Starting phenix.real_space_refine on Tue Mar 11 20:01:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j52_61140/03_2025/9j52_61140.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j52_61140/03_2025/9j52_61140.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j52_61140/03_2025/9j52_61140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j52_61140/03_2025/9j52_61140.map" model { file = "/net/cci-nas-00/data/ceres_data/9j52_61140/03_2025/9j52_61140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j52_61140/03_2025/9j52_61140.cif" } resolution = 3.1 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= -0.001 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 30 5.16 5 C 4462 2.51 5 N 1024 2.21 5 O 1072 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6593 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3186 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "B" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3186 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 14, 'TRANS': 367} Chain breaks: 1 Chain: "A" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 113 Unusual residues: {'PC1': 2, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'PC1': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.50, per 1000 atoms: 0.68 Number of scatterers: 6593 At special positions: 0 Unit cell: (123.05, 67.41, 75.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 5 15.00 O 1072 8.00 N 1024 7.00 C 4462 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: 1.69 Conformation dependent library (CDL) restraints added in 898.7 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 80.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 230 through 258 Processing helix chain 'A' and resid 265 through 295 removed outlier: 4.798A pdb=" N GLY A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N GLY A 275 " --> pdb=" O ILE A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 303 removed outlier: 3.564A pdb=" N ILE A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 336 Processing helix chain 'A' and resid 337 through 340 Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 367 through 384 removed outlier: 4.538A pdb=" N ALA A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 402 Processing helix chain 'A' and resid 403 through 420 removed outlier: 4.324A pdb=" N LEU A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.742A pdb=" N VAL A 451 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 471 removed outlier: 3.978A pdb=" N ARG A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN A 462 " --> pdb=" O LEU A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 503 removed outlier: 4.247A pdb=" N HIS A 476 " --> pdb=" O ARG A 472 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ASN A 479 " --> pdb=" O PRO A 475 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 532 removed outlier: 4.179A pdb=" N VAL A 509 " --> pdb=" O SER A 505 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N PHE A 517 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 529 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 532 " --> pdb=" O TRP A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 583 removed outlier: 3.750A pdb=" N TYR A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL A 567 " --> pdb=" O ILE A 563 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN A 576 " --> pdb=" O ALA A 572 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A 581 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 618 Proline residue: A 598 - end of helix removed outlier: 3.767A pdb=" N PHE A 609 " --> pdb=" O PHE A 605 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHE A 610 " --> pdb=" O VAL A 606 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU A 613 " --> pdb=" O PHE A 609 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 265 through 296 removed outlier: 4.371A pdb=" N GLY B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.592A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 