Starting phenix.real_space_refine on Wed Nov 13 23:52:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg0_51319/11_2024/9gg0_51319_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg0_51319/11_2024/9gg0_51319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg0_51319/11_2024/9gg0_51319.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg0_51319/11_2024/9gg0_51319.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg0_51319/11_2024/9gg0_51319_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9gg0_51319/11_2024/9gg0_51319_neut.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1482 2.51 5 N 444 2.21 5 O 453 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2385 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 795 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 3, 'TRANS': 103} Restraints were copied for chains: C, B Time building chain proxies: 4.19, per 1000 atoms: 1.76 Number of scatterers: 2385 At special positions: 0 Unit cell: (80.752, 121.128, 37.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 453 8.00 N 444 7.00 C 1482 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.59 Conformation dependent library (CDL) restraints added in 282.4 milliseconds 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 43.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 274 through 280 removed outlier: 6.343A pdb=" N VAL A 275 " --> pdb=" O GLN C 276 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ILE C 278 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE A 277 " --> pdb=" O ILE C 278 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LYS C 280 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASN A 279 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 284 through 289 removed outlier: 6.520A pdb=" N LEU A 284 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N VAL C 287 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN A 286 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER C 289 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLN A 288 " --> pdb=" O SER C 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 296 through 301 removed outlier: 6.865A pdb=" N ILE A 297 " --> pdb=" O ASN B 296 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS B 298 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N HIS A 299 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 9.141A pdb=" N ASN A 296 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 10.027A pdb=" N HIS C 299 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N LYS A 298 " --> pdb=" O HIS C 299 " (cutoff:3.500A) removed outlier: 8.505A pdb=" N LEU C 301 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL A 300 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 306 through 310 removed outlier: 6.492A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.631A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 314 removed outlier: 6.899A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.285A pdb=" N VAL A 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N LYS C 321 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER A 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.117A pdb=" N SER A 324 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.793A pdb=" N ILE A 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 336 through 341 removed outlier: 6.425A pdb=" N GLN A 336 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL B 339 " --> pdb=" O GLN A 336 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU A 338 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N SER B 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LYS A 340 " --> pdb=" O SER B 341 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.745A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 349 through 354 removed outlier: 6.008A pdb=" N VAL A 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LYS C 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER A 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 369 through 376 removed outlier: 6.447A pdb=" N LYS A 370 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N THR C 373 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU A 372 " --> pdb=" O THR C 373 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS C 375 " --> pdb=" O GLU A 372 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N HIS A 374 " --> pdb=" O LYS C 375 " (cutoff:3.500A) 44 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 539 1.33 - 1.45: 487 1.45 - 1.57: 1380 1.57 - 1.69: 0 1.69 - 1.81: 6 Bond restraints: 2412 Sorted by residual: bond pdb=" CA SER B 305 " pdb=" CB SER B 305 " ideal model delta sigma weight residual 1.529 1.486 0.043 1.64e-02 3.72e+03 6.90e+00 bond pdb=" CA SER A 305 " pdb=" CB SER A 305 " ideal