Starting phenix.real_space_refine on Wed Sep 17 03:07:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0z_26268/09_2025/7u0z_26268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0z_26268/09_2025/7u0z_26268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7u0z_26268/09_2025/7u0z_26268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0z_26268/09_2025/7u0z_26268.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7u0z_26268/09_2025/7u0z_26268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0z_26268/09_2025/7u0z_26268.map" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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 1545 2.51 5 N 465 2.21 5 O 471 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2487 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "C" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Time building chain proxies: 0.92, per 1000 atoms: 0.37 Number of scatterers: 2487 At special positions: 0 Unit cell: (68.868, 110.189, 35.5818, 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 471 8.00 N 465 7.00 C 1545 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: 0.20 Conformation dependent library (CDL) restraints added in 96.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 570 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 275 through 278 removed outlier: 6.499A pdb=" N VAL B 275 " --> pdb=" O GLN A 276 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N ILE A 278 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE B 277 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 284 through 287 removed outlier: 6.565A pdb=" N LEU B 284 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL A 287 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN B 286 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 294 through 299 removed outlier: 6.866A pdb=" N ASP C 295 " --> pdb=" O LYS B 294 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ASN B 296 " --> pdb=" O ASP C 295 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ASP B 295 " --> pdb=" O ASN A 296 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N LYS A 298 " --> pdb=" O ASP B 295 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE B 297 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 307 through 310 removed outlier: 6.792A pdb=" N ILE B 308 " --> pdb=" O VAL A 309 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 313 through 314 removed outlier: 7.051A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 317 through 322 removed outlier: 6.695A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N SER C 320 " --> pdb=" O LYS B 317 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR B 319 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N CYS C 322 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS B 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 removed outlier: 6.607A pdb=" N HIS B 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 340 through 345 removed outlier: 6.191A pdb=" N LYS B 340 " --> pdb=" O SER C 341 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS C 343 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU B 342 " --> pdb=" O LYS C 343 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ASP C 345 " --> pdb=" O GLU B 342 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU B 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 348 through 354 removed outlier: 6.654A pdb=" N ASP B 348 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N GLN C 351 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 350 " --> pdb=" O GLN C 351 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N LYS C 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N SER B 352 " --> pdb=" O LYS C 353 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 357 through 360 removed outlier: 6.543A pdb=" N LEU B 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE C 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASN B 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 368 through 373 removed outlier: 6.173A pdb=" N ASN B 368 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N ILE A 371 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LYS B 370 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N THR A 373 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU B 372 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 376 through 379 removed outlier: 6.345A pdb=" N THR B 377 " --> pdb=" O PHE A 378 " (cutoff:3.500A) 42 hydrogen bonds defined for protein. 126 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: 0.34 Time building geometry restraints manager: 0.