361 removed outlier: 3.930A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 384 through 387 Processing helix chain 'B' and resid 390 through 419 removed outlier: 3.580A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N VAL B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 406 " --> pdb=" O SER B 402 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 Processing helix chain 'B' and resid 453 through 462 removed outlier: 3.816A pdb=" N ARG B 459 " --> pdb=" O PRO B 455 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN B 462 " --> pdb=" O LEU B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 471 Processing helix chain 'B' and resid 472 through 503 removed outlier: 4.193A pdb=" N HIS B 476 " --> pdb=" O ARG B 472 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ASN B 479 " --> pdb=" O PRO B 475 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N PHE B 487 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 532 removed outlier: 3.733A pdb=" N LEU B 513 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU B 526 " --> pdb=" O SER B 522 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP B 528 " --> pdb=" O TYR B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 580 removed outlier: 4.330A pdb=" N TYR B 559 " --> pdb=" O GLN B 555 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE B 571 " --> pdb=" O VAL B 567 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 578 " --> pdb=" O THR B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 618 Proline residue: B 598 - end of helix removed outlier: 3.805A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 623 removed outlier: 3.933A pdb=" N GLU B 622 " --> pdb=" O ASN B 619 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE B 623 " --> pdb=" O CYS B 620 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 619 through 623' 430 hydrogen bonds defined for protein. 1284 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: 1.79 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 992 1.32 - 1.44: 2062 1.44 - 1.57: 3694 1.57 - 1.69: 10 1.69 - 1.81: 42 Bond restraints: 6800 Sorted by residual: bond pdb=" C ILE A 454 " pdb=" N PRO A 455 " ideal model delta sigma weight residual 1.335 1.348 -0.014 1.19e-02 7.06e+03 1.33e+00 bond pdb=" C ALA A 337 " pdb=" N PRO A 338 " ideal model delta sigma weight residual 1.334 1.357 -0.023 2.34e-02 1.83e+03 9.86e-01 bond pdb=" CA ILE B 342 " pdb=" C ILE B 342 " ideal model delta sigma weight residual 1.526 1.519 0.007 7.90e-03 1.60e+04 8.82e-01 bond pdb=" CA LEU B 259 " pdb=" C LEU B 259 " ideal model delta sigma weight residual 1.532 1.524 0.009 9.60e-03 1.09e+04 8.53e-01 bond pdb=" CG GLN B 399 " pdb=" CD GLN B 399 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.00e-01 ... (remaining 6795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 8908 1.29 - 2.59: 244 2.59 - 3.88: 35 3.88 - 5.18: 14 5.18 - 6.47: 7 Bond angle restraints: 9208 Sorted by residual: angle pdb=" C LYS A 422 " pdb=" N TRP A 423 " pdb=" CA TRP A 423 " ideal model delta sigma weight residual 121.54 127.40 -5.86 1.91e+00 2.74e-01 9.41e+00 angle pdb=" C CYS B 453 " pdb=" N ILE B 454 " pdb=" CA ILE B 454 " ideal model delta sigma weight residual 120.33 122.47 -2.14 8.00e-01 1.56e+00 7.17e+00 angle pdb=" C VAL B 447 " pdb=" N ARG B 448 " pdb=" CA ARG B 448 " ideal model delta sigma weight residual 120.38 124.01 -3.63 1.37e+00 5.33e-01 7.01e+00 angle pdb=" N LEU B 464 " pdb=" CA LEU B 464 " pdb=" C LEU B 464 " ideal model delta sigma weight residual 113.12 109.83 3.29 1.25e+00 6.40e-01 6.91e+00 angle pdb=" C ILE B 454 " pdb=" CA ILE B 454 " pdb=" CB ILE B 454 " ideal model delta sigma weight residual 114.00 110.92 3.08 1.31e+00 5.83e-01 5.54e+00 ... (remaining 9203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 3600 17.43 - 34.86: 244 34.86 - 52.30: 58 52.30 - 69.73: 13 69.73 - 87.16: 3 Dihedral angle restraints: 3918 sinusoidal: 1668 harmonic: 2250 Sorted by residual: dihedral pdb=" CA CYS B 463 " pdb=" C CYS B 463 " pdb=" N LEU B 464 " pdb=" CA LEU B 464 " ideal model delta harmonic sigma weight residual 180.00 160.68 19.32 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA GLU B 260 " pdb=" C GLU B 260 " pdb=" N THR B 261 " pdb=" CA THR B 261 " ideal model delta harmonic sigma weight residual 180.00 -161.96 -18.04 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA SER A 578 " pdb=" C SER A 578 " pdb=" N ILE A 579 " pdb=" CA ILE A 579 " ideal model delta harmonic sigma weight residual -180.00 -163.24 -16.76 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 3915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 500 0.025 - 0.050: 307 0.050 - 0.075: 119 0.075 - 0.099: 40 0.099 - 0.124: 20 Chirality restraints: 986 Sorted by residual: chirality pdb=" CA ILE B 342 " pdb=" N ILE B 342 " pdb=" C ILE B 342 " pdb=" CB ILE B 342 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA TRP B 266 " pdb=" N TRP B 266 " pdb=" C TRP B 266 " pdb=" CB TRP B 266 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA PRO B 554 " pdb=" N PRO B 554 " pdb=" C PRO B 554 " pdb=" CB PRO B 554 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 983 not shown) Planarity restraints: 1098 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 337 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 338 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 338 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 338 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 266 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO A 267 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 567 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C VAL A 567 " 0.024 2.00e-02 2.50e+03 pdb=" O VAL A 567 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE A 568 " -0.008 2.00e-02 2.50e+03 ... (remaining 1095 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 110 2.66 - 3.22: 6718 3.22 - 3.78: 10471 3.78 - 4.34: 14351 4.34 - 4.90: 23284 Nonbonded interactions: 54934 Sorted by model distance: nonbonded pdb=" O ILE B 271 " pdb=" OH TYR B 352 " model vdw 2.100 3.040 nonbonded pdb=" O LYS B 482 " pdb=" OG1 THR B 485 " model vdw 2.147 3.040 nonbonded pdb=" N ASN A 479 " pdb=" OD1 ASN A 479 " model vdw 2.184 3.120 nonbonded pdb=" NH1 ARG A 570 " pdb=" O2 PO4 A 803 " model vdw 2.202 3.120 nonbonded pdb=" OD2 ASP A 529 " pdb=" NH2 ARG A 570 " model vdw 2.217 3.120 ... (remaining 54929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 229 through 624 or resid 801 through 802)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.670 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 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 0.028 6800 Z= 0.247 Angle : 0.554 6.471 9208 Z= 0.307 Chirality : 0.038 0.124 986 Planarity : 0.005 0.052 1098 Dihedral : 12.860 87.159 2466 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.48 % Favored : 93.39 % Rotamer: Outliers : 2.36 % Allowed : 6.19 % Favored : 91.45 % 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: 0.50 (0.31), residues: 756 helix: 1.11 (0.22), residues: 562 sheet: None (None), residues: 0 loop : -1.95 (0.45), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 607 HIS 0.003 0.001 HIS A 476 PHE 0.016 0.001 PHE A 517 TYR 0.011 0.001 TYR B 367 ARG 0.003 0.000 ARG B 459 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.682 Fit side-chains REVERT: A 258 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7054 (mmtm) REVERT: A 270 ARG cc_start: 0.7674 (mtm180) cc_final: 0.6154 (mtp-110) REVERT: A 398 ASP cc_start: 0.8567 (m-30) cc_final: 0.8275 (m-30) REVERT: A 399 GLN cc_start: 0.8609 (mm110) cc_final: 0.8331 (mm110) REVERT: A 590 ASP cc_start: 0.8269 (m-30) cc_final: 0.7664 (m-30) REVERT: B 290 TYR cc_start: 0.8325 (t80) cc_final: 0.7902 (t80) REVERT: B 357 PHE cc_start: 0.8228 (t80) cc_final: 0.7203 (m-10) REVERT: B 364 LYS cc_start: 0.8201 (mttt) cc_final: 0.7904 (mtpt) REVERT: B 416 PHE cc_start: 0.8667 (t80) cc_final: 0.8369 (t80) REVERT: B 487 PHE cc_start: 