Starting phenix.real_space_refine on Sun Mar 10 15:00:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/03_2024/7u0z_26268.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/03_2024/7u0z_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/03_2024/7u0z_26268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/03_2024/7u0z_26268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/03_2024/7u0z_26268.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/03_2024/7u0z_26268.pdb" } 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 Residue "B GLU 372": "OE1" <-> "OE2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "A GLU 372": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 1.69, per 1000 atoms: 0.68 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 - 3.50 Amino acid : False - 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: 0.88 Conformation dependent library (CDL) restraints added in 414.3 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: 0.35 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: 0.64 Time building geometry restraints manager: 0.98 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: 102.27 - 108.07: 136 108.07 - 113.88: 1430 113.88 - 119.68: 602 119.68 - 125.49: 1168 125.49 - 131.29: 30 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 2.520 nonbonded pdb=" OE1 GLN C 288 " pdb=" OG SER C 320 " model vdw 2.282 2.440 nonbonded pdb=" OE1 GLN B 288 " pdb=" OG SER B 320 " model vdw 2.283 2.440 nonbonded pdb=" OD1 ASN B 296 " pdb=" NZ LYS B 298 " model vdw 2.308 2.520 nonbonded pdb=" OD1 ASN C 296 " pdb=" NZ LYS C 298 " model vdw 2.308 2.520 ... (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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.390 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.570 Find NCS groups from input model: 0.140 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.700 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.272 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: 0.0881 time to fit residues: 3.3335 Evaluate side-chains 11 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 0.0060 chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 overall best weight: 3.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN A 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 2520 Z= 0.398 Angle : 0.693 6.988 3366 Z= 0.365 Chirality : 0.052 0.138 375 Planarity : 0.004 0.019 435 Dihedral : 4.754 13.438 336 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.35 % Allowed : 7.72 % Favored : 91.93 % 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: -2.65 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS C 374 PHE 0.014 0.004 PHE B 346 TYR 0.022 0.006 TYR A 310 ARG 0.002 0.001 ARG B 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 15 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.318 Fit side-chains REVERT: B 300 VAL cc_start: 0.7996 (t) cc_final: 0.7767 (t) REVERT: C 295 ASP cc_start: 0.7358 (p0) cc_final: 0.6974 (p0) REVERT: C 376 LEU cc_start: 0.7661 (mm) cc_final: 0.6671 (pt) outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.0670 time to fit residues: 1.8056 Evaluate side-chains 12 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.8980 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2520 Z= 0.215 Angle : 0.572 6.116 3366 Z= 0.288 Chirality : 0.048 0.129 375 Planarity : 0.003 0.019 435 Dihedral : 4.515 12.987 336 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % 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: -2.55 (0.41), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.011 0.003 PHE B 346 TYR 0.013 0.003 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 21 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.311 Fit side-chains REVERT: B 300 VAL cc_start: 0.7870 (t) cc_final: 0.7650 (t) REVERT: C 376 LEU cc_start: 0.7240 (mm) cc_final: 0.6667 (pt) outliers start: 1 outliers final: 1 residues processed: 21 average time/residue: 0.0953 time to fit residues: 2.9118 Evaluate side-chains 12 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 11 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 31 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 2520 Z= 0.406 Angle : 0.686 6.964 3366 Z= 0.355 Chirality : 0.052 0.147 375 Planarity : 0.004 0.020 435 Dihedral : 4.939 13.942 336 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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: -2.80 (0.41), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 329 PHE 0.022 0.003 PHE C 346 TYR 0.026 0.006 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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 fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.334 Fit side-chains REVERT: B 368 ASN cc_start: 0.6177 (m110) cc_final: 0.5476 (t0) REVERT: C 295 ASP cc_start: 0.7692 (p0) cc_final: 0.7336 (p0) REVERT: C 376 LEU cc_start: 0.7686 (mm) cc_final: 0.6837 (pt) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0788 time to fit residues: 2.2837 Evaluate side-chains 10 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3337 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= 0.249 Angle : 0.606 6.161 3366 Z= 0.306 Chirality : 0.049 0.163 375 Planarity : 0.003 0.021 435 Dihedral : 4.715 13.984 336 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % 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: -2.70 (0.41), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 374 PHE 0.012 0.003 PHE A 346 TYR 0.016 0.004 TYR A 310 ARG 0.000 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 fitting. rotamer outliers: 0 poor density : 17 time to evaluate : 0.314 Fit side-chains REVERT: C 376 LEU cc_start: 0.7456 (mm) cc_final: 0.6823 (pt) REVERT: A 338 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7225 (tm-30) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0682 time to fit residues: 1.9961 Evaluate side-chains 12 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 18 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 17 optimal weight: 0.0060 overall best weight: 6.