Starting phenix.real_space_refine on Tue Feb 11 20:31:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j52_61140/02_2025/9j52_61140.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j52_61140/02_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_61140/02_2025/9j52_61140.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j52_61140/02_2025/9j52_61140.map" model { file = "/net/cci-nas-00/data/ceres_data/9j52_61140/02_2025/9j52_61140.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j52_61140/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 4.33, per 1000 atoms: 0.66 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: 1.76 Conformation dependent library (CDL) restraints added in 828.8 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: 0.61 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: 1.64 Time building geometry restraints manager: 2.00 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: 1.440 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: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.220 Find NCS groups from input model: 0.240 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.210 ------------------------------------------------------------------------------- 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 : 0.739 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: 0.1490 time to fit residues: 37.2630 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 : 0.764 ------------------------------------------------------------------------------- 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 = 0.158586 restraints weight = 9104.807| |-----------------------------------------------------------------------------| 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 : 0.737 Fit side-chains REVERT: A 258 LYS cc_start: 0.7676 (mmtt) cc_final: 0.7224 (mmtm) REVERT: A 270 ARG cc_start: 0.7683 (mtm180) cc_final: 0.6839 (mtp-110) REVERT: A 301 LEU cc_start: 0.8394 (mt) cc_final: 0.8008 (tp) REVERT: A 323 LEU cc_start: 0.8102 (mt) cc_final: 0.7718 (mt) REVERT: A 398 ASP cc_start: 0.8561 (m-30) cc_final: 0.8199 (m-30) REVERT: B 290 TYR cc_start: 0.8301 (t80) cc_final: 0.8032 (t80) REVERT: B 352 TYR cc_start: 0.7874 (m-80) cc_final: 0.7255 (m-80) REVERT: B 357 PHE cc_start: 0.8248 (t80) cc_final: 0.7542 (m-10) REVERT: B 364 LYS cc_start: 0.8175 (mttt) cc_final: 0.7894 (mtpt) REVERT: B 408 MET cc_start: 0.8345 (mmm) cc_final: 0.8054 (mmm) REVERT: B 487 PHE cc_start: 0.7294 (m-10) cc_final: 0.6471 (t80) REVERT: B 538 ASP cc_start: 0.8860 (t70) cc_final: 0.8476 (t0) REVERT: B 549 GLU cc_start: 0.6931 (mp0) cc_final: 0.6666 (mm-30) REVERT: B 555 GLN cc_start: 0.7509 (mm-40) cc_final: 0.7264 (mm-40) outliers start: 19 outliers final: 9 residues processed: 163 average time/residue: 0.1582 time to fit residues: 36.0772 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 : 0.752 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 55 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 46 optimal weight: 0.0060 chunk 24 optimal weight: 0.6980 overall best weight: 0.4114 ------------------------------------------------------------------------------- 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 B 288 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.187842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.159254 restraints weight = 9315.046| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.35 r_work: 0.3808 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6800 Z= 0.178 Angle : 0.528 6.760 9208 Z= 0.279 Chirality : 0.040 0.141 986 Planarity : 0.005 0.053 1098 Dihedral : 11.443 74.889 1038 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.51 % Allowed : 12.98 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.15 (0.31), residues: 756 helix: 1.62 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.03 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 528 HIS 0.004 0.001 HIS A 587 PHE 0.020 0.001 PHE A 517 TYR 0.017 0.001 TYR B 496 ARG 0.005 0.000 ARG A 604 *********************** 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 170 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.866 Fit side-chains REVERT: A 258 LYS cc_start: 0.7677 (mmtt) cc_final: 0.7275 (mmtm) REVERT: A 270 ARG cc_start: 0.7586 (mtm180) cc_final: 0.6829 (mtp180) REVERT: A 301 LEU cc_start: 0.8348 (mt) cc_final: 0.8067 (tp) REVERT: A 323 LEU cc_start: 0.8104 (mt) cc_final: 