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 834 1.34 - 1.46: 229 1.46 - 1.57: 1451 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 2520 Sorted by residual: bond pdb=" CB VAL C 337 " pdb=" CG2 VAL C 337 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CB VAL B 337 " pdb=" CG2 VAL B 337 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.88e+00 bond pdb=" CB VAL A 337 " pdb=" CG2 VAL A 337 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 bond pdb=" CB ASP C 295 " pdb=" CG ASP C 295 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.87e+00 bond pdb=" CB ASP A 295 " pdb=" CG ASP A 295 " ideal model delta sigma weight residual 1.516 1.482 0.034 2.50e-02 1.60e+03 1.84e+00 ... (remaining 2515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 3316 2.30 - 4.59: 39 4.59 - 6.89: 8 6.89 - 9.18: 0 9.18 - 11.48: 3 Bond angle restraints: 3366 Sorted by residual: angle pdb=" CA LEU A 376 " pdb=" CB LEU A 376 " pdb=" CG LEU A 376 " ideal model delta sigma weight residual 116.30 127.78 -11.48 3.50e+00 8.16e-02 1.08e+01 angle pdb=" CA LEU B 376 " pdb=" CB LEU B 376 " pdb=" CG LEU B 376 " ideal model delta sigma weight residual 116.30 127.75 -11.45 3.50e+00 8.16e-02 1.07e+01 angle pdb=" CA LEU C 376 " pdb=" CB LEU C 376 " pdb=" CG LEU C 376 " ideal model delta sigma weight residual 116.30 127.73 -11.43 3.50e+00 8.16e-02 1.07e+01 angle pdb=" N GLY B 333 " pdb=" CA GLY B 333 " pdb=" C GLY B 333 " ideal model delta sigma weight residual 110.71 114.94 -4.23 1.53e+00 4.27e-01 7.63e+00 angle pdb=" N GLY A 333 " pdb=" CA GLY A 333 " pdb=" C GLY A 333 " ideal model delta sigma weight residual 110.71 114.91 -4.20 1.53e+00 4.27e-01 7.55e+00 ... (remaining 3361 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.30: 1219 8.30 - 16.60: 197 16.60 - 24.90: 69 24.90 - 33.19: 48 33.19 - 41.49: 15 Dihedral angle restraints: 1548 sinusoidal: 648 harmonic: 900 Sorted by residual: dihedral pdb=" CA PHE B 346 " pdb=" C PHE B 346 " pdb=" N LYS B 347 " pdb=" CA LYS B 347 " ideal model delta harmonic sigma weight residual 180.00 -167.00 -13.00 0 5.00e+00 4.00e-02 6.76e+00 dihedral pdb=" CA PHE C 346 " pdb=" C PHE C 346 " pdb=" N LYS C 347 " pdb=" CA LYS C 347 " ideal model delta harmonic sigma weight residual -180.00 -167.00 -13.00 0 5.00e+00 4.00e-02 6.76e+00 dihedral pdb=" CA PHE A 346 " pdb=" C PHE A 346 " pdb=" N LYS A 347 " pdb=" CA LYS A 347 " ideal model delta harmonic sigma weight residual -180.00 -167.00 -13.00 0 5.00e+00 4.00e-02 6.76e+00 ... (remaining 1545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 260 0.046 - 0.093: 67 0.093 - 0.139: 42 0.139 - 0.185: 3 0.185 - 0.231: 3 Chirality restraints: 375 Sorted by residual: chirality pdb=" CB VAL C 337 " pdb=" CA VAL C 337 " pdb=" CG1 VAL C 337 " pdb=" CG2 VAL C 337 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB VAL B 337 " pdb=" CA VAL B 337 " pdb=" CG1 VAL B 337 " pdb=" CG2 VAL B 337 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB VAL A 337 " pdb=" CA VAL A 337 " pdb=" CG1 VAL A 337 " pdb=" CG2 VAL A 337 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 372 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " 0.006 2.00e-02 2.50e+03 9.35e-03 1.53e+00 pdb=" CG PHE B 346 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 346 " 0.006 2.00e-02 2.50e+03 9.28e-03 1.51e+00 pdb=" CG PHE C 346 " 0.007 2.00e-02 2.50e+03 pdb=" CD1 PHE C 346 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE C 346 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 346 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE C 346 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 346 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.006 2.00e-02 2.50e+03 9.20e-03 1.48e+00 pdb=" CG PHE A 346 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " -0.000 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 51 2.70 - 3.25: 2287 3.25 - 3.80: 3624 3.80 - 4.35: 4724 4.35 - 4.90: 8693 Nonbonded interactions: 19379 Sorted by model distance: nonbonded pdb=" NE2 GLN A 288 " pdb=" OG SER A 320 " model vdw 2.146 3.120 nonbonded pdb=" OE1 GLN C 288 " pdb=" OG SER C 320 " model vdw 2.282 3.040 nonbonded pdb=" OE1 GLN B 288 " pdb=" OG SER B 320 " model vdw 2.283 3.040 nonbonded pdb=" OD1 ASN B 296 " pdb=" NZ LYS B 298 " model vdw 2.308 3.120 nonbonded pdb=" OD1 ASN C 296 " pdb=" NZ LYS C 298 " model vdw 2.308 3.120 ... (remaining 19374 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: 0.01 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'A' } 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 group one per residue 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: 2.880 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.970 Find NCS groups from input model: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 2520 Z= 0.165 Angle : 0.749 11.479 3366 Z= 0.382 Chirality : 0.054 0.231 375 Planarity : 0.003 0.022 435 Dihedral : 11.444 41.492 978 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.57 (0.41), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.95 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.007 0.002 TYR C 310 PHE 0.018 0.007 PHE B 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2520) covalent geometry : angle 0.74896 ( 3366) hydrogen bonds : bond 0.12609 ( 42) hydrogen bonds : angle 7.42496 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.103 Fit side-chains REVERT: C 376 LEU cc_start: 0.7667 (mm) cc_final: 0.6724 (pt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0336 time to fit residues: 1.2459 Evaluate side-chains 11 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** 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 = 0.4347 r_free = 0.4347 target = 0.184208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.103583 restraints weight = 4760.