Starting phenix.real_space_refine on Wed Mar 5 15:49:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7u0z_26268/03_2025/7u0z_26268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7u0z_26268/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7u0z_26268/03_2025/7u0z_26268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7u0z_26268/03_2025/7u0z_26268.map" model { file = "/net/cci-nas-00/data/ceres_data/7u0z_26268/03_2025/7u0z_26268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7u0z_26268/03_2025/7u0z_26268.cif" } resolution = 4.2 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= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 2.75, per 1000 atoms: 1.11 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: 0.69 Conformation dependent library (CDL) restraints added in 291.8 milliseconds 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: 0.34 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: 0.75 Time building geometry restraints manager: 0.68 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: 0.02 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 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: 3.400 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.110 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:3.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.040 ------------------------------------------------------------------------------- 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= 0.339 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 (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: -2.57 (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 HIS 0.003 0.001 HIS A 362 PHE 0.018 0.007 PHE B 346 TYR 0.007 0.002 TYR C 310 ARG 0.001 0.000 ARG A 379 *********************** 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 : 0.278 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: 0.0873 time to fit residues: 3.1785 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 : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 15 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN B 288 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 279 ASN A 286 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.170589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.090846 restraints weight = 4871.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.092057 restraints weight = 3786.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.092893 restraints weight = 3200.106| |-----------------------------------------------------------------------------| r_work (final): 0.4007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 2520 Z= 0.459 Angle : 0.768 7.294 3366 Z= 0.409 Chirality : 0.054 0.151 375 Planarity : 0.005 0.020 435 Dihedral : 5.171 14.466 336 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.05 % Allowed : 7.72 % Favored : 91.23 % 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: -2.77 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 329 PHE 0.016 0.005 PHE C 346 TYR 0.027 0.007 TYR A 310 ARG 0.002 0.001 ARG A 349 *********************** 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: 3 poor density : 15 time to evaluate : 0.314 Fit side-chains REVERT: C 376 LEU cc_start: 0.7828 (mm) cc_final: 0.6771 (pt) REVERT: A 286 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7288 (t0) outliers start: 3 outliers final: 2 residues processed: 18 average time/residue: 0.0633 time to fit residues: 2.0044 Evaluate side-chains 12 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.164285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.084762 restraints weight = 4865.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.085469 restraints weight = 3932.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.086274 restraints weight = 3453.415| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 2520 Z= 0.423 Angle : 0.740 6.875 3366 Z= 0.386 Chirality : 0.053 0.169 375 Planarity : 0.004 0.020 435 Dihedral : 5.446 14.036 336 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.35 % Allowed : 4.56 % Favored : 95.09 % 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: -3.03 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 329 PHE 0.022 0.004 PHE B 346 TYR 0.027 0.006 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** 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 18 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.310 Fit side-chains REVERT: B 368 ASN cc_start: 0.5764 (m110) cc_final: 0.5058 (t0) REVERT: C 338 GLU cc_start: 0.7366 (tp30) cc_final: 0.7157 (tp30) REVERT: C 376 LEU cc_start: 0.7655 (mm) cc_final: 0.6802 (pt) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.0738 time to fit residues: 2.2145 Evaluate side-chains 10 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 32 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.4190 r_free = 0.4190 target = 0.090873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.071408 restraints weight = 5260.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.072772 restraints weight = 3678.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.073703 restraints weight = 2895.483| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2520 Z= 0.291 Angle : 0.664 6.245 3366 Z= 0.340 Chirality : 0.050 0.135 375 Planarity : 0.003 0.020 435 Dihedral : 5.114 13.719 336 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -3.01 (0.39), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.005 0.002 PHE C 346 TYR 0.021 0.005 TYR A 310 ARG 0.001 0.000 ARG C 379 *********************** 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 18 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.394 Fit side-chains REVERT: B 368 ASN cc_start: 0.5486 (m110) cc_final: 0.5193 (t0) REVERT: C 376 LEU cc_start: 0.7573 (mm) cc_final: 0.6769 (pt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0974 time to fit residues: 2.7543 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 : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 21 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 0.0470 chunk 29 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 overall best weight: 1.7284 ------------------------------------------------------------------------------- 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 = 0.4258 r_free = 0.4258 target = 0.175877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.093223 restraints weight = 4860.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.094006 restraints weight = 4044.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.094338 restraints weight = 3586.844| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2520 Z= 0.195 Angle : 0.587 6.187 3366 Z= 0.296 Chirality : 0.049 0.137 375 Planarity : 0.003 0.024 435 Dihedral : 4.709 13.865 336 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -2.97 (0.39), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.26 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.009 0.002 PHE C 346 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** 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 17 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.303 Fit side-chains REVERT: B 295 ASP cc_start: 0.7261 (p0) cc_final: 0.6958 (p0) REVERT: C 376 LEU cc_start: 0.7565 (mm) cc_final: 0.6818 (pt) REVERT: A 368 ASN cc_start: 0.6638 (m110) cc_final: 0.6294 (t0) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0782 time to fit residues: 2.1589 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 : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.170697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.090078 restraints weight = 4866.