Starting phenix.real_space_refine on Tue Mar 3 14:00:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sde_23517/03_2026/7sde_23517_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sde_23517/03_2026/7sde_23517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sde_23517/03_2026/7sde_23517_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sde_23517/03_2026/7sde_23517_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sde_23517/03_2026/7sde_23517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sde_23517/03_2026/7sde_23517.map" } resolution = 3.2 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= 0.003 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 32 5.16 5 C 3748 2.51 5 N 943 2.21 5 O 1011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5734 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3856 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 3 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 3, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 77 Chain: "B" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1878 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 5, 'TRANS': 232} Chain breaks: 5 Unresolved non-hydrogen bonds: 163 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 13, 'GLU:plan': 5, 'PHE:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 3, 'GLN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 1.23, per 1000 atoms: 0.21 Number of scatterers: 5734 At special positions: 0 Unit cell: (68.096, 80.864, 105.336, 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 32 16.00 O 1011 8.00 N 943 7.00 C 3748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.41 Conformation dependent library (CDL) restraints added in 413.2 milliseconds 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1414 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 0 sheets defined 61.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 removed outlier: 3.660A pdb=" N LEU A 30 " --> pdb=" O GLU A 26 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 53 removed outlier: 3.793A pdb=" N LEU A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.971A pdb=" N VAL A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 4.030A pdb=" N LEU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP A 91 " --> pdb=" O LEU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 116 Processing helix chain 'A' and resid 126 through 140 removed outlier: 3.775A pdb=" N ALA A 138 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 229 through 239 removed outlier: 3.502A pdb=" N ILE A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 261 removed outlier: 3.920A pdb=" N CYS A 253 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'A' and resid 279 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 292 through 302 removed outlier: 4.036A pdb=" N SER A 298 " --> pdb=" O ALA A 294 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 4.481A pdb=" N LEU A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 362 " --> pdb=" O CYS A 358 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 391 Processing helix chain 'A' and resid 394 through 403 removed outlier: 3.936A pdb=" N PHE A 402 " --> pdb=" O PHE A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.565A pdb=" N THR A 421 " --> pdb=" O LEU A 417 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LEU A 426 " --> pdb=" O LEU A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 442 removed outlier: 3.918A pdb=" N LEU A 442 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.540A pdb=" N PHE A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS A 449 " --> pdb=" O GLY A 445 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 457 removed outlier: 3.950A pdb=" N LEU A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 496 removed outlier: 4.087A pdb=" N ILE A 479 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 518 Processing helix chain 'A' and resid 518 through 529 removed outlier: 4.073A pdb=" N ARG A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS A 527 " --> pdb=" O ARG A 523 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 529 " --> pdb=" O TRP A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 removed outlier: 3.505A pdb=" N GLN A 544 " --> pdb=" O PRO A 540 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N MET A 545 " --> pdb=" O ILE A 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 217 Processing helix chain 'B' and resid 219 through 225 Processing helix chain 'B' and resid 245 through 253 Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.513A pdb=" N MET B 292 " --> pdb=" O LEU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 removed outlier: 3.541A pdb=" N ARG B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N PHE B 306 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASP B 317 " --> pdb=" O CYS B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 339 through 346 Processing helix chain 'B' and resid 354 through 366 removed outlier: 4.065A pdb=" N LEU B 358 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 removed outlier: 3.663A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 404 through 416 Processing helix chain 'B' and resid 432 through 441 removed outlier: 3.753A pdb=" N CYS B 436 " --> pdb=" O TYR B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 462 removed outlier: 4.018A pdb=" N LEU B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) 248 hydrogen bonds defined for protein. 738 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: 0.76 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1785 1.34 - 1.46: 1133 1.46 - 1.58: 2893 1.58 - 1.70: 0 1.70 - 1.82: 45 Bond restraints: 5856 Sorted by residual: bond pdb=" CA GLU A 193 " pdb=" C GLU A 193 " ideal model delta sigma weight residual 1.524 1.556 -0.032 1.24e-02 6.50e+03 6.64e+00 bond pdb=" CA LEU A 192 " pdb=" C LEU A 192 " ideal model delta sigma weight residual 1.522 1.545 -0.023 1.25e-02 6.40e+03 3.33e+00 bond pdb=" N TYR A 20 " pdb=" CA TYR A 20 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.31e+00 bond pdb=" C MET A 241 " pdb=" O MET A 241 " ideal model delta sigma weight residual 1.244 1.226 0.018 1.00e-02 1.00e+04 3.15e+00 bond pdb=" CA ALA B 323 " pdb=" C ALA B 323 " ideal model delta sigma weight residual 1.530 1.511 0.020 1.23e-02 6.61e+03 2.58e+00 ... (remaining 5851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 7720 2.64 - 5.28: 174 5.28 - 7.92: 23 7.92 - 10.57: 2 10.57 - 13.21: 1 Bond angle restraints: 7920 Sorted by residual: angle pdb=" N LYS A 146 " pdb=" CA LYS A 146 " pdb=" C LYS A 146 " ideal model delta sigma weight residual 110.24 123.45 -13.21 1.47e+00 4.63e-01 8.07e+01 angle pdb=" N GLN A 194 " pdb=" CA GLN A 194 " pdb=" C GLN A 194 " ideal model delta sigma weight residual 112.57 119.12 -6.55 1.13e+00 7.83e-01 3.36e+01 angle pdb=" N ARG A 364 " pdb=" CA ARG A 364 " pdb=" C ARG A 364 " ideal model delta sigma weight residual 113.12 106.11 7.01 1.25e+00 6.40e-01 3.15e+01 angle pdb=" C ASP A 91 " pdb=" N PRO A 92 " pdb=" CA PRO A 92 " ideal model delta sigma weight residual 119.24 124.34 -5.10 1.04e+00 9.25e-01 2.40e+01 angle pdb=" N LYS A 146 " pdb=" CA LYS A 146 " pdb=" CB LYS A 146 " ideal model delta sigma weight residual 109.48 102.06 7.42 1.55e+00 4.16e-01 2.29e+01 ... (remaining 7915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3072 17.64 - 35.28: 307 35.28 - 52.92: 102 52.92 - 70.56: 28 70.56 - 88.20: 7 Dihedral angle restraints: 3516 sinusoidal: 1356 harmonic: 2160 Sorted by residual: dihedral pdb=" N TYR A 20 " pdb=" C TYR A 20 " pdb=" CA TYR A 20 " pdb=" CB TYR A 20 " ideal model delta harmonic sigma weight residual 122.80 135.03 -12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" C TYR A 20 " pdb=" N TYR A 20 " pdb=" CA TYR A 20 " pdb=" CB TYR A 20 " ideal model delta harmonic sigma weight residual -122.60 -134.70 12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" CA GLU B 398 " pdb=" C GLU B 398 " pdb=" N PHE B 399 " pdb=" CA PHE B 399 " ideal model delta harmonic sigma weight residual 180.00 162.12 17.88 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 3513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 847 0.098 - 0.195: 52 0.195 - 0.293: 9 0.293 - 0.390: 2 0.390 - 0.488: 1 Chirality restraints: 911 Sorted by residual: chirality pdb=" CA TYR A 20 " pdb=" N TYR A 20 " pdb=" C TYR A 20 " pdb=" CB TYR A 20 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.95e+00 chirality pdb=" CA ILE A 435 " pdb=" N ILE A 435 " pdb=" C ILE A 435 " pdb=" CB ILE A 435 " both_signs ideal model delta sigma weight residual False 2.43 2.80 -0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CA TRP A 240 " pdb=" N TRP A 240 " pdb=" C TRP A 240 " pdb=" CB TRP A 240 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 ... (remaining 908 not shown) Planarity restraints: 993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 279 " -0.012 2.00e-02 2.50e+03 2.31e-02 5.34e+00 pdb=" C SER A 279 " 0.040 2.00e-02 2.50e+03 pdb=" O SER A 279 " -0.015 2.00e-02 2.50e+03 pdb=" N PRO A 280 