model delta sigma weight residual 1.529 1.487 0.042 1.64e-02 3.72e+03 6.64e+00 bond pdb=" CA SER C 305 " pdb=" CB SER C 305 " ideal model delta sigma weight residual 1.529 1.487 0.042 1.64e-02 3.72e+03 6.61e+00 bond pdb=" CA SER C 352 " pdb=" CB SER C 352 " ideal model delta sigma weight residual 1.530 1.492 0.037 1.57e-02 4.06e+03 5.57e+00 bond pdb=" CA SER A 352 " pdb=" CB SER A 352 " ideal model delta sigma weight residual 1.530 1.493 0.037 1.57e-02 4.06e+03 5.49e+00 ... (remaining 2407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 2224 1.25 - 2.50: 734 2.50 - 3.74: 201 3.74 - 4.99: 39 4.99 - 6.24: 21 Bond angle restraints: 3219 Sorted by residual: angle pdb=" N PRO C 332 " pdb=" CA PRO C 332 " pdb=" CB PRO C 332 " ideal model delta sigma weight residual 103.35 106.45 -3.10 8.70e-01 1.32e+00 1.27e+01 angle pdb=" N PRO A 332 " pdb=" CA PRO A 332 " pdb=" CB PRO A 332 " ideal model delta sigma weight residual 103.35 106.45 -3.10 8.70e-01 1.32e+00 1.27e+01 angle pdb=" N PRO B 332 " pdb=" CA PRO B 332 " pdb=" CB PRO B 332 " ideal model delta sigma weight residual 103.35 106.45 -3.10 8.70e-01 1.32e+00 1.27e+01 angle pdb=" C ASP C 295 " pdb=" N ASN C 296 " pdb=" CA ASN C 296 " ideal model delta sigma weight residual 122.29 116.46 5.83 1.65e+00 3.67e-01 1.25e+01 angle pdb=" C ASP A 295 " pdb=" N ASN A 296 " pdb=" CA ASN A 296 " ideal model delta sigma weight residual 122.29 116.47 5.82 1.65e+00 3.67e-01 1.25e+01 ... (remaining 3214 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.84: 1297 15.84 - 31.68: 146 31.68 - 47.52: 18 47.52 - 63.37: 12 63.37 - 79.21: 3 Dihedral angle restraints: 1476 sinusoidal: 609 harmonic: 867 Sorted by residual: dihedral pdb=" CA GLY C 365 " pdb=" C GLY C 365 " pdb=" N GLY C 366 " pdb=" CA GLY C 366 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA GLY A 365 " pdb=" C GLY A 365 " pdb=" N GLY A 366 " pdb=" CA GLY A 366 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA GLY B 365 " pdb=" C GLY B 365 " pdb=" N GLY B 366 " pdb=" CA GLY B 366 " ideal model delta harmonic sigma weight residual 180.00 156.75 23.25 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 1473 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.080: 240 0.080 - 0.159: 114 0.159 - 0.239: 9 0.239 - 0.318: 0 0.318 - 0.397: 3 Chirality restraints: 366 Sorted by residual: chirality pdb=" CA ASN B 296 " pdb=" N ASN B 296 " pdb=" C ASN B 296 " pdb=" CB ASN B 296 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ASN A 296 " pdb=" N ASN A 296 " pdb=" C ASN A 296 " pdb=" CB ASN A 296 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA ASN C 296 " pdb=" N ASN C 296 " pdb=" C ASN C 296 " pdb=" CB ASN C 296 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 363 not shown) Planarity restraints: 411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 304 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLY C 304 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY C 304 " 0.022 2.00e-02 2.50e+03 pdb=" N SER C 305 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 304 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C GLY A 304 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY A 304 " 0.022 2.00e-02 2.50e+03 pdb=" N SER A 305 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 304 " 0.016 2.00e-02 2.50e+03 3.28e-02 1.07e+01 pdb=" C GLY B 304 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY B 304 " 0.022 2.00e-02 2.50e+03 pdb=" N SER B 305 " 0.019 2.00e-02 2.50e+03 ... (remaining 408 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1400 3.07 - 3.53: 2329 3.53 - 3.99: 3476 3.99 - 4.44: 3686 4.44 - 4.90: 7653 Nonbonded interactions: 18544 Sorted by model distance: nonbonded pdb=" N SER B 305 " pdb=" O SER B 305 " model vdw 2.615 2.496 nonbonded pdb=" N SER A 305 " pdb=" O SER A 305 " model vdw 2.615 2.496 nonbonded pdb=" N SER C 305 " pdb=" O SER C 305 " model vdw 2.615 2.496 nonbonded pdb=" N LEU A 315 " pdb=" O ASP B 314 " model vdw 2.630 3.120 nonbonded pdb=" O ASP A 314 " pdb=" N LEU C 315 " model vdw 2.630 3.120 ... (remaining 18539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.550 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.000 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 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:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 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 : 0.008 0.043 2412 Z= 0.573 Angle : 1.406 6.240 3219 Z= 0.876 Chirality : 0.086 0.397 366 Planarity : 0.008 0.033 411 Dihedral : 14.688 79.206 930 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.39), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.30), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS C 299 PHE 0.007 0.004 PHE B 346 TYR 0.019 0.012 TYR B 310 