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4680 r_free = 0.4680 target = 0.105069 restraints weight = 3492.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.106332 restraints weight = 2853.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.107167 restraints weight = 2474.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.107416 restraints weight = 2231.251| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2520 Z= 0.168 Angle : 0.621 6.014 3366 Z= 0.321 Chirality : 0.049 0.131 375 Planarity : 0.003 0.019 435 Dihedral : 4.386 12.086 336 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.41), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 349 TYR 0.016 0.005 TYR B 310 PHE 0.014 0.003 PHE B 346 HIS 0.004 0.001 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 2520) covalent geometry : angle 0.62143 ( 3366) hydrogen bonds : bond 0.02229 ( 42) hydrogen bonds : angle 5.10350 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.113 Fit side-chains REVERT: C 295 ASP cc_start: 0.7075 (p0) cc_final: 0.6853 (p0) REVERT: C 338 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7014 (tp30) REVERT: C 376 LEU cc_start: 0.7686 (mm) cc_final: 0.6719 (pt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0299 time to fit residues: 0.8938 Evaluate side-chains 8 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.168754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.092981 restraints weight = 4853.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.094349 restraints weight = 3690.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.095238 restraints weight = 3057.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.095250 restraints weight = 2696.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.095787 restraints weight = 2689.950| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2520 Z= 0.168 Angle : 0.605 6.187 3366 Z= 0.314 Chirality : 0.050 0.133 375 Planarity : 0.003 0.017 435 Dihedral : 4.640 13.209 336 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.70 % Allowed : 4.91 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.71 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 379 TYR 0.019 0.005 TYR A 310 PHE 0.016 0.004 PHE B 378 HIS 0.003 0.001 HIS C 329 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 2520) covalent geometry : angle 0.60512 ( 3366) hydrogen bonds : bond 0.02145 ( 42) hydrogen bonds : angle 4.56678 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 18 time to evaluate : 0.104 Fit side-chains REVERT: C 338 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7115 (tm-30) REVERT: C 376 LEU cc_start: 0.7520 (mm) cc_final: 0.6709 (pt) REVERT: A 286 ASN cc_start: 0.7606 (OUTLIER) cc_final: 0.7295 (t0) outliers start: 2 outliers final: 1 residues processed: 20 average time/residue: 0.0302 time to fit residues: 0.9692 Evaluate side-chains 11 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 9 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 30 optimal weight: 6.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.158583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.081431 restraints weight = 4963.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.081367 restraints weight = 4699.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.081406 restraints weight = 4385.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.081440 restraints weight = 4452.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.081543 restraints weight = 4307.259| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 2520 Z= 0.328 Angle : 0.814 7.302 3366 Z= 0.428 Chirality : 0.056 0.173 375 Planarity : 0.004 0.016 435 Dihedral : 5.467 14.429 336 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.35 % Allowed : 7.02 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 349 TYR 0.036 0.008 TYR A 310 PHE 0.015 0.004 PHE C 346 HIS 0.009 0.003 HIS B 329 Details of bonding type rmsd covalent geometry : bond 0.00745 ( 2520) covalent geometry : angle 0.81352 ( 3366) hydrogen bonds : bond 0.02466 ( 42) hydrogen bonds : angle 5.00311 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.098 Fit side-chains REVERT: B 378 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.5860 (m-10) REVERT: C 376 LEU cc_start: 0.7957 (mm) cc_final: 0.6812 (pt) outliers start: 1 outliers final: 0 residues processed: 15 average time/residue: 0.0312 time to fit residues: 0.7923 Evaluate side-chains 11 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 10 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.168999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.089824 restraints weight = 4790.