0.7757 (mt) REVERT: B 357 PHE cc_start: 0.8158 (t80) cc_final: 0.7349 (m-10) REVERT: B 364 LYS cc_start: 0.8156 (mttt) cc_final: 0.7914 (mtpt) REVERT: B 408 MET cc_start: 0.8305 (mmm) cc_final: 0.8012 (mmm) REVERT: B 485 THR cc_start: 0.8262 (p) cc_final: 0.7087 (m) REVERT: B 487 PHE cc_start: 0.7322 (m-10) cc_final: 0.6541 (t80) REVERT: B 549 GLU cc_start: 0.7098 (mp0) cc_final: 0.6609 (mm-30) REVERT: B 555 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7273 (mm-40) outliers start: 17 outliers final: 9 residues processed: 159 average time/residue: 0.1571 time to fit residues: 34.6840 Evaluate side-chains 142 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 133 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 591 ILE Chi-restraints excluded: chain A residue 617 LEU 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: 4.9990 chunk 45 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 70 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 73 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.6298 ------------------------------------------------------------------------------- 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 499 HIS A 587 HIS ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.186779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.158078 restraints weight = 9321.333| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.33 r_work: 0.3787 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6800 Z= 0.211 Angle : 0.542 6.742 9208 Z= 0.286 Chirality : 0.040 0.135 986 Planarity : 0.005 0.053 1098 Dihedral : 11.291 74.552 1034 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.06 % Allowed : 15.49 % Favored : 82.45 % 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: 1.13 (0.31), residues: 756 helix: 1.62 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.09 (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 0.020 0.001 PHE A 517 TYR 0.016 0.001 TYR B 524 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 : 0.710 Fit side-chains REVERT: A 258 LYS cc_start: 0.7731 (mmtt) cc_final: 0.7326 (mmtm) REVERT: A 270 ARG cc_start: 0.7557 (mtm180) cc_final: 0.6872 (mtp180) REVERT: A 323 LEU cc_start: 0.8120 (mt) cc_final: 0.7778 (mt) REVERT: A 622 GLU cc_start: 0.6782 (pp20) cc_final: 0.6494 (pp20) REVERT: B 357 PHE cc_start: 0.8121 (t80) cc_final: 0.7401 (m-10) REVERT: B 364 LYS cc_start: 0.8143 (mttt) cc_final: 0.7905 (mtpt) REVERT: B 408 MET cc_start: 0.8373 (mmm) cc_final: 0.8034 (mmm) REVERT: B 487 PHE cc_start: 0.7309 (m-10) cc_final: 0.6510 (t80) REVERT: B 555 GLN cc_start: 0.7592 (mm-40) cc_final: 0.7326 (mm-40) outliers start: 14 outliers final: 9 residues processed: 147 average time/residue: 0.1628 time to fit residues: 33.0281 Evaluate side-chains 148 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.674 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.185370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.156483 restraints weight = 9239.830| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.30 r_work: 0.3769 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2000 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= 0.248 Angle : 0.557 6.843 9208 Z= 0.292 Chirality : 0.040 0.143 986 Planarity : 0.005 0.053 1098 Dihedral : 11.334 74.045 1034 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.80 % Allowed : 15.49 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.31), residues: 756 helix: 1.59 (0.21), residues: 572 sheet: None (None), residues: 0 loop : -2.09 (0.45), residues: 184 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 0.020 0.002 PHE A 517 TYR 0.014 0.001 TYR B 496 ARG 0.004 0.000 ARG A 603 *********************** 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: 19 poor density : 145 time to evaluate : 0.757 Fit side-chains REVERT: A 258 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7305 (mmtm) REVERT: A 270 ARG cc_start: 0.7619 (mtm180) cc_final: 0.6834 (mtp180) REVERT: A 590 ASP cc_start: 0.8038 (m-30) cc_final: 0.7583 (t0) REVERT: A 622 GLU cc_start: 0.6900 (pp20) cc_final: 0.6570 (pp20) REVERT: B 357 PHE cc_start: 0.8227 (t80) cc_final: 0.7534 (m-10) REVERT: B 364 LYS cc_start: 0.8148 (mttt) cc_final: 0.7908 (mtpt) REVERT: B 408 MET cc_start: 0.8435 (mmm) cc_final: 0.8028 (mmm) REVERT: B 452 GLN cc_start: 0.8213 (tm-30) cc_final: 0.7829 (tm-30) REVERT: B 487 PHE cc_start: 0.7350 (m-10) cc_final: 0.6514 (t80) REVERT: B 508 MET cc_start: 0.6970 (mmt) cc_final: 0.6654 (mmt) REVERT: B 549 GLU cc_start: 0.6912 (mp0) cc_final: 0.6588 (mm-30) REVERT: B 555 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7471 (mm-40) outliers start: 19 outliers final: 13 residues processed: 153 average time/residue: 0.1523 time to fit residues: 32.7521 Evaluate side-chains 149 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 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 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 = 0.4235 r_free = 0.4235 target = 0.186117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.157290 restraints weight = 9195.770| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.30 r_work: 0.3778 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2117 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= 0.232 Angle : 0.558 6.548 9208 Z= 0.294 Chirality : 0.040 0.152 986 Planarity : 0.005 0.054 1098 Dihedral : 11.317 74.124 1034 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.51 % Allowed : 16.67 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.18 (0.31), residues: 756 helix: 1.69 (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 0.020 0.001 PHE A 596 TYR 0.015 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 163 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.665 Fit side-chains REVERT: A 258 LYS cc_start: 0.7738 (mmtt) cc_final: 0.7327 (mmtm) REVERT: A 270 ARG cc_start: 0.7595 (mtm180) cc_final: 0.6818 (mtp180) REVERT: A 489 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7650 (tpp) REVERT: A 590 ASP cc_start: 0.8020 (m-30) cc_final: 0.7572 (t0) REVERT: A 622 GLU cc_start: 0.6971 (pp20) cc_final: 0.6631 (pp20) REVERT: B 301 LEU cc_start: 0.8506 (tt) cc_final: 0.8195 (tt) REVERT: B 357 PHE cc_start: 0.8186 (t80) cc_final: 0.7525 (m-10) REVERT: B 364 LYS cc_start: 0.8134 (mttt) cc_final: 0.7898 (mtpt) REVERT: B 408 MET cc_start: 0.8395 (mmm) cc_final: 0.8014 (mmm) REVERT: B 487 PHE cc_start: 0.7308 (m-10) cc_final: 0.6511 (t80) REVERT: B 549 GLU cc_start: 0.7045 (mp0) cc_final: 0.6696 (mm-30) REVERT: B 555 GLN cc_start: 0.7732 (mm-40) cc_final: 0.7475 (mm-40) outliers start: 17 outliers final: 15 residues processed: 151 average time/residue: 0.1536 time to fit residues: 32.3218 Evaluate side-chains 149 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 363 THR 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: 0.4980 chunk 63 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 32 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.187391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158709 restraints weight = 9195.001| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 2.30 r_work: 0.3795 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.2208 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= 0.208 Angle : 0.555 7.065 9208 Z= 0.294 Chirality : 0.040 0.165 986 Planarity : 0.005 0.054 1098 Dihedral : 11.213 74.518 1034 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.65 % Allowed : 17.40 % Favored : 79.94 % 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: 1.29 (0.31), residues: 756 helix: 1.75 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.82 (0.45), residues: 198 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 0.017 0.001 PHE A 517 TYR 0.020 0.001 TYR B 518 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 168 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.697 Fit side-chains REVERT: A 248 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7815 (m-40) REVERT: A 258 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7273 (mmtm) REVERT: A 270 ARG cc_start: 0.7594 (mtm180) cc_final: 0.6819 (mtp180) REVERT: A 489 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7532 (tpp) REVERT: A 590 ASP cc_start: 0.8019 (m-30) cc_final: 0.7571 (t0) REVERT: A 622 GLU cc_start: 0.6978 (pp20) cc_final: 0.6641 (pp20) REVERT: B 301 LEU cc_start: 0.8575 (tt) cc_final: 0.8259 (tt) REVERT: B 352 TYR cc_start: 0.8182 (m-80) cc_final: 0.7422 (m-80) REVERT: B 357 PHE cc_start: 0.8125 (t80) cc_final: 0.7533 (m-10) REVERT: B 364 LYS cc_start: 0.8122 (mttt) cc_final: 0.7891 (mtpt) REVERT: B 408 MET cc_start: 0.8388 (mmm) cc_final: 0.8018 (mmm) REVERT: B 487 PHE cc_start: 0.7307 (m-10) cc_final: 0.6526 (t80) REVERT: B 549 GLU cc_start: 0.6946 (mp0) cc_final: 0.6532 (mm-30) REVERT: B 555 GLN cc_start: 0.7706 (mm-40) cc_final: 0.7396 (mm-40) REVERT: B 573 TRP cc_start: 0.7767 (t60) cc_final: 0.7554 (t60) outliers start: 18 outliers final: 13 residues processed: 156 average time/residue: 0.1630 time to fit residues: 35.6053 Evaluate side-chains 154 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 363 THR Chi-restraints excluded: chain A residue 489 MET 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: 1.