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 193 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C GLU A 193 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU A 193 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 194 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 411 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C SER A 411 " 0.029 2.00e-02 2.50e+03 pdb=" O SER A 411 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 412 " -0.010 2.00e-02 2.50e+03 ... (remaining 990 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 591 2.74 - 3.28: 5984 3.28 - 3.82: 8827 3.82 - 4.36: 11087 4.36 - 4.90: 18709 Nonbonded interactions: 45198 Sorted by model distance: nonbonded pdb=" O SER A 458 " pdb=" OG SER A 458 " model vdw 2.201 3.040 nonbonded pdb=" O PHE A 461 " pdb=" NH2 ARG A 522 " model vdw 2.213 3.120 nonbonded pdb=" N GLU A 473 " pdb=" OE1 GLU A 473 " model vdw 2.216 3.120 nonbonded pdb=" O PHE A 50 " pdb=" NE2 GLN A 54 " model vdw 2.232 3.120 nonbonded pdb=" CD2 LEU A 438 " pdb=" OE1 GLU A 451 " model vdw 2.278 3.460 ... (remaining 45193 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.120 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.460 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 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 0.032 5856 Z= 0.241 Angle : 0.918 13.208 7920 Z= 0.621 Chirality : 0.057 0.488 911 Planarity : 0.003 0.037 993 Dihedral : 17.029 88.204 2102 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.28 % Allowed : 10.62 % Favored : 89.09 % Rotamer: Outliers : 8.60 % Allowed : 16.69 % Favored : 74.71 % Cbeta Deviations : 0.14 % 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: -4.65 (0.25), residues: 706 helix: -2.68 (0.21), residues: 412 sheet: None (None), residues: 0 loop : -3.61 (0.29), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 387 TYR 0.009 0.001 TYR A 82 PHE 0.011 0.001 PHE A 413 TRP 0.012 0.002 TRP B 200 HIS 0.002 0.001 HIS A 46 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 5856) covalent geometry : angle 0.91771 ( 7920) hydrogen bonds : bond 0.23533 ( 248) hydrogen bonds : angle 8.55749 ( 738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 116 time to evaluate : 0.214 Fit side-chains revert: symmetry clash REVERT: A 146 LYS cc_start: 0.7400 (pttt) cc_final: 0.7088 (mtmm) REVERT: A 300 TYR cc_start: 0.7788 (OUTLIER) cc_final: 0.6979 (m-10) REVERT: A 451 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6616 (tt0) REVERT: A 507 GLU cc_start: 0.7164 (mp0) cc_final: 0.6827 (mp0) REVERT: A 508 GLN cc_start: 0.7407 (OUTLIER) cc_final: 0.7159 (pt0) REVERT: A 545 MET cc_start: 0.7802 (mtp) cc_final: 0.7541 (mtp) outliers start: 52 outliers final: 29 residues processed: 157 average time/residue: 0.0752 time to fit residues: 15.3949 Evaluate side-chains 121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 89 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 440 GLU Chi-restraints excluded: chain A residue 451 GLU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 489 LEU Chi-restraints excluded: chain A residue 497 ILE Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 511 MET Chi-restraints excluded: chain A residue 523 ARG Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 27 optimal weight: 0.0020 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 46 HIS A 90 ASN A 94 ASN A 134 GLN A 227 GLN ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 345 GLN A 383 GLN A 495 HIS B 201 HIS B 206 ASN B 211 GLN B 277 ASN ** B 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 389 GLN B 407 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.177747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.150070 restraints weight = 7465.391| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 1.80 r_work: 0.3780 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3651 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5856 Z= 0.140 Angle : 0.619 8.713 7920 Z= 0.316 Chirality : 0.041 0.164 911 Planarity : 0.004 0.050 993 Dihedral : 8.775 55.234 837 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.46 % Allowed : 18.35 % Favored : 77.19 % 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: -2.86 (0.28), residues: 706 helix: -1.06 (0.24), residues: 435 sheet: None (None), residues: 0 loop : -3.27 (0.30), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 186 TYR 0.026 0.002 TYR A 257 PHE 0.013 0.002 PHE B 348 TRP 0.013 0.002 TRP A 240 HIS 0.008 0.001 HIS A 495 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5856) covalent