Starting phenix.real_space_refine on Thu Mar 6 09:33:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sde_23517/03_2025/7sde_23517_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sde_23517/03_2025/7sde_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sde_23517/03_2025/7sde_23517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sde_23517/03_2025/7sde_23517.map" model { file = "/net/cci-nas-00/data/ceres_data/7sde_23517/03_2025/7sde_23517_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sde_23517/03_2025/7sde_23517_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 2, 'ASP:plan': 6, 'TYR:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3} 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: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 13} Unresolved non-hydrogen planarities: 119 Time building chain proxies: 3.70, per 1000 atoms: 0.65 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: 1.24 Conformation dependent library (CDL) restraints added in 622.8 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: 0.56 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: 1.36 Time building geometry restraints manager: 1.51 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: 0.010 Normalize map: mean=0, sd=1: 1.440 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.510 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.980 ------------------------------------------------------------------------------- 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= 0.239 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.012 0.002 TRP B 200 HIS 0.002 0.001 HIS A 46 PHE 0.011 0.001 PHE A 413 TYR 0.009 0.001 TYR A 82 ARG 0.001 0.000 ARG A 387 *********************** 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 : 0.719 Fit side-chains revert: symmetry clash REVERT: A 146 LYS cc_start: 0.7399 (pttt) cc_final: 0.7085 (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: 0.7163 (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: 0.7542 (mtp) outliers start: 52 outliers final: 29 residues processed: 157 average time/residue: 0.1805 time to fit residues: 36.4777 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 : 0.691 ------------------------------------------------------------------------------- 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 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 28 optimal weight: 0.0070 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.0010 chunk 33 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 overall best weight: 0.2782 ------------------------------------------------------------------------------- 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 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 GLN B 389 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.181188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.153286 restraints weight = 7352.557| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 1.88 r_work: 0.3810 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3679 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2178 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= 0.163 Angle : 0.598 8.484 7920 Z= 0.304 Chirality : 0.040 0.170 911 Planarity : 0.004 0.051 993 Dihedral : 8.546 58.944 837 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 4.13 % Allowed : 17.52 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.29), residues: 706 helix: -0.91 (0.24), residues: 431 sheet: None (None), residues: 0 loop : -3.18 (0.30), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 200 HIS 0.008 0.001 HIS A 495 PHE 0.012 0.001 PHE A 55 TYR 0.027 0.002 TYR A 257 ARG 0.007 0.000 ARG A 186 *********************** 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 146 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.650 Fit side-chains REVERT: A 51 LEU cc_start: 0.7204 (OUTLIER) cc_final: 0.6986 (mm) REVERT: A 227 GLN cc_start: 0.8343 (tp40) cc_final: 0.8103 (mm-40) REVERT: A 441 ASN cc_start: 0.6604 (m-40) cc_final: 0.3652 (m110) REVERT: A 447 SER cc_start: 0.7420 (m) cc_final: 0.7121 (t) REVERT: A 451 GLU cc_start: 0.7601 (tt0) cc_final: 0.7269 (mt-10) REVERT: A 516 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7514 (tt0) REVERT: A 545 MET cc_start: 0.7972 (mtp) cc_final: 0.7740 (mtp) REVERT: B 389 GLN cc_start: 0.7541 (mt0) cc_final: 0.7317 (mt0) outliers start: 25 outliers final: 11 residues processed: 140 average time/residue: 0.1671 time to fit residues: 31.4751 Evaluate side-chains 112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 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 281 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 46 optimal weight: 9.9990 chunk 52 optimal weight: 0.0040 chunk 6 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 chunk 38 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 0.3668 ------------------------------------------------------------------------------- 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 339 ASN B 407 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.180721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.153849 restraints weight = 7399.959| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 1.80 r_work: 0.3799 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5856 Z= 0.146 Angle : 0.545 8.608 7920 Z= 0.272 Chirality : 0.039 0.132 911 Planarity : 0.004 0.042 993 Dihedral : 5.773 50.578 788 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 2.31 % Allowed : 20.