0.7327 (m-10) cc_final: 0.6399 (t80) REVERT: B 538 ASP cc_start: 0.8741 (t70) cc_final: 0.8461 (t0) REVERT: B 555 GLN cc_start: 0.7512 (mm-40) cc_final: 0.7261 (mm-40) outliers start: 16 outliers final: 7 residues processed: 179 average time/residue: 0.1475 time to fit residues: 37.0411 Evaluate side-chains 135 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 128 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 393 ASP Chi-restraints excluded: chain A residue 394 PHE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 393 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 10.0000 chunk 57 optimal weight: 0.0970 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 38 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 0.0570 chunk 36 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 315 HIS A 387 HIS ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 544 ASN A 587 HIS B 288 ASN B 387 HIS B 399 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.187722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158585 restraints weight = 9104.795| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.37 r_work: 0.3789 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6800 Z= 0.181 Angle : 0.546 6.562 9208 Z= 0.291 Chirality : 0.040 0.132 986 Planarity : 0.005 0.054 1098 Dihedral : 11.763 75.763 1047 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.80 % Allowed : 11.06 % Favored : 86.14 % 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: 1.14 (0.31), residues: 756 helix: 1.63 (0.22), residues: 560 sheet: None (None), residues: 0 loop : -1.89 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 528 HIS 0.004 0.001 HIS A 476 PHE 0.024 0.001 PHE A 517 TYR 0.017 0.001 TYR B 496 ARG 0.004 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.775 Fit side-chains REVERT: A 258 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7225 (mmtm) REVERT: A 270 ARG cc_start: 0.7682 (mtm180) cc_final: 0.6839 (mtp-110) REVERT: A 301 LEU cc_start: 0.8396 (mt) cc_final: 0.8009 (tp) REVERT: A 323 LEU cc_start: 0.8101 (mt) cc_final: 0.7718 (mt) REVERT: A 398 ASP cc_start: 0.8560 (m-30) cc_final: 0.8196 (m-30) REVERT: B 290 TYR cc_start: 0.8304 (t80) cc_final: 0.8034 (t80) REVERT: B 352 TYR cc_start: 0.7875 (m-80) cc_final: 0.7256 (m-80) REVERT: B 357 PHE cc_start: 0.8250 (t80) cc_final: 0.7543 (m-10) REVERT: B 364 LYS cc_start: 0.8174 (mttt) cc_final: 0.7893 (mtpt) REVERT: B 408 MET cc_start: 0.8345 (mmm) cc_final: 0.8055 (mmm) REVERT: B 487 PHE cc_start: 0.7295 (m-10) cc_final: 0.6472 (t80) REVERT: B 538 ASP cc_start: 0.8862 (t70) cc_final: 0.8479 (t0) REVERT: B 549 GLU cc_start: 0.6927 (mp0) cc_final: 0.6664 (mm-30) REVERT: B 555 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7261 (mm-40) outliers start: 19 outliers final: 9 residues processed: 163 average time/residue: 0.1558 time to fit residues: 35.7713 Evaluate side-chains 144 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 564 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 587 HIS A 619 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.185765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.156862 restraints weight = 9325.962| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.38 r_work: 0.3777 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6800 Z= 0.226 Angle : 0.553 7.137 9208 Z= 0.290 Chirality : 0.040 0.143 986 Planarity : 0.005 0.053 1098 Dihedral : 11.573 74.464 1038 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.80 % Allowed : 13.27 % Favored : 83.92 % 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: 1.04 (0.31), residues: 756 helix: 1.53 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.04 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 528 HIS 0.003 0.001 HIS A 587 PHE 0.021 0.002 PHE A 517 TYR 0.016 0.001 TYR B 496 ARG 0.004 0.000 ARG A 603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.739 Fit side-chains REVERT: A 258 LYS cc_start: 0.7703 (mmtt) cc_final: 0.7294 (mmtm) REVERT: A 270 ARG cc_start: 0.7607 (mtm180) cc_final: 0.6844 (mtp180) REVERT: A 301 LEU cc_start: 0.8391 (mt) cc_final: 0.8127 (tp) REVERT: A 323 LEU cc_start: 0.8167 (mt) cc_final: 0.7833 (mt) REVERT: A 398 ASP cc_start: 0.8613 (m-30) cc_final: 0.8356 (m-30) REVERT: B 290 TYR cc_start: 0.8381 (t80) cc_final: 0.8125 (t80) REVERT: B 357 PHE cc_start: 0.8227 (t80) cc_final: 0.7498 (m-10) REVERT: B 364 LYS cc_start: 0.8175 (mttt) cc_final: 0.7918 (mtpt) REVERT: B 408 MET cc_start: 0.8392 (mmm) cc_final: 0.8071 (mmm) REVERT: B 487 PHE cc_start: 0.7371 (m-10) cc_final: 0.6504 (t80) REVERT: B 538 ASP cc_start: 0.8829 (t70) cc_final: 0.8470 (t0) REVERT: B 549 GLU cc_start: 0.7095 (mp0) cc_final: 0.6454 (mm-30) REVERT: B 555 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7345 (mm-40) outliers start: 19 outliers final: 11 residues processed: 153 average time/residue: 0.1633 time to fit residues: 34.5370 Evaluate side-chains 142 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 479 ASN Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 0.1980 chunk 58 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 7 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 288 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN A 499 HIS A 587 HIS ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.186856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.158059 restraints weight = 9313.410| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.32 r_work: 0.3790 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6800 Z= 0.195 Angle : 0.537 6.566 9208 Z= 0.283 Chirality : 0.040 0.141 986 Planarity : 0.005 0.053 1098 Dihedral : 11.346 74.754 1036 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.06 % Allowed : 15.63 % Favored : 82.30 % 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: 1.17 (0.31), residues: 756 helix: 1.64 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.07 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 528 HIS 0.006 0.001 HIS A 587 PHE 0.021 0.001 PHE A 517 TYR 0.015 0.001 TYR B 496 ARG 0.004 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 144 time to evaluate : 0.779 Fit side-chains REVERT: A 258 LYS cc_start: 0.7724 (mmtt) cc_final: 0.7318 (mmtm) REVERT: A 270 ARG cc_start: 0.7607 (mtm180) cc_final: 0.6917 (mtp180) REVERT: A 622 GLU cc_start: 0.7096 (pt0) cc_final: 0.6779 (pp20) REVERT: B 301 LEU cc_start: 0.8525 (tt) cc_final: 0.8172 (tt) REVERT: B 357 PHE cc_start: 0.8148 (t80) cc_final: 0.7541 (m-10) REVERT: B 364 LYS cc_start: 0.8158 (mttt) cc_final: 0.7918 (mtpt) REVERT: B 408 MET cc_start: 0.8370 (mmm) cc_final: 0.8026 (mmm) REVERT: B 487 PHE cc_start: 0.7310 (m-10) cc_final: 0.6507 (t80) REVERT: B 538 ASP cc_start: 0.8809 (t70) cc_final: 0.8597 (t0) REVERT: B 555 GLN cc_start: 0.7679 (mm-40) cc_final: 0.7429 (mm-40) outliers start: 14 outliers final: 10 residues processed: 147 average time/residue: 0.1621 time to fit residues: 33.1868 Evaluate side-chains 145 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 72 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 74 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 499 HIS A 587 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.187214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158563 restraints weight = 9242.484| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.31 r_work: 0.3795 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 6800 Z= 0.198 Angle : 0.535 6.311 9208 Z= 0.282 Chirality : 0.039 0.148 986 Planarity : 0.005 0.053 1098 Dihedral : 11.259 74.731 1034 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.51 % Allowed : 15.93 % Favored : 81.56 % 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: 1.21 (0.31), residues: 756 helix: 1.67 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.05 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 607 HIS 0.006 0.001 HIS A 587 PHE 0.019 0.001 PHE A 517 TYR 0.015 0.001 TYR B 496 ARG 0.004 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.684 