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.090811 restraints weight = 4036.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.091422 restraints weight = 3561.376| |-----------------------------------------------------------------------------| r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2520 Z= 0.214 Angle : 0.577 5.802 3366 Z= 0.294 Chirality : 0.048 0.131 375 Planarity : 0.003 0.027 435 Dihedral : 4.648 13.910 336 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -2.99 (0.39), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 329 PHE 0.006 0.002 PHE B 378 TYR 0.017 0.004 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** 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 16 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.326 Fit side-chains REVERT: C 376 LEU cc_start: 0.7603 (mm) cc_final: 0.6885 (pt) REVERT: A 368 ASN cc_start: 0.6728 (m110) cc_final: 0.6435 (t0) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0809 time to fit residues: 2.1486 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 : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4153 r_free = 0.4153 target = 0.087746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.068733 restraints weight = 5654.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.070023 restraints weight = 3917.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.070681 restraints weight = 3088.954| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 2520 Z= 0.300 Angle : 0.632 6.311 3366 Z= 0.326 Chirality : 0.050 0.127 375 Planarity : 0.004 0.026 435 Dihedral : 4.902 14.733 336 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.39), 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 HIS 0.007 0.002 HIS A 329 PHE 0.006 0.002 PHE B 378 TYR 0.022 0.005 TYR A 310 ARG 0.002 0.000 ARG B 379 *********************** 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 9 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.304 Fit side-chains REVERT: B 295 ASP cc_start: 0.7431 (p0) cc_final: 0.6979 (p0) REVERT: B 368 ASN cc_start: 0.5758 (m110) cc_final: 0.5158 (t0) REVERT: C 376 LEU cc_start: 0.7852 (mm) cc_final: 0.6974 (pt) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0601 time to fit residues: 1.1774 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 19 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 18 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 28 optimal weight: 0.0270 chunk 11 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 25 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- 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 = 0.4171 r_free = 0.4171 target = 0.088878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.070076 restraints weight = 5462.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.071401 restraints weight = 3784.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.072223 restraints weight = 2960.973| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2520 Z= 0.252 Angle : 0.604 6.000 3366 Z= 0.309 Chirality : 0.049 0.132 375 Planarity : 0.004 0.031 435 Dihedral : 4.779 14.824 336 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: -3.17 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 329 PHE 0.006 0.002 PHE B 378 TYR 0.019 0.004 TYR A 310 ARG 0.001 0.000 ARG A 379 *********************** 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 14 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.320 Fit side-chains REVERT: B 295 ASP cc_start: 0.7598 (p0) cc_final: 0.7099 (p0) REVERT: B 368 ASN cc_start: 0.6058 (m110) cc_final: 0.5286 (t0) REVERT: C 376 LEU cc_start: 0.7993 (mm) cc_final: 0.7216 (pt) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0731 time to fit residues: 1.8005 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 : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.4196 r_free = 0.4196 target = 0.170423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.086739 restraints weight = 4840.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.087227 restraints weight = 4225.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.087227 restraints weight = 3874.686| |-----------------------------------------------------------------------------| r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.4720 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= 0.241 Angle : 0.613 7.675 3366 Z= 0.312 Chirality : 0.049 0.130 375 Planarity : 0.004 0.033 435 Dihedral : 4.756 15.026 336 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 329 PHE 0.005 0.002 PHE C 346 TYR 0.019 0.004 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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 10 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.319 Fit side-chains REVERT: B 295 ASP cc_start: 0.7499 (p0) cc_final: 0.6956 (p0) REVERT: B 368 ASN cc_start: 0.5937 (m110) cc_final: 0.5041 (t0) REVERT: C 376 LEU cc_start: 0.8033 (mm) cc_final: 0.7194 (pt) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0775 time to fit residues: 1.5236 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 : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- 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 276 GLN ** C 362 HIS ** 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 = 0.4146 r_free = 0.4146 target = 0.165449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.080891 restraints weight = 4926.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.081132 restraints weight = 4492.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.081238 restraints weight = 4259.631| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2520 Z= 0.371 Angle : 0.701 8.145 3366 Z= 0.361 Chirality : 0.052 0.166 375 Planarity : 0.004 0.032 435 Dihedral : 5.162 15.855 336 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.60 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 329 PHE 0.008 0.003 PHE C 378 TYR 0.029 0.006 TYR A 310 ARG 0.001 0.000 ARG A 349 ********************** 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 11 residues out of total 285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.321 Fit side-chains REVERT: B 295 ASP cc_start: 0.7487 (p0) cc_final: 0.6904 (p0) REVERT: B 368 ASN cc_start: 0.5922 (m110) cc_final: 0.5272 (t0) REVERT: C 376 LEU cc_start: 0.8187 (mm) cc_final: 0.7388 (pt) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0666 time to fit residues: 1.4691 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 : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 329 HIS ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** 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 = 0.4207 r_free = 0.4207 target = 0.090434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.071789 restraints weight = 5385.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.073200 restraints weight = 3624.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.074089 restraints weight = 2789.168| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2520 Z= 0.165 Angle : 0.588 7.782 3366 Z= 0.296 Chirality : 0.049 0.154 375 Planarity : 0.004 0.036 435 Dihedral : 4.637 14.543 336 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.35 % Allowed : 0.35 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.37), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 299 PHE 0.009 0.002 PHE A 346 TYR 0.010 0.003 TYR A 310 ARG 0.001 0.000 ARG C 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1113.39 seconds wall clock time: 20 minutes 16.97 seconds (1216.97 seconds total)