ARG 0.003 0.001 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.315 Fit side-chains REVERT: A 356 SER cc_start: 0.9064 (p) cc_final: 0.8772 (p) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.8180 time to fit residues: 24.7549 Evaluate side-chains 22 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.0070 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2412 Z= 0.203 Angle : 0.531 3.587 3219 Z= 0.281 Chirality : 0.051 0.144 366 Planarity : 0.002 0.019 411 Dihedral : 5.190 15.321 324 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.10 % Allowed : 8.79 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.40), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 299 PHE 0.005 0.001 PHE C 346 TYR 0.003 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.295 Fit side-chains REVERT: A 356 SER cc_start: 0.9156 (p) cc_final: 0.8905 (p) REVERT: B 356 SER cc_start: 0.9193 (p) cc_final: 0.8987 (p) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.3385 time to fit residues: 8.7021 Evaluate side-chains 22 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 20 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain C residue 296 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 5.9990 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 296 ASN A 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2412 Z= 0.158 Angle : 0.468 3.466 3219 Z= 0.248 Chirality : 0.050 0.144 366 Planarity : 0.002 0.015 411 Dihedral : 4.730 15.281 324 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.56 % Allowed : 10.26 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.41), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.67 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.004 0.001 PHE C 346 TYR 0.003 0.001 TYR C 310 ARG 0.000 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.345 Fit side-chains REVERT: A 356 SER cc_start: 0.9219 (p) cc_final: 0.8958 (p) REVERT: B 325 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8107 (tt) outliers start: 7 outliers final: 2 residues processed: 26 average time/residue: 0.4488 time to fit residues: 12.6769 Evaluate side-chains 24 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 21 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 296 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 374 HIS B 362 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2412 Z= 0.289 Angle : 0.537 3.740 3219 Z= 0.283 Chirality : 0.052 0.155 366 Planarity : 0.002 0.018 411 Dihedral : 5.144 15.733 324 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.83 % Allowed : 13.19 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.007 0.002 PHE A 346 TYR 0.006 0.002 TYR C 310 ARG 0.000 0.000 ARG C 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.308 Fit side-chains REVERT: A 356 SER cc_start: 0.9207 (p) cc_final: 0.8972 (p) REVERT: B 325 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8129 (tt) outliers start: 5 outliers final: 4 residues processed: 23 average time/residue: 0.6028 time to fit residues: 14.8221 Evaluate side-chains 27 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 296 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2412 Z= 0.367 Angle : 0.581 4.043 3219 Z= 0.306 Chirality : 0.053 0.156 366 Planarity : 0.003 0.021 411 Dihedral : 5.370 16.549 324 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.93 % Allowed : 13.19 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.009 0.002 PHE A 346 TYR 0.006 0.002 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.293 Fit side-chains REVERT: A 347 LYS cc_start: 0.7988 (tttt) cc_final: 0.7711 (mtmp) REVERT: A 356 SER cc_start: 0.9205 (p) cc_final: 0.8974 (p) REVERT: B 325 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8188 (tt) REVERT: C 347 LYS cc_start: 0.8012 (tttt) cc_final: 0.7623 (mmpt) outliers start: 8 outliers final: 4 residues processed: 28 average time/residue: 0.8698 time to fit residues: 25.4162 Evaluate side-chains 30 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 296 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 0.1980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 336 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 2412 Z= 0.331 Angle : 0.558 3.854 3219 Z= 0.293 Chirality : 0.052 0.156 366 Planarity : 0.002 0.021 411 Dihedral : 5.278 16.883 324 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.56 % Allowed : 13.92 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.009 0.002 PHE A 346 TYR 0.006 0.002 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.290 Fit side-chains REVERT: A 347 LYS cc_start: 0.7945 (tttt) cc_final: 0.7655 (mtmp) REVERT: A 356 SER cc_start: 0.9221 (p) cc_final: 0.8988 (p) REVERT: B 325 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8181 (tt) REVERT: C 347 LYS