERT: C 418 GLN cc_start: 0.8833 (tt0) cc_final: 0.8395 (tm-30) REVERT: D 408 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7994 (tm) REVERT: D 505 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7920 (ttmm) REVERT: D 507 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.7517 (t80) REVERT: A 61 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8659 (mm) outliers start: 20 outliers final: 10 residues processed: 140 average time/residue: 0.4158 time to fit residues: 63.4118 Evaluate side-chains 135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 95 optimal weight: 0.0870 chunk 84 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 50 optimal weight: 0.0170 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.076122 restraints weight = 14277.607| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.84 r_work: 0.2901 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8782 Z= 0.129 Angle : 0.582 10.163 11948 Z= 0.286 Chirality : 0.041 0.154 1427 Planarity : 0.004 0.053 1480 Dihedral : 7.516 74.341 1301 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 1.68 % Allowed : 29.37 % Favored : 68.95 % 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: 2.59 (0.26), residues: 1132 helix: 2.59 (0.18), residues: 788 sheet: -0.18 (0.70), residues: 60 loop : -0.43 (0.41), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 425 TYR 0.018 0.001 TYR B 439 PHE 0.008 0.001 PHE C 423 TRP 0.036 0.001 TRP B 415 HIS 0.011 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 8781) covalent geometry : angle 0.58222 / 0.29 (11948) hydrogen bonds : bond 0.03327 / 2.15 ( 636) hydrogen bonds : angle 3.76068 / 2.78 ( 1863) Misc. bond : bond 0.00204 / 0.11 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2264 Ramachandran restraints generated. 1132 Oldfield, 0 Emsley, 1132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.298 Fit side-chains REVERT: B 412 LEU cc_start: 0.9222 (mm) cc_final: 0.8916 (mm) REVERT: C 371 GLU cc_start: 0.8040 (mp0) cc_final: 0.7494 (mm-30) REVERT: C 381 ASP cc_start: 0.8593 (t0) cc_final: 0.8279 (t0) REVERT: C 418 GLN cc_start: 0.8818 (tt0) cc_final: 0.8392 (tm-30) REVERT: D 408 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7989 (tm) REVERT: D 507 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7427 (t80) REVERT: A 61 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8622 (mm) outliers start: 15 outliers final: 10 residues processed: 139 average time/residue: 0.3730 time to fit residues: 56.5850 Evaluate side-chains 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 507 PHE Chi-restraints excluded: chain C residue 214 MET Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 411 ILE Chi-restraints excluded: chain D residue 507 PHE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.0980 chunk 94 optimal weight: 0.0060 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 291 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.105537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.077433 restraints weight = 14168.420| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.82 r_work: 0.2925 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8782 Z= 0.125 Angle : 0.579 10.117 11948 Z= 0.285 Chirality : 0.040 0.156 1427 Planarity : 0.004 0.053 1480 Dihedral : 7.343 77.228 1301 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.89 % Favored : 95.85 % Rotamer: Outliers : 1.68 % Allowed : 29.26 % Favored : 69.06 % 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: 2.59 (0.26), residues: 1132 helix: 2.59 (0.18), residues: 790 sheet: -0.12 (0.70), residues: 60 loop : -0.44 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 425 TYR 0.017 0.001 TYR A 106 PHE 0.013 0.001 PHE B 480 TRP 0.033 0.001 TRP B 415 HIS 0.010 0.001 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8781) covalent geometry : angle 0.57902 / 0.28 (11948) hydrogen bonds : bond 0.03289 / 2.12 ( 636) hydrogen bonds : angle 3.73781 / 2.77 ( 1863) Misc. bond : bond 0.00210 / 0.11 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2256.88 seconds wall clock time: 39 minutes 17.58 seconds (2357.58 seconds total)