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.090530 restraints weight = 4043.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.091133 restraints weight = 3620.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.091281 restraints weight = 3331.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.091569 restraints weight = 3223.083| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2520 Z= 0.134 Angle : 0.620 5.620 3366 Z= 0.311 Chirality : 0.049 0.143 375 Planarity : 0.003 0.022 435 Dihedral : 4.905 13.667 336 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.95 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.014 0.003 TYR A 310 PHE 0.015 0.003 PHE A 346 HIS 0.004 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 2520) covalent geometry : angle 0.62031 ( 3366) hydrogen bonds : bond 0.01648 ( 42) hydrogen bonds : angle 4.39908 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.145 Fit side-chains REVERT: C 376 LEU cc_start: 0.7477 (mm) cc_final: 0.6809 (pt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0362 time to fit residues: 1.3846 Evaluate side-chains 11 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 26 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.0040 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 28 optimal weight: 0.0970 overall best weight: 2.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 288 GLN ** 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 = 0.4221 r_free = 0.4221 target = 0.171262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.089121 restraints weight = 4852.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.089536 restraints weight = 4171.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.090222 restraints weight = 3836.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.090476 restraints weight = 3547.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.090476 restraints weight = 3389.121| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2520 Z= 0.142 Angle : 0.600 5.889 3366 Z= 0.304 Chirality : 0.049 0.137 375 Planarity : 0.004 0.032 435 Dihedral : 4.723 13.777 336 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.06 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.32 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 379 TYR 0.018 0.004 TYR A 310 PHE 0.013 0.003 PHE A 346 HIS 0.003 0.001 HIS A 329 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2520) covalent geometry : angle 0.60033 ( 3366) hydrogen bonds : bond 0.01695 ( 42) hydrogen bonds : angle 4.24804 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.103 Fit side-chains REVERT: C 376 LEU cc_start: 0.7665 (mm) cc_final: 0.6876 (pt) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0283 time to fit residues: 0.6576 Evaluate side-chains 9 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.0370 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 8.9990 chunk 32 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 overall best weight: 1.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.174022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.091207 restraints weight = 4828.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.092024 restraints weight = 4010.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.092442 restraints weight = 3572.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.092443 restraints weight = 3337.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.092443 restraints weight = 3336.462| |-----------------------------------------------------------------------------| r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2520 Z= 0.127 Angle : 0.568 5.609 3366 Z= 0.288 Chirality : 0.049 0.138 375 Planarity : 0.003 0.027 435 Dihedral : 4.556 14.170 336 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.11 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 379 TYR 0.013 0.003 TYR A 310 PHE 0.012 0.002 PHE A 346 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 2520) covalent geometry : angle 0.56773 ( 3366) hydrogen bonds : bond 0.01355 ( 42) hydrogen bonds : angle 4.05482 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.105 Fit side-chains REVERT: C 376 LEU cc_start: 0.7921 (mm) cc_final: 0.7060 (pt) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0308 time to fit residues: 0.6745 Evaluate side-chains 8 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 25 optimal weight: 0.0670 chunk 26 optimal weight: 4.9990 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.9524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.170680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.089316 restraints weight = 4884.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.090079 restraints weight = 4100.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.090338 restraints weight = 3671.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.090771 restraints weight = 3467.