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.31), residues: 706 helix: -0.01 (0.26), residues: 438 sheet: None (None), residues: 0 loop : -2.87 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 240 HIS 0.004 0.001 HIS A 261 PHE 0.018 0.001 PHE B 396 TYR 0.018 0.001 TYR A 20 ARG 0.002 0.000 ARG B 304 *********************** 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 128 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.705 Fit side-chains revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8300 (tp40) cc_final: 0.8082 (mm-40) REVERT: A 363 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7713 (tt) REVERT: A 447 SER cc_start: 0.7447 (m) cc_final: 0.6809 (t) REVERT: A 477 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6975 (tp) REVERT: B 369 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8491 (pp) REVERT: B 450 ILE cc_start: 0.7400 (mp) cc_final: 0.6881 (mp) outliers start: 14 outliers final: 8 residues processed: 123 average time/residue: 0.1715 time to fit residues: 28.0222 Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 276 LEU 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 35 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.0070 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.179652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.152168 restraints weight = 7564.571| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 1.80 r_work: 0.3800 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3672 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5856 Z= 0.164 Angle : 0.573 14.963 7920 Z= 0.277 Chirality : 0.040 0.123 911 Planarity : 0.004 0.044 993 Dihedral : 5.128 50.329 782 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 2.98 % Allowed : 20.83 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.31), residues: 706 helix: 0.37 (0.26), residues: 432 sheet: None (None), residues: 0 loop : -2.64 (0.32), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 240 HIS 0.003 0.001 HIS A 261 PHE 0.011 0.001 PHE B 348 TYR 0.019 0.001 TYR A 20 ARG 0.005 0.000 ARG A 387 *********************** 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 125 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8304 (tp40) cc_final: 0.8097 (mm-40) REVERT: A 447 SER cc_start: 0.7769 (m) cc_final: 0.7319 (t) REVERT: A 477 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7067 (tp) REVERT: B 339 ASN cc_start: 0.7731 (t0) cc_final: 0.5947 (m110) REVERT: B 369 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8470 (pp) REVERT: B 450 ILE cc_start: 0.7472 (mp) cc_final: 0.6900 (mp) outliers start: 18 outliers final: 11 residues processed: 122 average time/residue: 0.1567 time to fit residues: 26.0076 Evaluate side-chains 107 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 277 SER Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 318 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 chunk 6 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 389 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.179261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.152182 restraints weight = 7378.610| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 1.76 r_work: 0.3791 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3668 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5856 Z= 0.167 Angle : 0.568 14.950 7920 Z= 0.275 Chirality : 0.039 0.120 911 Planarity : 0.004 0.044 993 Dihedral : 4.925 47.649 780 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.64 % Allowed : 20.66 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.32), residues: 706 helix: 0.58 (0.26), residues: 434 sheet: None (None), residues: 0 loop : -2.52 (0.33), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 200 HIS 0.003 0.001 HIS A 261 PHE 0.012 0.001 PHE B 307 TYR 0.019 0.001 TYR A 20 ARG 0.005 0.000 ARG A 275 *********************** 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 132 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLN cc_start: 0.8334 (tp40) cc_final: 0.8133 (mm-40) REVERT: A 300 TYR cc_start: 0.7810 (OUTLIER) cc_final: 0.7410 (m-10) REVERT: A 363 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7754 (tt) REVERT: A 447 SER cc_start: 0.7549 (m) cc_final: 0.7315 (t) REVERT: A 477 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7107 (mp) REVERT: A 545 MET cc_start: 0.7613 (mtp) cc_final: 0.7245 (mtp) REVERT: B 336 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7921 (mt-10) REVERT: B 369 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8465 (pp) REVERT: B 450 ILE cc_start: 0.7433 (mp) cc_final: 0.6850 (mp) outliers start: 22 outliers final: 12 residues processed: 125 average time/residue: 0.1659 time to fit residues: 27.5065 Evaluate side-chains 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 300 TYR Chi-restraints excluded: chain A residue 304 ASN 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 477 LEU Chi-restraints excluded: chain A residue 531 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 336 GLU 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 36 optimal weight: 0.5980 chunk 63 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4279 r_free = 0.4279 target = 