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 67 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 3 optimal weight: 0.0000 chunk 48 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.4182 ------------------------------------------------------------------------------- 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 310 ASN B 399 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.188105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.159818 restraints weight = 9189.348| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 2.29 r_work: 0.3804 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2321 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= 0.198 Angle : 0.559 7.752 9208 Z= 0.295 Chirality : 0.040 0.177 986 Planarity : 0.005 0.054 1098 Dihedral : 11.103 74.868 1034 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.51 % Allowed : 17.99 % 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: 1.37 (0.31), residues: 756 helix: 1.81 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.79 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 528 HIS 0.007 0.001 HIS A 587 PHE 0.017 0.001 PHE A 596 TYR 0.021 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 156 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.807 Fit side-chains REVERT: A 258 LYS cc_start: 0.7671 (mmtt) cc_final: 0.7249 (mmtm) REVERT: A 270 ARG cc_start: 0.7620 (mtm180) cc_final: 0.6836 (mtp180) REVERT: A 489 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7512 (tpp) REVERT: A 590 ASP cc_start: 0.7905 (m-30) cc_final: 0.7481 (t0) REVERT: A 622 GLU cc_start: 0.6968 (pp20) cc_final: 0.6623 (pp20) REVERT: B 301 LEU cc_start: 0.8567 (tt) cc_final: 0.8262 (tt) REVERT: B 357 PHE cc_start: 0.8124 (t80) cc_final: 0.7514 (m-10) REVERT: B 364 LYS cc_start: 0.8102 (mttt) cc_final: 0.7872 (mtpt) REVERT: B 408 MET cc_start: 0.8316 (mmm) cc_final: 0.8020 (mmm) REVERT: B 487 PHE cc_start: 0.7228 (m-10) cc_final: 0.6527 (t80) REVERT: B 538 ASP cc_start: 0.8814 (t70) cc_final: 0.8473 (t0) REVERT: B 549 GLU cc_start: 0.6918 (mp0) cc_final: 0.6389 (mm-30) REVERT: B 555 GLN cc_start: 0.7612 (mm-40) cc_final: 0.7332 (mm-40) outliers start: 17 outliers final: 13 residues processed: 143 average time/residue: 0.1650 time to fit residues: 32.7575 Evaluate side-chains 150 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.786 ------------------------------------------------------------------------------- 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 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 326 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: 0.0770 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.187280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.158669 restraints weight = 9310.398| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.31 r_work: 0.3789 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6800 Z= 0.223 Angle : 0.570 8.201 9208 Z= 0.301 Chirality : 0.041 0.176 986 Planarity : 0.005 0.053 1098 Dihedral : 11.076 74.377 1034 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.21 % Allowed : 18.14 % Favored : 79.65 % 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: 1.33 (0.31), residues: 756 helix: 1.77 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.79 (0.45), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 528 HIS 0.003 0.001 HIS A 476 PHE 0.036 0.001 PHE A 596 TYR 0.020 0.001 TYR B 518 ARG 0.005 0.000 ARG A 603 *********************** 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: 15 poor density : 141 time to evaluate : 0.701 Fit side-chains REVERT: A 258 LYS cc_start: 0.7680 (mmtt) cc_final: 0.7288 (mmtm) REVERT: A 270 ARG cc_start: 0.7631 (mtm180) cc_final: 0.6786 (mtp180) REVERT: A 489 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7441 (tpp) REVERT: A 590 ASP cc_start: 0.7951 (m-30) cc_final: 0.7533 (t0) REVERT: A 622 GLU cc_start: 0.6976 (pp20) cc_final: 0.6628 (pp20) REVERT: B 357 PHE cc_start: 0.8134 (t80) cc_final: 0.7506 (m-10) REVERT: B 364 LYS cc_start: 0.8119 (mttt) cc_final: 0.7881 (mtpt) REVERT: B 408 MET cc_start: 0.8393 (mmm) cc_final: 0.8030 (mmm) REVERT: B 487 PHE cc_start: 0.7263 (m-10) cc_final: 0.6540 (t80) REVERT: B 533 ASP cc_start: 0.7946 (m-30) cc_final: 0.7534 (m-30) REVERT: B 538 ASP cc_start: 0.8792 (t70) cc_final: 0.8541 (t0) REVERT: B 549 GLU cc_start: 0.6970 (mp0) cc_final: 0.6289 (mm-30) REVERT: B 555 GLN cc_start: 0.7655 (mm-40) cc_final: 0.7221 (mm-40) outliers start: 15 outliers final: 12 residues processed: 146 average time/residue: 0.1530 time to fit residues: 31.0051 Evaluate side-chains 147 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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 363 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 36 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 0.0980 chunk 43 optimal weight: 0.6980 chunk 64 optimal weight: 5.9990 chunk 46 optimal weight: 0.2980 chunk 45 optimal weight: 0.0070 chunk 38 optimal weight: 0.3980 overall best weight: 0.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN A 499 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.191305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.163202 restraints weight = 9323.191| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.33 r_work: 0.3843 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6800 Z= 0.176 Angle : 0.546 7.671 9208 Z= 0.291 Chirality : 0.040 0.192 986 Planarity : 0.004 0.054 1098 Dihedral : 10.730 75.699 1034 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.62 % Allowed : 19.62 % Favored : 78.76 % 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: 1.50 (0.31), residues: 756 helix: 1.90 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.72 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 528 HIS 0.004 0.001 HIS A 476 PHE 0.014 0.001 PHE B 610 TYR 0.019 0.001 TYR B 518 ARG 0.005 0.000 ARG A 603 ********************** 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 170 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.739 Fit side-chains REVERT: A 258 LYS cc_start: 0.7682 (mmtt) cc_final: 0.6635 (tttm) REVERT: A 270 ARG cc_start: 0.7517 (mtm180) cc_final: 0.6712 (mtp180) REVERT: A 302 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 489 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7299 (tpp) REVERT: A 590 ASP cc_start: 0.7915 (m-30) cc_final: 0.7497 (t0) REVERT: A 622 GLU cc_start: 0.6943 (pp20) cc_final: 0.6607 (pp20) REVERT: B 305 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5847 (mt) REVERT: B 357 PHE cc_start: 0.8023 (t80) cc_final: 0.7526 (m-10) REVERT: B 364 LYS cc_start: 0.8112 (mttt) cc_final: 0.7889 (mtpt) REVERT: B 408 MET cc_start: 0.8265 (mmm) cc_final: 0.7954 (mmm) REVERT: B 487 PHE cc_start: 0.6956 (m-10) cc_final: 0.6473 (t80) REVERT: B 549 GLU cc_start: 0.6982 (mp0) cc_final: 0.6559 (mm-30) REVERT: B 555 GLN cc_start: 0.7507 (mm-40) cc_final: 0.7120 (mm-40) outliers start: 11 outliers final: 7 residues processed: 162 average time/residue: 0.1481 time to fit residues: 33.8202 Evaluate side-chains 150 residues out of total 678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.740 ------------------------------------------------------------------------------- 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 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 B residue 305 LEU Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 377 LEU 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: 0.0770 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 499 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.189060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.160789 restraints weight = 9375.216| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.32 r_work: 0.3817 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6800 Z= 0.211 Angle : 0.578 8.232 9208 Z= 0.306 Chirality : 0.041 0.184 986 Planarity : 0.005 0.054 1098 Dihedral : 10.774 75.435 1034 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.33 % Allowed : 21.53 % Favored : 77.14 % 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: 1.49 (0.31), residues: 756 helix: 1.91 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -1.78 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 528 HIS 0.006 0.001 HIS B 387 PHE 0.029 0.001 PHE A 596 TYR 0.014 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: 3106.70 seconds wall clock time: 56 minutes 3.63 seconds (3363.63 seconds total)