Starting phenix.real_space_refine on Wed Mar 5 15:41:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gg0_51319/03_2025/9gg0_51319_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gg0_51319/03_2025/9gg0_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/cci-nas-00/data/ceres_data/9gg0_51319/03_2025/9gg0_51319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gg0_51319/03_2025/9gg0_51319.map" model { file = "/net/cci-nas-00/data/ceres_data/9gg0_51319/03_2025/9gg0_51319_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gg0_51319/03_2025/9gg0_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-5624/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: 2.50, per 1000 atoms: 1.05 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: 0.51 Conformation dependent library (CDL) restraints added in 325.0 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: 0.39 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: 0.53 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' 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: 3.680 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.390 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- 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 : 0.261 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: 0.7684 time to fit residues: 23.2999 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 : 0.272 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.135378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.102974 restraints weight = 2686.419| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.46 r_work: 0.3489 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 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 : 0.262 Fit side-chains REVERT: A 356 SER cc_start: 0.9075 (p) cc_final: 0.8752 (p) REVERT: B 356 SER cc_start: 0.9186 (p) cc_final: 0.8933 (p) REVERT: C 356 SER cc_start: 0.9131 (p) cc_final: 0.8920 (p) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.3244 time to fit residues: 8.3088 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 : 0.262 ------------------------------------------------------------------------------- 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 11 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 0.2980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 A 374 HIS ** C 296 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 = 0.3993 r_free = 0.3993 target = 0.134617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.102323 restraints weight = 2654.416| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.41 r_work: 0.3483 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2412 Z= 0.197 Angle : 0.495 3.584 3219 Z= 0.262 Chirality : 0.051 0.149 366 Planarity : 0.002 0.015 411 Dihedral : 4.908 15.548 324 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -2.19 (0.41), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 362 PHE 0.005 0.001 PHE C 346 TYR 0.004 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 29 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.289 Fit side-chains REVERT: A 356 SER cc_start: 0.9140 (p) cc_final: 0.8824 (p) REVERT: B 325 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7939 (tt) REVERT: B 356 SER cc_start: 0.9194 (p) cc_final: 0.8955 (p) outliers start: 7 outliers final: 2 residues processed: 25 average time/residue: 0.4303 time to fit residues: 11.7188 Evaluate side-chains 23 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 13 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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 ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.129221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.096850 restraints weight = 2663.785| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.38 r_work: 0.3383 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 2412 Z= 0.452 Angle : 0.630 4.371 3219 Z= 0.332 Chirality : 0.054 0.159 366 Planarity : 0.003 0.021 411 Dihedral : 5.548 16.609 324 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: -2.11 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 362 PHE 0.010 0.003 PHE A 346 TYR 0.006 0.003 TYR C 310 ARG 0.000 0.000 ARG B 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 31 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.260 Fit side-chains REVERT: A 347 LYS cc_start: 0.7588 (tttt) cc_final: 0.7338 (mtmp) REVERT: A 356 SER cc_start: 0.9161 (p) cc_final: 0.8863 (p) REVERT: B 325 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7967 (tt) REVERT: B 347 LYS cc_start: 0.8011 (tttt) cc_final: 0.7762 (mtmp) REVERT: B 356 SER cc_start: 0.9218 (p) cc_final: 0.9001 (p) REVERT: C 347 LYS cc_start: 0.7621 (tttt) cc_final: 0.7316 (mmpt) outliers start: 5 outliers final: 4 residues processed: 27 average time/residue: 0.7575 time to fit residues: 21.4220 Evaluate side-chains 31 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 16 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.135103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.102435 restraints weight = 2688.281| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.44 r_work: 0.3472 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2412 Z= 0.196 Angle : 0.488 3.662 3219 Z= 0.257 Chirality : 0.050 0.146 366 Planarity : 0.002 0.019 411 Dihedral : 4.953 16.152 324 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.56 % Allowed : 12.45 % 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: -2.12 (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 B 299 PHE 0.006 0.002 PHE C 346 TYR 0.004 0.001 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 30 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.298 Fit side-chains REVERT: A 356 SER cc_start: 0.9164 (p) cc_final: 0.8869 (p) REVERT: B 325 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7940 (tt) REVERT: B 356 SER cc_start: 0.9198 (p) cc_final: 0.8980 (p) outliers start: 7 outliers final: 4 residues processed: 26 average time/residue: 0.5813 time to fit residues: 16.0968 Evaluate side-chains 28 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 5 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 22 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.136029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103732 restraints weight = 2602.682| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 2.42 r_work: 0.3499 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1921 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= 0.166 Angle : 0.465 3.562 3219 Z= 0.243 Chirality : 0.050 0.144 366 Planarity : 