geometry : angle 0.61936 ( 7920) hydrogen bonds : bond 0.04077 ( 248) hydrogen bonds : angle 4.68107 ( 738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8369 (tp40) cc_final: 0.8146 (mm-40) REVERT: A 262 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5688 (tt0) REVERT: A 447 SER cc_start: 0.7451 (m) cc_final: 0.6970 (t) REVERT: A 516 GLU cc_start: 0.7784 (tm-30) cc_final: 0.7487 (tt0) REVERT: A 545 MET cc_start: 0.7861 (mtp) cc_final: 0.7561 (mtp) outliers start: 27 outliers final: 16 residues processed: 135 average time/residue: 0.0668 time to fit residues: 12.0119 Evaluate side-chains 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 238 GLU Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 506 LYS Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 41 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.0020 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.0870 overall best weight: 0.3566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 339 ASN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.180698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.153773 restraints weight = 7358.154| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 1.79 r_work: 0.3804 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3677 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5856 Z= 0.106 Angle : 0.555 8.857 7920 Z= 0.275 Chirality : 0.039 0.128 911 Planarity : 0.004 0.043 993 Dihedral : 6.561 53.549 794 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.14 % Allowed : 19.83 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.67 (0.31), residues: 706 helix: -0.10 (0.26), residues: 438 sheet: None (None), residues: 0 loop : -2.85 (0.32), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.016 0.001 TYR A 20 PHE 0.014 0.001 PHE B 396 TRP 0.012 0.002 TRP B 200 HIS 0.004 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00228 ( 5856) covalent geometry : angle 0.55473 ( 7920) hydrogen bonds : bond 0.03341 ( 248) hydrogen bonds : angle 4.02289 ( 738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.226 Fit side-chains REVERT: A 227 GLN cc_start: 0.8320 (tp40) cc_final: 0.8098 (mm-40) REVERT: A 262 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6035 (tt0) REVERT: A 363 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7688 (tt) REVERT: A 447 SER cc_start: 0.7775 (m) cc_final: 0.7307 (t) REVERT: B 369 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8467 (pp) REVERT: B 450 ILE cc_start: 0.7318 (mp) cc_final: 0.6774 (mp) outliers start: 19 outliers final: 12 residues processed: 126 average time/residue: 0.0678 time to fit residues: 11.3132 Evaluate side-chains 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 276 LEU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 369 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 23 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.176572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.149132 restraints weight = 7405.180| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.77 r_work: 0.3750 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3623 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5856 Z= 0.146 Angle : 0.613 14.916 7920 Z= 0.295 Chirality : 0.041 0.125 911 Planarity : 0.004 0.045 993 Dihedral : 5.691 50.352 784 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.97 % Allowed : 20.17 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.31), residues: 706 helix: 0.14 (0.26), residues: 437 sheet: None (None), residues: 0 loop : -2.65 (0.33), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 387 TYR 0.020 0.002 TYR B 432 PHE 0.016 0.002 PHE B 348 TRP 0.010 0.002 TRP A 240 HIS 0.003 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5856) covalent geometry : angle 0.61296 ( 7920) hydrogen bonds : bond 0.03566 ( 248) hydrogen bonds : angle 4.01175 ( 738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.228 Fit side-chains revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8443 (tp40) cc_final: 0.8230 (mm-40) REVERT: A 262 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5909 (tt0) REVERT: A 363 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7794 (tt) REVERT: A 441 ASN cc_start: 0.6951 (m-40) cc_final: 0.6011 (m-40) REVERT: A 447 SER cc_start: 0.7523 (m) cc_final: 0.7135 (t) REVERT: B 369 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8474 (pp) REVERT: B 450 ILE cc_start: 0.7326 (mp) cc_final: 0.6786 (mp) outliers start: 24 outliers final: 15 residues processed: 