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.090771 restraints weight = 3279.138| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2520 Z= 0.124 Angle : 0.576 6.260 3366 Z= 0.290 Chirality : 0.049 0.135 375 Planarity : 0.004 0.031 435 Dihedral : 4.464 13.873 336 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 349 TYR 0.017 0.004 TYR A 310 PHE 0.011 0.002 PHE A 346 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 2520) covalent geometry : angle 0.57558 ( 3366) hydrogen bonds : bond 0.01402 ( 42) hydrogen bonds : angle 4.09013 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.079 Fit side-chains REVERT: C 376 LEU cc_start: 0.7982 (mm) cc_final: 0.7102 (pt) outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0253 time to fit residues: 0.3710 Evaluate side-chains 5 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 0.0010 chunk 26 optimal weight: 0.5980 chunk 20 optimal weight: 6.9990 chunk 2 optimal weight: 0.5980 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.171766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.090038 restraints weight = 4836.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.090349 restraints weight = 4032.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.091125 restraints weight = 3721.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.091608 restraints weight = 3381.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4478 r_free = 0.4478 target = 0.091608 restraints weight = 3130.613| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2520 Z= 0.106 Angle : 0.550 6.072 3366 Z= 0.276 Chirality : 0.048 0.134 375 Planarity : 0.004 0.030 435 Dihedral : 4.384 13.749 336 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 379 TYR 0.012 0.003 TYR A 310 PHE 0.012 0.002 PHE A 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2520) covalent geometry : angle 0.55019 ( 3366) hydrogen bonds : bond 0.01260 ( 42) hydrogen bonds : angle 3.99506 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.108 Fit side-chains REVERT: C 295 ASP cc_start: 0.7567 (p0) cc_final: 0.7347 (p0) REVERT: C 376 LEU cc_start: 0.7954 (mm) cc_final: 0.7151 (pt) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0192 time to fit residues: 0.3816 Evaluate side-chains 5 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 12 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 21 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.170854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.088156 restraints weight = 4939.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.088793 restraints weight = 4150.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.089340 restraints weight = 3714.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.089482 restraints weight = 3431.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.089485 restraints weight = 3312.310| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2520 Z= 0.123 Angle : 0.563 6.196 3366 Z= 0.282 Chirality : 0.049 0.131 375 Planarity : 0.004 0.030 435 Dihedral : 4.391 14.088 336 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.21 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 349 TYR 0.016 0.004 TYR A 310 PHE 0.012 0.002 PHE A 346 HIS 0.003 0.001 HIS A 362 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 2520) covalent geometry : angle 0.56302 ( 3366) hydrogen bonds : bond 0.01291 ( 42) hydrogen bonds : angle 4.01799 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 648 Ramachandran restraints generated. 324 Oldfield, 0 Emsley, 324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.108 Fit side-chains REVERT: C 295 ASP cc_start: 0.7586 (p0) cc_final: 0.7372 (p0) REVERT: C 376 LEU cc_start: 0.8049 (mm) cc_final: 0.7204 (pt) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0246 time to fit residues: 0.5069 Evaluate side-chains 6 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.170120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.087820 restraints weight = 4867.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.088454 restraints weight = 4154.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.088683 restraints weight = 3723.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.089199 restraints weight = 3534.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.089199 restraints weight = 3339.405| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.4640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2520 Z= 0.121 Angle : 0.566 6.891 3366 Z= 0.283 Chirality : 0.049 0.132 375 Planarity : 0.004 0.032 435 Dihedral : 4.388 14.339 336 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 349 TYR 0.015 0.004 TYR A 310 PHE 0.012 0.002 PHE A 346 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2520) covalent geometry : angle 0.56641 ( 3366) hydrogen bonds : bond 0.01199 ( 42) hydrogen bonds : angle 3.95309 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 622.98 seconds wall clock time: 11 minutes 28.27 seconds (688.27 seconds total)