0.184238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.157236 restraints weight = 7424.658| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 1.72 r_work: 0.3852 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5856 Z= 0.206 Angle : 0.599 16.212 7920 Z= 0.291 Chirality : 0.041 0.121 911 Planarity : 0.004 0.045 993 Dihedral : 4.979 45.769 780 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.47 % Allowed : 20.99 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.32), residues: 706 helix: 0.65 (0.26), residues: 434 sheet: None (None), residues: 0 loop : -2.44 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 200 HIS 0.003 0.001 HIS A 261 PHE 0.015 0.002 PHE B 348 TYR 0.021 0.002 TYR B 432 ARG 0.003 0.000 ARG A 275 *********************** 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 127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 TYR cc_start: 0.7770 (OUTLIER) cc_final: 0.7414 (m-10) REVERT: A 363 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7856 (tt) REVERT: A 447 SER cc_start: 0.7570 (m) cc_final: 0.7336 (t) REVERT: A 457 LYS cc_start: 0.7212 (ptpt) cc_final: 0.6880 (pttm) REVERT: A 477 LEU cc_start: 0.7617 (OUTLIER) cc_final: 0.7204 (mp) REVERT: B 369 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8461 (pp) REVERT: B 450 ILE cc_start: 0.7487 (mp) cc_final: 0.6921 (mp) outliers start: 21 outliers final: 11 residues processed: 120 average time/residue: 0.1634 time to fit residues: 26.0192 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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 300 TYR 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 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 18 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 354 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 = 0.4250 r_free = 0.4250 target = 0.181240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.154007 restraints weight = 7496.323| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.73 r_work: 0.3811 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5856 Z= 0.260 Angle : 0.642 14.814 7920 Z= 0.315 Chirality : 0.042 0.123 911 Planarity : 0.004 0.045 993 Dihedral : 4.942 40.267 778 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 3.80 % Allowed : 21.32 % Favored : 74.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.32), residues: 706 helix: 0.55 (0.26), residues: 440 sheet: None (None), residues: 0 loop : -2.43 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 200 HIS 0.003 0.001 HIS A 261 PHE 0.020 0.002 PHE B 348 TYR 0.021 0.002 TYR A 20 ARG 0.002 0.000 ARG A 275 *********************** 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 117 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7156 (m-80) REVERT: A 300 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7473 (m-10) REVERT: A 363 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7883 (tt) REVERT: A 477 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7261 (mp) REVERT: A 497 ILE cc_start: 0.7178 (OUTLIER) cc_final: 0.6848 (tp) REVERT: A 545 MET cc_start: 0.7612 (mtp) cc_final: 0.7207 (mtm) REVERT: B 369 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8480 (pp) REVERT: B 450 ILE cc_start: 0.7392 (mp) cc_final: 0.6853 (mp) outliers start: 23 outliers final: 12 residues processed: 110 average time/residue: 0.2241 time to fit residues: 33.6441 Evaluate side-chains 106 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 300 TYR 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 497 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 43 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 40 optimal weight: 7.9990 chunk 1 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4275 r_free = 0.4275 target = 0.183536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.157002 restraints weight = 7371.189| |-----------------------------------------------------------------------------| r_work (start): 0.3970 rms_B_bonded: 1.70 r_work: 0.3854 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3724 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3088 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= 0.191 Angle : 0.593 14.355 7920 Z= 0.290 Chirality : 0.040 0.123 911 Planarity : 0.004 0.046 993 Dihedral : 4.733 35.361 778 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.32), residues: 706 helix: 0.81 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -2.37 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 200 HIS 0.003 0.001 HIS A 261 PHE 0.016 0.001 PHE A 272 TYR 0.020 0.001 TYR B 432 ARG 0.006 0.000 ARG A 387 *********************** 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 119 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 99 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7856 (tt) REVERT: A 477 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7276 (mp) REVERT: A 545 MET cc_start: 0.7549 (mtp) cc_final: 0.7142 (mtm) REVERT: B 369 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8488 (pp) REVERT: B 450 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.6846 (mp) outliers start: 20 outliers final: 14 residues processed: 112 average time/residue: 0.1727 time to fit residues: 25.7824 Evaluate side-chains 112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.683 ------------------------------------------------------------------------------- 