119 average time/residue: 0.0616 time to fit residues: 10.0577 Evaluate side-chains 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 336 GLU Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 21 optimal weight: 0.0050 chunk 49 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 0.0270 chunk 69 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.6054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.178791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.150163 restraints weight = 7508.103| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.91 r_work: 0.3757 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5856 Z= 0.118 Angle : 0.590 14.926 7920 Z= 0.282 Chirality : 0.039 0.123 911 Planarity : 0.004 0.045 993 Dihedral : 5.409 48.798 782 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.47 % Allowed : 21.49 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.32), residues: 706 helix: 0.44 (0.26), residues: 434 sheet: None (None), residues: 0 loop : -2.50 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 275 TYR 0.018 0.001 TYR A 20 PHE 0.012 0.001 PHE B 307 TRP 0.012 0.002 TRP B 200 HIS 0.002 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 5856) covalent geometry : angle 0.59011 ( 7920) hydrogen bonds : bond 0.03172 ( 248) hydrogen bonds : angle 3.81260 ( 738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 262 GLU cc_start: 0.6167 (OUTLIER) cc_final: 0.5398 (tt0) REVERT: A 363 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7788 (tt) REVERT: A 441 ASN cc_start: 0.7022 (m-40) cc_final: 0.6176 (m-40) REVERT: A 447 SER cc_start: 0.7544 (m) cc_final: 0.7170 (t) REVERT: A 477 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7036 (tp) REVERT: B 369 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8457 (pp) REVERT: B 450 ILE cc_start: 0.7400 (mp) cc_final: 0.6842 (mp) outliers start: 21 outliers final: 11 residues processed: 121 average time/residue: 0.0621 time to fit residues: 10.2983 Evaluate side-chains 112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.0980 chunk 12 optimal weight: 2.9990 chunk 70 optimal weight: 0.0970 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.185604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.158975 restraints weight = 7454.299| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.71 r_work: 0.3865 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3737 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5856 Z= 0.112 Angle : 0.577 14.480 7920 Z= 0.282 Chirality : 0.039 0.123 911 Planarity : 0.004 0.045 993 Dihedral : 5.256 50.277 782 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.47 % Allowed : 21.32 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.32), residues: 706 helix: 0.62 (0.26), residues: 434 sheet: None (None), residues: 0 loop : -2.37 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 275 TYR 0.020 0.001 TYR B 432 PHE 0.011 0.001 PHE B 343 TRP 0.012 0.002 TRP B 200 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5856) covalent geometry : angle 0.57664 ( 7920) hydrogen bonds : bond 0.03111 ( 248) hydrogen bonds : angle 3.74223 ( 738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 105 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: A 262 GLU cc_start: 0.6318 (OUTLIER) cc_final: 0.5568 (tt0) REVERT: A 447 SER cc_start: 0.7526 (m) cc_final: 0.7304 (t) REVERT: A 457 LYS cc_start: 0.7296 (ptpt) cc_final: 0.7067 (pttm) REVERT: A 477 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7179 (mp) REVERT: B 369 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8456 (pp) REVERT: B 450 ILE cc_start: 0.7471 (mp) cc_final: 0.6906 (mp) outliers start: 21 outliers final: 12 residues processed: 120 average time/residue: 0.0656 time to fit residues: 10.6615 Evaluate side-chains 115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 99 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 0.0370 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.0170 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN B 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.187386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.161041 restraints weight = 7416.112| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.72 r_work: 0.3882 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5856 Z= 0.106 Angle : 0.578 15.316 7920 Z= 0.278 Chirality : 0.039 0.123 911 Planarity : 0.003 0.045 993 Dihedral : 4.767 51.209 780 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.64 % Allowed : 22.48 