Fit side-chains REVERT: A 258 LYS cc_start: 0.7728 (mmtt) cc_final: 0.7323 (mmtm) REVERT: A 270 ARG cc_start: 0.7585 (mtm180) cc_final: 0.6855 (mtp180) REVERT: A 622 GLU cc_start: 0.7147 (pt0) cc_final: 0.6841 (pp20) REVERT: B 301 LEU cc_start: 0.8500 (tt) cc_final: 0.8164 (tt) REVERT: B 357 PHE cc_start: 0.8163 (t80) cc_final: 0.7542 (m-10) REVERT: B 364 LYS cc_start: 0.8138 (mttt) cc_final: 0.7900 (mtpt) REVERT: B 408 MET cc_start: 0.8360 (mmm) cc_final: 0.7979 (mmm) REVERT: B 487 PHE cc_start: 0.7294 (m-10) cc_final: 0.6509 (t80) REVERT: B 508 MET cc_start: 0.6959 (mmt) cc_final: 0.6641 (mmt) REVERT: B 538 ASP cc_start: 0.8766 (t70) cc_final: 0.8384 (t0) REVERT: B 549 GLU cc_start: 0.7029 (mp0) cc_final: 0.6489 (mm-30) REVERT: B 555 GLN cc_start: 0.7678 (mm-40) cc_final: 0.7414 (mm-40) outliers start: 17 outliers final: 13 residues processed: 153 average time/residue: 0.1514 time to fit residues: 32.3100 Evaluate side-chains 152 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 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 248 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 587 HIS ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.186458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.157996 restraints weight = 9188.796| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.29 r_work: 0.3786 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 6800 Z= 0.231 Angle : 0.560 7.066 9208 Z= 0.295 Chirality : 0.040 0.157 986 Planarity : 0.005 0.053 1098 Dihedral : 11.265 74.439 1034 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.51 % Allowed : 16.52 % Favored : 80.97 % 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: 1.23 (0.31), residues: 756 helix: 1.74 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -1.99 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 607 HIS 0.006 0.001 HIS A 587 PHE 0.019 0.001 PHE A 517 TYR 0.016 0.001 TYR B 496 ARG 0.005 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.742 Fit side-chains REVERT: A 258 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7332 (mmtm) REVERT: A 270 ARG cc_start: 0.7584 (mtm180) cc_final: 0.6836 (mtp180) REVERT: A 622 GLU cc_start: 0.7181 (pt0) cc_final: 0.6870 (pp20) REVERT: B 301 LEU cc_start: 0.8502 (tt) cc_final: 0.8180 (tt) REVERT: B 357 PHE cc_start: 0.8160 (t80) cc_final: 0.7548 (m-10) REVERT: B 364 LYS cc_start: 0.8126 (mttt) cc_final: 0.7893 (mtpt) REVERT: B 408 MET cc_start: 0.8368 (mmm) cc_final: 0.7956 (mmm) REVERT: B 487 PHE cc_start: 0.7302 (m-10) cc_final: 0.6520 (t80) REVERT: B 538 ASP cc_start: 0.8739 (t70) cc_final: 0.8361 (t0) REVERT: B 549 GLU cc_start: 0.6932 (mp0) cc_final: 0.6464 (mm-30) REVERT: B 555 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7442 (mm-40) outliers start: 17 outliers final: 15 residues processed: 144 average time/residue: 0.1656 time to fit residues: 33.5882 Evaluate side-chains 150 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 355 MET Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 0.5980 chunk 32 optimal weight: 0.0980 chunk 27 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 48 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 587 HIS ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.187462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.159056 restraints weight = 9177.321| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.29 r_work: 0.3795 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6800 Z= 0.213 Angle : 0.559 7.666 9208 Z= 0.293 Chirality : 0.040 0.165 986 Planarity : 0.005 0.054 1098 Dihedral : 11.197 74.626 1034 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.36 % Allowed : 17.40 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.31), residues: 756 helix: 1.74 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -1.98 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 607 HIS 0.006 0.001 HIS A 587 PHE 0.018 0.001 PHE A 517 TYR 0.015 0.001 TYR B 496 ARG 0.005 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.748 