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 GLN ** C 307 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 2520 Z= 0.522 Angle : 0.815 8.171 3366 Z= 0.421 Chirality : 0.057 0.214 375 Planarity : 0.005 0.018 435 Dihedral : 5.479 15.700 336 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 0.35 % Allowed : 2.81 % Favored : 96.84 % 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: -3.25 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.003 HIS A 329 PHE 0.021 0.006 PHE C 378 TYR 0.038 0.008 TYR A 310 ARG 0.002 0.000 ARG A 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 14 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 13 time to evaluate : 0.332 Fit side-chains REVERT: C 376 LEU cc_start: 0.7934 (mm) cc_final: 0.7091 (pt) REVERT: C 378 PHE cc_start: 0.7162 (OUTLIER) cc_final: 0.6204 (m-80) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.0729 time to fit residues: 1.8016 Evaluate side-chains 10 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 9 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 2 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2520 Z= 0.229 Angle : 0.620 6.243 3366 Z= 0.314 Chirality : 0.050 0.154 375 Planarity : 0.003 0.021 435 Dihedral : 5.033 15.167 336 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -2.96 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 362 PHE 0.017 0.004 PHE A 346 TYR 0.015 0.004 TYR A 310 ARG 0.001 0.000 ARG C 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 16 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 16 time to evaluate : 0.287 Fit side-chains REVERT: C 300 VAL cc_start: 0.7863 (t) cc_final: 0.7638 (t) REVERT: C 376 LEU cc_start: 0.7971 (mm) cc_final: 0.7265 (pt) REVERT: A 291 CYS cc_start: 0.7245 (p) cc_final: 0.6958 (t) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0651 time to fit residues: 1.8207 Evaluate side-chains 10 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2520 Z= 0.364 Angle : 0.707 7.291 3366 Z= 0.360 Chirality : 0.052 0.202 375 Planarity : 0.004 0.027 435 Dihedral : 5.267 15.883 336 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.35 % Favored : 87.65 % 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 (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: -3.16 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.31), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 329 PHE 0.012 0.003 PHE B 346 TYR 0.028 0.006 TYR A 310 ARG 0.001 0.000 ARG C 349 *********************** 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 11 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.304 Fit side-chains REVERT: C 376 LEU cc_start: 0.8013 (mm) cc_final: 0.7345 (pt) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0663 time to fit residues: 1.4280 Evaluate side-chains 7 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.0030 chunk 19 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 21 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 20.0000 overall best weight: 5.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 2520 Z= 0.433 Angle : 0.782 7.670 3366 Z= 0.402 Chirality : 0.055 0.239 375 Planarity : 0.005 0.027 435 Dihedral : 5.733 17.392 336 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % 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: -3.49 (0.39), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS A 329 PHE 0.013 0.004 PHE B 346 TYR 0.033 0.007 TYR A 310 ARG 0.001 0.000 ARG B 379 *********************** 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 11 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.312 Fit side-chains REVERT: C 376 LEU cc_start: 0.8169 (mm) cc_final: 0.7467 (pt) outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0671 time to fit residues: 1.4534 Evaluate side-chains 6 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 2520 Z= 0.424 Angle : 0.777 7.914 3366 Z= 0.396 Chirality : 0.055 0.176 375 Planarity : 0.004 0.027 435 Dihedral : 5.740 16.426 336 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.36 % Favored : 83.64 % 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: -3.69 (0.38), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.81 (0.29), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS A 329 PHE 0.019 0.004 PHE B 346 TYR 0.031 0.007 TYR A 310 ARG 0.001 0.000 ARG B 379 ********************** 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 fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.317 Fit side-chains REVERT: C 376 LEU cc_start: 0.8133 (mm) cc_final: 0.7479 (pt) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0711 time to fit residues: 1.4204 Evaluate side-chains 7 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 0.0050 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 20.0000 chunk 12 optimal weight: 0.0870 chunk 32 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 31 optimal weight: 0.0470 chunk 6 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 overall best weight: 2.0274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN ** B 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 307 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.170005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.085127 restraints weight = 4869.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.085706 restraints weight = 4197.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.085712 restraints weight = 3801.768| |-----------------------------------------------------------------------------| r_work (final): 0.3929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.5175 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= 0.224 Angle : 0.636 6.954 3366 Z= 0.318 Chirality : 0.051 0.145 375 Planarity : 0.004 0.031 435 Dihedral : 5.168 15.634 336 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 13.40 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 (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: -3.35 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 299 PHE 0.017 0.003 PHE B 346 TYR 0.016 0.004 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: 952.73 seconds wall clock time: 18 minutes 3.13 seconds (1083.13 seconds total)