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.32), residues: 706 helix: 0.83 (0.26), residues: 442 sheet: None (None), residues: 0 loop : -2.29 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 275 TYR 0.016 0.001 TYR A 20 PHE 0.009 0.001 PHE B 348 TRP 0.013 0.002 TRP B 200 HIS 0.004 0.001 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 5856) covalent geometry : angle 0.57818 ( 7920) hydrogen bonds : bond 0.02907 ( 248) hydrogen bonds : angle 3.62004 ( 738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 103 time to evaluate : 0.207 Fit side-chains revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: A 262 GLU cc_start: 0.6225 (OUTLIER) cc_final: 0.5711 (tt0) REVERT: A 363 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7811 (tt) REVERT: A 447 SER cc_start: 0.7618 (m) cc_final: 0.7385 (t) REVERT: A 477 LEU cc_start: 0.7855 (tp) cc_final: 0.7464 (mp) REVERT: B 292 MET cc_start: 0.7771 (ttp) cc_final: 0.7534 (ttt) REVERT: B 369 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8477 (pp) REVERT: B 450 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.6842 (mp) outliers start: 22 outliers final: 14 residues processed: 119 average time/residue: 0.0645 time to fit residues: 10.3041 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 95 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 54 optimal weight: 6.9990 chunk 50 optimal weight: 0.0370 chunk 69 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.0980 chunk 44 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 60 optimal weight: 0.0270 chunk 14 optimal weight: 0.0000 overall best weight: 0.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 342 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.188723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.162255 restraints weight = 7335.254| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 1.73 r_work: 0.3909 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3784 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5856 Z= 0.095 Angle : 0.566 14.989 7920 Z= 0.271 Chirality : 0.038 0.121 911 Planarity : 0.003 0.045 993 Dihedral : 4.514 52.860 778 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.98 % Allowed : 22.31 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.33), residues: 706 helix: 1.06 (0.26), residues: 438 sheet: None (None), residues: 0 loop : -2.26 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 387 TYR 0.019 0.001 TYR B 432 PHE 0.009 0.001 PHE A 214 TRP 0.013 0.002 TRP B 200 HIS 0.002 0.000 HIS B 342 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 5856) covalent geometry : angle 0.56572 ( 7920) hydrogen bonds : bond 0.02684 ( 248) hydrogen bonds : angle 3.53019 ( 738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7756 (OUTLIER) cc_final: 0.7392 (m-80) REVERT: A 262 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5717 (tt0) REVERT: A 363 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7789 (tt) REVERT: A 447 SER cc_start: 0.7565 (m) cc_final: 0.6935 (t) REVERT: A 477 LEU cc_start: 0.7745 (tp) cc_final: 0.7332 (mp) REVERT: A 545 MET cc_start: 0.7474 (mtp) cc_final: 0.7111 (mtm) REVERT: B 292 MET cc_start: 0.7869 (ttp) cc_final: 0.7652 (ttt) REVERT: B 369 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8492 (pp) REVERT: B 450 ILE cc_start: 0.7319 (OUTLIER) cc_final: 0.6774 (mp) outliers start: 18 outliers final: 11 residues processed: 116 average time/residue: 0.0681 time to fit residues: 10.4713 Evaluate side-chains 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 112 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 15 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 0.1980 chunk 58 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 12 optimal weight: 0.0040 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 50 optimal weight: 0.0870 overall best weight: 0.2570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.188871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.162487 restraints weight = 7287.397| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.70 r_work: 0.3905 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3781 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5856 Z= 0.096 Angle : 0.570 14.660 7920 Z= 0.273 Chirality : 0.039 0.134 911 Planarity : 0.003 0.045 993 Dihedral : 4.431 51.886 776 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.31 % Allowed : 22.64 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.33), residues: 706 helix: 1.16 (0.26), residues: 438 sheet: None (None), residues: 