Starting phenix.real_space_refine (version: dev) on Tue Nov 29 11:52:43 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/11_2022/7u0z_26268.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/11_2022/7u0z_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_26268/11_2022/7u0z_26268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/11_2022/7u0z_26268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/11_2022/7u0z_26268.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u0z_26268/11_2022/7u0z_26268.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4778/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: 1.91, per 1000 atoms: 0.77 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: 0.98 Conformation dependent library (CDL) restraints added in 371.1 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: 0.18 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: 0.51 Time building geometry restraints manager: 1.07 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 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. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 7.700 Check model and map are aligned: 0.040 Convert atoms to be neutral: 0.020 Process input model: 12.730 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 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 : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer Outliers : 0.00 % 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 *********************** 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 : 0.321 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0778 time to fit residues: 2.9218 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4352 ------------------------------------------------------------------------------- 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: 0.8980 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 2.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2520 Z= 0.283 Angle : 0.628 6.331 3366 Z= 0.325 Chirality : 0.049 0.130 375 Planarity : 0.003 0.018 435 Dihedral : 4.410 11.843 336 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer Outliers : 0.00 % 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: -2.55 (0.41), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.93 (0.31), residues: 324 *********************** 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 14 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 14 time to evaluate : 0.295 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0694 time to fit residues: 1.7654 Evaluate side-chains 6 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.299 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4162 ------------------------------------------------------------------------------- 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: 0.3980 chunk 8 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 chunk 3 optimal weight: 0.7980 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 GLN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2520 Z= 0.239 Angle : 0.578 5.976 3366 Z= 0.293 Chirality : 0.049 0.135 375 Planarity : 0.003 0.018 435 Dihedral : 4.429 12.981 336 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.41), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.31), residues: 324 *********************** 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 fitting. rotamer outliers: 1 poor density : 17 time to evaluate : 0.339 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.0756 time to fit residues: 2.2430 Evaluate side-chains 9 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0268 time to fit residues: 0.5005 ------------------------------------------------------------------------------- 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: 0.9990 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 20.0000 chunk 31 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2795 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= 0.254 Angle : 0.583 6.035 3366 Z= 0.294 Chirality : 0.048 0.139 375 Planarity : 0.003 0.019 435 Dihedral : 4.430 12.948 336 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer Outliers : 0.00 % 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: -2.64 (0.41), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.31), residues: 324 *********************** 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 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 outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0727 time to fit residues: 2.0667 Evaluate side-chains 10 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4892 ------------------------------------------------------------------------------- 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: 6.9990 chunk 27 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 6.9990 chunk 28 optimal weight: 0.0070 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 7 optimal weight: 7.9990 overall best weight: 1.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 GLN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** 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: 0.7337 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 2520 Z= 0.196 Angle : 0.559 5.992 3366 Z= 0.278 Chirality : 0.048 0.153 375 Planarity : 0.003 0.021 435 Dihedral : 4.356 13.597 336 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.00 % 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: -2.67 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.31), residues: 324 *********************** 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 18 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.339 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0750 time to fit residues: 2.2313 Evaluate side-chains 8 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4374 ------------------------------------------------------------------------------- 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: 4.9990 chunk 26 optimal weight: 6.9990 chunk 14 optimal weight: 0.0870 chunk 2 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 16 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 2520 Z= 0.271 Angle : 0.602 6.216 3366 Z= 0.303 Chirality : 0.050 0.166 375 Planarity : 0.003 0.024 435 Dihedral : 4.488 13.720 336 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer Outliers : 0.00 % 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: -2.70 (0.41), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.31), residues: 324 *********************** 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 15 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.327 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0704 time to fit residues: 1.8780 Evaluate side-chains 7 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.329 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4518 ------------------------------------------------------------------------------- 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: 6.9990 chunk 19 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- 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 276 GLN ** C 288 GLN ** 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: 0.7472 moved from start: 0.3791 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= 0.308 Angle : 0.652 7.014 3366 Z= 0.329 Chirality : 0.051 0.164 375 Planarity : 0.003 0.024 435 Dihedral : 4.763 14.697 336 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.00 % 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: -2.90 (0.39), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.30), residues: 324 *********************** 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 18 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.362 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0891 time to fit residues: 2.5683 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4594 ------------------------------------------------------------------------------- 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: 0.0570 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 0.0030 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.6114 ------------------------------------------------------------------------------- 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: 0.7415 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 2520 Z= 0.186 Angle : 0.573 6.016 3366 Z= 0.285 Chirality : 0.049 0.146 375 Planarity : 0.003 0.026 435 Dihedral : 4.423 14.193 336 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.00 % 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: -2.85 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.30), residues: 324 *********************** 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 12 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.329 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0754 time to fit residues: 1.6844 Evaluate side-chains 6 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5267 ------------------------------------------------------------------------------- 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: 3.9990 chunk 19 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 26 optimal weight: 0.0570 chunk 2 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 overall best weight: 2.5104 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4245 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= 0.243 Angle : 0.605 6.275 3366 Z= 0.303 Chirality : 0.050 0.145 375 Planarity : 0.003 0.026 435 Dihedral : 4.533 14.717 336 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 0.00 % 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: -2.92 (0.40), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.31), residues: 324 *********************** 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 : 0.336 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0834 time to fit residues: 1.6935 Evaluate side-chains 4 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 4 time to evaluate : 0.339 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4640 ------------------------------------------------------------------------------- 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: 6.9990 chunk 26 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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: 0.7517 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 2520 Z= 0.303 Angle : 0.663 6.897 3366 Z= 0.336 Chirality : 0.051 0.144 375 Planarity : 0.004 0.025 435 Dihedral : 4.764 15.455 336 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer Outliers : 0.00 % 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: -3.17 (0.39), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.30), residues: 324 ********************** 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 12 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.345 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0751 time to fit residues: 1.6678 Evaluate side-chains 5 residues out of total 285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4536 ------------------------------------------------------------------------------- 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: 5.9990 chunk 22 optimal weight: 0.0020 chunk 0 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 31 optimal weight: 0.0370 chunk 6 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 0.5666 ------------------------------------------------------------------------------- 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 329 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.176136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.092183 restraints weight = 4749.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.093063 restraints weight = 3978.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.093659 restraints weight = 3494.214| |-----------------------------------------------------------------------------| r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 2520 Z= 0.143 Angle : 0.564 5.923 3366 Z= 0.281 Chirality : 0.049 0.142 375 Planarity : 0.003 0.026 435 Dihedral : 4.248 13.838 336 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.00 % 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: -3.01 (0.39), residues: 324 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.30), residues: 324 =============================================================================== Job complete usr+sys time: 965.66 seconds wall clock time: 18 minutes 42.25 seconds (1122.25 seconds total)