Fit side-chains REVERT: A 258 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7246 (mmtm) REVERT: A 270 ARG cc_start: 0.7575 (mtm180) cc_final: 0.6821 (mtp180) REVERT: B 301 LEU cc_start: 0.8510 (tt) cc_final: 0.8212 (tt) REVERT: B 357 PHE cc_start: 0.8136 (t80) cc_final: 0.7535 (m-10) REVERT: B 364 LYS cc_start: 0.8119 (mttt) cc_final: 0.7887 (mtpt) REVERT: B 408 MET cc_start: 0.8332 (mmm) cc_final: 0.7941 (mmm) REVERT: B 487 PHE cc_start: 0.7263 (m-10) cc_final: 0.6487 (t80) REVERT: B 538 ASP cc_start: 0.8764 (t70) cc_final: 0.8416 (t0) REVERT: B 549 GLU cc_start: 0.6937 (mp0) cc_final: 0.6453 (mm-30) REVERT: B 555 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7430 (mm-40) outliers start: 16 outliers final: 14 residues processed: 152 average time/residue: 0.1542 time to fit residues: 32.7637 Evaluate side-chains 152 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.0010 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 499 HIS A 587 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.186780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.158274 restraints weight = 9224.483| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.29 r_work: 0.3790 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6800 Z= 0.220 Angle : 0.563 7.812 9208 Z= 0.297 Chirality : 0.041 0.188 986 Planarity : 0.005 0.053 1098 Dihedral : 11.133 74.500 1034 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.21 % Allowed : 17.99 % Favored : 79.79 % 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: 1.26 (0.31), residues: 756 helix: 1.76 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -1.96 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 607 HIS 0.006 0.001 HIS A 587 PHE 0.021 0.001 PHE A 596 TYR 0.020 0.001 TYR B 518 ARG 0.006 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.736 Fit side-chains REVERT: A 248 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7703 (m110) REVERT: A 258 LYS cc_start: 0.7692 (mmtt) cc_final: 0.7276 (mmtm) REVERT: A 270 ARG cc_start: 0.7585 (mtm180) cc_final: 0.6794 (mtp180) REVERT: B 301 LEU cc_start: 0.8577 (tt) cc_final: 0.8275 (tt) REVERT: B 357 PHE cc_start: 0.8127 (t80) cc_final: 0.7533 (m-10) REVERT: B 364 LYS cc_start: 0.8115 (mttt) cc_final: 0.7882 (mtpt) REVERT: B 408 MET cc_start: 0.8346 (mmm) cc_final: 0.7962 (mmm) REVERT: B 487 PHE cc_start: 0.7314 (m-10) cc_final: 0.6535 (t80) REVERT: B 538 ASP cc_start: 0.8749 (t70) cc_final: 0.8403 (t0) REVERT: B 549 GLU cc_start: 0.6966 (mp0) cc_final: 0.6391 (mm-30) REVERT: B 555 GLN cc_start: 0.7713 (mm-40) cc_final: 0.7402 (mm-40) REVERT: B 573 TRP cc_start: 0.7765 (t60) cc_final: 0.7517 (t60) outliers start: 15 outliers final: 12 residues processed: 144 average time/residue: 0.1583 time to fit residues: 31.6905 Evaluate side-chains 148 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 34 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 499 HIS A 587 HIS B 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.187292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.158696 restraints weight = 9288.065| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.32 r_work: 0.3792 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 6800 Z= 0.211 Angle : 0.573 8.072 9208 Z= 0.303 Chirality : 0.042 0.298 986 Planarity : 0.005 0.054 1098 Dihedral : 11.069 74.497 1034 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.92 % Allowed : 18.58 % Favored : 79.50 % 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: 1.27 (0.31), residues: 756 helix: 1.75 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -1.91 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 528 HIS 0.009 0.001 HIS A 587 PHE 0.017 0.001 PHE B 354 TYR 0.021 0.001 TYR B 518 ARG 0.006 0.000 ARG B 293 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.659 Fit side-chains REVERT: A 258 LYS cc_start: 0.7673 (mmtt) cc_final: 0.6603 (tttm) REVERT: A 270 ARG cc_start: 0.7576 (mtm180) cc_final: 0.6786 (mtp180) REVERT: B 357 PHE cc_start: 0.8122 (t80) cc_final: 0.7517 (m-10) REVERT: B 364 LYS cc_start: 0.8114 (mttt) cc_final: 0.7878 (mtpt) REVERT: B 408 MET cc_start: 0.8266 (mmm) cc_final: 0.7912 (mmm) REVERT: B 487 PHE cc_start: 0.7293 (m-10) cc_final: 0.6537 (t80) REVERT: B 549 GLU cc_start: 0.6915 (mp0) cc_final: 0.6504 (mm-30) REVERT: B 555 GLN cc_start: 0.7607 (mm-40) cc_final: 0.7329 (mm-40) REVERT: B 573 TRP cc_start: 0.7773 (t60) cc_final: 0.7500 (t60) outliers start: 13 outliers final: 12 residues processed: 146 average time/residue: 0.1501 time to fit residues: 30.6036 Evaluate side-chains 149 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 336 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain A residue 620 CYS Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 7 optimal weight: 0.0040 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 38 optimal weight: 0.0010 overall best weight: 0.3198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN A 499 HIS A 587 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.189458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.160914 restraints weight = 9394.159| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 2.35 r_work: 0.3813 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6800 Z= 0.189 Angle : 0.567 7.865 9208 Z= 0.302 Chirality : 0.041 0.187 986 Planarity : 0.004 0.054 1098 Dihedral : 10.889 75.200 1034 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.62 % Allowed : 19.03 % Favored : 79.35 % 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: 1.38 (0.31), residues: 756 helix: 1.83 (0.21), residues: 560 sheet: None (None), residues: 0 loop : -1.87 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 528 HIS 0.009 0.001 HIS A 587 PHE 0.025 0.001 PHE A 596 TYR 0.021 0.001 TYR B 518 ARG 0.006 0.000 ARG B 293 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.729 Fit side-chains REVERT: A 258 LYS cc_start: 0.7675 (mmtt) cc_final: 0.6608 (tttm) REVERT: A 270 ARG cc_start: 0.7578 (mtm180) cc_final: 0.6794 (mtp180) REVERT: B 305 LEU cc_start: 0.6216 (OUTLIER) cc_final: 0.5885 (mt) REVERT: B 357 PHE cc_start: 0.8104 (t80) cc_final: 0.7504 (m-10) REVERT: B 364 LYS cc_start: 0.8109 (mttt) cc_final: 0.7876 (mtpt) REVERT: B 408 MET cc_start: 0.8276 (mmm) cc_final: 0.7934 (mmm) REVERT: B 487 PHE cc_start: 0.7192 (m-10) cc_final: 0.6531 (t80) REVERT: B 549 GLU cc_start: 0.6950 (mp0) cc_final: 0.6491 (mm-30) REVERT: B 555 GLN cc_start: 0.7587 (mm-40) cc_final: 0.7147 (mm-40) outliers start: 11 outliers final: 9 residues processed: 151 average time/residue: 0.1461 time to fit residues: 31.0556 Evaluate side-chains 151 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 591 ILE Chi-restraints excluded: chain A residue 608 ASN Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 305 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 491 THR Chi-restraints excluded: chain B residue 574 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN ** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 499 HIS A 587 HIS ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.186975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.158061 restraints weight = 9336.926| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.33 r_work: 0.3781 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6800 Z= 0.246 Angle : 0.606 8.582 9208 Z= 0.318 Chirality : 0.042 0.210 986 Planarity : 0.005 0.053 1098 Dihedral : 11.007 74.080 1034 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.92 % Allowed : 19.47 % Favored : 78.61 % 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: 1.35 (0.31), residues: 756 helix: 1.78 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -1.74 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 528 HIS 0.010 0.001 HIS A 587 PHE 0.043 0.002 PHE A 596 TYR 0.021 0.001 TYR B 518 ARG 0.005 0.000 ARG A 603 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3335.00 seconds wall clock time: 58 minutes 12.58 seconds (3492.58 seconds total)