0 loop : -2.19 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 387 TYR 0.015 0.001 TYR A 20 PHE 0.015 0.001 PHE A 272 TRP 0.012 0.002 TRP B 200 HIS 0.004 0.000 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 5856) covalent geometry : angle 0.57016 ( 7920) hydrogen bonds : bond 0.02695 ( 248) hydrogen bonds : angle 3.54416 ( 738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 104 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7373 (m-80) REVERT: A 262 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5993 (tm-30) REVERT: A 363 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7746 (tt) REVERT: A 447 SER cc_start: 0.7696 (m) cc_final: 0.7244 (t) REVERT: A 477 LEU cc_start: 0.7711 (tp) cc_final: 0.7316 (mp) REVERT: A 545 MET cc_start: 0.7509 (mtp) cc_final: 0.7094 (mtm) REVERT: B 292 MET cc_start: 0.7922 (ttp) cc_final: 0.7713 (ttt) REVERT: B 369 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8439 (pp) REVERT: B 450 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.6787 (mp) outliers start: 20 outliers final: 11 residues processed: 118 average time/residue: 0.0707 time to fit residues: 11.0770 Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 64 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 HIS A 261 HIS ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN B 354 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.184848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.157779 restraints weight = 7535.243| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.76 r_work: 0.3850 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5856 Z= 0.143 Angle : 0.629 15.899 7920 Z= 0.303 Chirality : 0.041 0.127 911 Planarity : 0.004 0.043 993 Dihedral : 4.730 56.817 776 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.31 % Allowed : 22.31 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.32), residues: 706 helix: 0.95 (0.26), residues: 438 sheet: None (None), residues: 0 loop : -2.24 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 387 TYR 0.020 0.002 TYR A 20 PHE 0.017 0.002 PHE B 348 TRP 0.008 0.002 TRP A 240 HIS 0.004 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 5856) covalent geometry : angle 0.62918 ( 7920) hydrogen bonds : bond 0.03307 ( 248) hydrogen bonds : angle 3.78872 ( 738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1412 Ramachandran restraints generated. 706 Oldfield, 0 Emsley, 706 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: A 262 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5778 (tm-30) REVERT: A 363 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7808 (tt) REVERT: A 477 LEU cc_start: 0.7703 (tp) cc_final: 0.7315 (mp) REVERT: A 545 MET cc_start: 0.7542 (mtp) cc_final: 0.7189 (mtm) REVERT: B 369 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8512 (pp) REVERT: B 450 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.6869 (mp) outliers start: 20 outliers final: 13 residues processed: 111 average time/residue: 0.0675 time to fit residues: 10.1213 Evaluate side-chains 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 118 PHE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 277 SER Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 361 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 277 ASN Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 450 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 35 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.185428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.158351 restraints weight = 7420.559| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.75 r_work: 0.3858 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5856 Z= 0.115 Angle : 0.603 15.591 7920 Z= 0.290 Chirality : 0.040 0.120 911 Planarity : 0.004 0.043 993 Dihedral : 4.675 55.854 776 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.52 % Favored : 93.48 % Rotamer: Outliers : 2.81 % Allowed : 22.98 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.32), residues: 706 helix: 1.00 (0.26), residues: 440 sheet: None (None), residues: 0 loop : -2.17 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 387 TYR 0.018 0.001 TYR A 20 PHE 0.013 0.001 PHE A 55 TRP 0.009 0.001 TRP B 200 HIS 0.010 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 5856) covalent geometry : angle 0.60255 ( 7920) hydrogen bonds : bond 0.03018 ( 248) hydrogen bonds : angle 3.71565 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1543.17 seconds wall clock time: 27 minutes 9.08 seconds (1629.08 seconds total)