cc_start: 0.8017 (tttt) cc_final: 0.7640 (mmpt) outliers start: 7 outliers final: 4 residues processed: 25 average time/residue: 0.7229 time to fit residues: 19.0857 Evaluate side-chains 27 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 296 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 13 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2412 Z= 0.172 Angle : 0.468 3.586 3219 Z= 0.247 Chirality : 0.050 0.145 366 Planarity : 0.002 0.019 411 Dihedral : 4.812 15.802 324 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.20 % Allowed : 14.65 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 299 PHE 0.006 0.001 PHE C 346 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.281 Fit side-chains REVERT: A 356 SER cc_start: 0.9245 (p) cc_final: 0.9000 (p) REVERT: B 325 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8151 (tt) outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.5022 time to fit residues: 13.5597 Evaluate side-chains 27 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 296 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 17 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2412 Z= 0.158 Angle : 0.459 3.807 3219 Z= 0.241 Chirality : 0.050 0.143 366 Planarity : 0.002 0.018 411 Dihedral : 4.603 15.190 324 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.83 % Allowed : 14.65 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 PHE 0.005 0.001 PHE C 346 TYR 0.007 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.292 Fit side-chains REVERT: A 356 SER cc_start: 0.9274 (p) cc_final: 0.9029 (p) REVERT: B 325 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8148 (tt) outliers start: 5 outliers final: 3 residues processed: 23 average time/residue: 0.4493 time to fit residues: 11.2997 Evaluate side-chains 25 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 325 LEU Chi-restraints excluded: chain C residue 296 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 0.0570 chunk 13 optimal weight: 0.2980 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 23 optimal weight: 0.0000 chunk 2 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 2412 Z= 0.094 Angle : 0.414 3.438 3219 Z= 0.219 Chirality : 0.049 0.134 366 Planarity : 0.002 0.017 411 Dihedral : 4.087 13.032 324 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.10 % Allowed : 15.38 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.63 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 362 PHE 0.003 0.001 PHE C 346 TYR 0.004 0.001 TYR A 310 ARG 0.000 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.290 Fit side-chains REVERT: A 356 SER cc_start: 0.9286 (p) cc_final: 0.9052 (p) REVERT: B 325 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8176 (tt) outliers start: 3 outliers final: 1 residues processed: 25 average time/residue: 0.5725 time to fit residues: 15.2869 Evaluate side-chains 24 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2412 Z= 0.164 Angle : 0.456 3.474 3219 Z= 0.240 Chirality : 0.050 0.144 366 Planarity : 0.002 0.018 411 Dihedral : 4.403 13.701 324 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.10 % Allowed : 17.22 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.64 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 299 PHE 0.005 0.001 PHE C 346 TYR 0.012 0.002 TYR A 310 ARG 0.001 0.000 ARG B 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 630 Ramachandran restraints generated. 315 Oldfield, 0 Emsley, 315 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.250 Fit side-chains REVERT: A 356 SER cc_start: 0.9302 (p) cc_final: 0.9063 (p) REVERT: B 325 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8180 (tt) outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.4221 time to fit residues: 11.8953 Evaluate side-chains 28 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 283 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 325 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 9.9990 chunk 16 optimal weight: 0.0980 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.3980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.132819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100645 restraints weight = 2619.312| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 2.38 r_work: 0.3462 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2412 Z= 0.267 Angle : 0.523 3.794 3219 Z= 0.274 Chirality : 0.051 0.151 366 Planarity : 0.002 0.019 411 Dihedral : 4.899 15.331 324 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.47 % Allowed : 16.85 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 330 PHE 0.007 0.002 PHE A 346 TYR 0.019 0.003 TYR A 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1382.58 seconds wall clock time: 25 minutes 46.69 seconds (1546.69 seconds total)