0.002 0.017 411 Dihedral : 4.686 15.279 324 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.83 % Allowed : 12.82 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (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 0.005 0.001 PHE C 346 TYR 0.004 0.001 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: 5 poor density : 24 time to evaluate : 0.274 Fit side-chains REVERT: A 356 SER cc_start: 0.9204 (p) cc_final: 0.8899 (p) REVERT: B 325 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.7923 (tt) REVERT: B 356 SER cc_start: 0.9200 (p) cc_final: 0.8995 (p) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.4104 time to fit residues: 11.1969 Evaluate side-chains 28 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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 8 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 0 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4030 r_free = 0.4030 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.104102 restraints weight = 2642.561| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.45 r_work: 0.3509 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.1999 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= 0.159 Angle : 0.461 3.466 3219 Z= 0.243 Chirality : 0.050 0.144 366 Planarity : 0.002 0.018 411 Dihedral : 4.627 14.831 324 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.83 % Allowed : 13.55 % Favored : 84.62 % 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 : -1.63 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 362 PHE 0.005 0.001 PHE C 346 TYR 0.008 0.002 TYR A 310 ARG 0.000 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: 5 poor density : 24 time to evaluate : 0.275 Fit side-chains REVERT: A 356 SER cc_start: 0.9211 (p) cc_final: 0.8912 (p) REVERT: B 325 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.7906 (tt) outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 0.4267 time to fit residues: 11.5921 Evaluate side-chains 27 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 23 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.135006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.102741 restraints weight = 2707.370| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 2.44 r_work: 0.3485 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2412 Z= 0.204 Angle : 0.481 3.626 3219 Z= 0.253 Chirality : 0.050 0.147 366 Planarity : 0.002 0.018 411 Dihedral : 4.777 15.253 324 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.83 % Allowed : 14.29 % 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: -2.15 (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 0.001 HIS A 299 PHE 0.006 0.002 PHE C 346 TYR 0.010 0.002 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 29 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.304 Fit side-chains REVERT: A 356 SER cc_start: 0.9210 (p) cc_final: 0.8921 (p) REVERT: B 325 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7920 (tt) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.4380 time to fit residues: 11.9267 Evaluate side-chains 28 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 21 optimal weight: 0.0970 chunk 29 optimal weight: 0.0770 chunk 7 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 27 optimal weight: 7.9990 overall best weight: 0.4936 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.142845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.110968 restraints weight = 2570.445| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.32 r_work: 0.3644 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2412 Z= 0.115 Angle : 0.430 3.410 3219 Z= 0.228 Chirality : 0.050 0.137 366 Planarity : 0.002 0.017 411 Dihedral : 4.323 13.968 324 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.20 % Allowed : 14.29 % 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: -2.17 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.65 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 299 PHE 0.004 0.001 PHE C 346 TYR 0.007 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 29 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.292 Fit side-chains REVERT: A 356 SER cc_start: 0.9202 (p) cc_final: 0.8929 (p) REVERT: B 325 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7954 (tt) outliers start: 6 outliers final: 4 residues processed: 24 average time/residue: 0.6081 time to fit residues: 15.5039 Evaluate side-chains 25 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 344 LEU 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 7 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.136253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.103937 restraints weight = 2641.793| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.45 r_work: 0.3507 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2412 Z= 0.185 Angle : 0.467 3.570 3219 Z= 0.247 Chirality : 0.050 0.146 366 Planarity : 0.002 0.018 411 Dihedral : 4.556 14.284 324 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.83 % Allowed : 15.38 % Favored : 82.78 % 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: -2.19 (0.42), residues: 315 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 362 PHE 0.005 0.001 PHE A 346 TYR 0.013 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 30 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.311 Fit side-chains REVERT: A 356 SER cc_start: 0.9219 (p) cc_final: 0.8939 (p) REVERT: B 325 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7952 (tt) outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.4259 time to fit residues: 11.6282 Evaluate side-chains 28 residues out of total 273 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 344 LEU 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 11 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.132696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.100376 restraints weight = 2669.836| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.41 r_work: 0.3452 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2013 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= 0.272 Angle : 0.524 3.812 3219 Z= 0.276 Chirality : 0.051 0.152 366 Planarity : 0.002 0.020 411 Dihedral : 4.956 15.393 324 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.83 % Allowed : 15.38 % Favored : 82.78 % 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 0.005 0.001 HIS B 362 PHE 0.007 0.002 PHE A 346 TYR 0.019 0.003 TYR A 310 ARG 0.000 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.58 seconds wall clock time: 36 minutes 28.98 seconds (2188.98 seconds total)