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 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 453 ILE 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 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 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 18 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 31 optimal weight: 0.0060 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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** B 342 HIS B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.184094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157657 restraints weight = 7407.014| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.70 r_work: 0.3847 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5856 Z= 0.181 Angle : 0.598 13.828 7920 Z= 0.292 Chirality : 0.040 0.120 911 Planarity : 0.004 0.047 993 Dihedral : 4.586 32.968 778 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.47 % Allowed : 22.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.32), residues: 706 helix: 0.90 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -2.30 (0.35), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 200 HIS 0.002 0.001 HIS A 261 PHE 0.015 0.001 PHE A 272 TYR 0.017 0.001 TYR A 20 ARG 0.005 0.000 ARG A 387 *********************** 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 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: A 300 TYR cc_start: 0.7715 (OUTLIER) cc_final: 0.7360 (m-10) REVERT: A 363 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7837 (tt) REVERT: A 477 LEU cc_start: 0.7791 (tp) cc_final: 0.7397 (mp) REVERT: A 545 MET cc_start: 0.7555 (mtp) cc_final: 0.7189 (mtm) REVERT: B 369 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8481 (pp) REVERT: B 450 ILE cc_start: 0.7467 (OUTLIER) cc_final: 0.6914 (mp) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 0.2320 time to fit residues: 33.8951 Evaluate side-chains 112 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 300 TYR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 336 ILE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 50 optimal weight: 0.0010 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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** 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 = 0.4293 r_free = 0.4293 target = 0.185173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.158793 restraints weight = 7508.400| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 1.72 r_work: 0.3862 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5856 Z= 0.171 Angle : 0.608 15.972 7920 Z= 0.292 Chirality : 0.040 0.194 911 Planarity : 0.004 0.047 993 Dihedral : 4.341 32.662 776 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 3.14 % Allowed : 22.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.33), residues: 706 helix: 0.99 (0.26), residues: 436 sheet: None (None), residues: 0 loop : -2.21 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 200 HIS 0.002 0.001 HIS A 261 PHE 0.020 0.001 PHE A 272 TYR 0.019 0.001 TYR B 432 ARG 0.005 0.000 ARG A 387 ********************** 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: 19 poor density : 98 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 PHE cc_start: 0.7843 (OUTLIER) cc_final: 0.7252 (m-80) REVERT: A 300 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: A 363 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7815 (tt) REVERT: A 477 LEU cc_start: 0.7714 (tp) cc_final: 0.7354 (mp) REVERT: A 545 MET cc_start: 0.7520 (mtp) cc_final: 0.7162 (mtm) REVERT: B 369 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8460 (pp) REVERT: B 450 ILE cc_start: 0.7466 (OUTLIER) cc_final: 0.6915 (mp) outliers start: 19 outliers final: 14 residues processed: 110 average time/residue: 0.1734 time to fit residues: 25.2338 Evaluate side-chains 115 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 300 TYR Chi-restraints excluded: chain A residue 304 ASN Chi-restraints excluded: chain A residue 336 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 71 random chunks: chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 0.2980 chunk 64 optimal weight: 0.0170 chunk 12 optimal weight: 0.0040 chunk 10 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 overall best weight: 0.3030 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.187042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.160985 restraints weight = 7452.171| |-----------------------------------------------------------------------------| r_work (start): 0.4009 rms_B_bonded: 1.72 r_work: 0.3891 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3762 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3448 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= 0.143 Angle : 0.595 15.602 7920 Z= 0.285 Chirality : 0.039 0.186 911 Planarity : 0.003 0.046 993 Dihedral : 4.190 31.857 776 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 3.14 % Allowed : 23.47 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.33), residues: 706 helix: 1.12 (0.26), residues: 437 sheet: None (None), residues: 0 loop : -2.22 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 200 HIS 0.002 0.000 HIS A 261 PHE 0.021 0.001 PHE A 272 TYR 0.015 0.001 TYR A 20 ARG 0.005 0.000 ARG A 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3384.76 seconds wall clock time: 59 minutes 54.89 seconds (3594.89 seconds total)