Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 3 01:25:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/10_2023/8orf_17122.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/10_2023/8orf_17122.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/10_2023/8orf_17122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/10_2023/8orf_17122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/10_2023/8orf_17122.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/10_2023/8orf_17122.pdb" } resolution = 2.5 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= 0.004 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: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1413 2.51 5 N 420 2.21 5 O 432 1.98 5 H 2382 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 4653 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1551 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1551 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 1551 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Time building chain proxies: 2.48, per 1000 atoms: 0.53 Number of scatterers: 4653 At special positions: 0 Unit cell: (83.93, 92.65, 35.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 432 8.00 N 420 7.00 C 1413 6.00 H 2382 1.00 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: 3.65 Conformation dependent library (CDL) restraints added in 388.3 milliseconds 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 45.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 283 removed outlier: 6.421A pdb=" N ILE B 278 " --> pdb=" O ASN C 279 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N LYS C 281 " --> pdb=" O ILE B 278 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYS B 280 " --> pdb=" O LYS C 281 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP C 283 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU B 282 " --> pdb=" O ASP C 283 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 286 through 289 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 299 removed outlier: 6.432A pdb=" N ILE B 297 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 310 removed outlier: 6.822A pdb=" N GLY B 304 " --> pdb=" O GLY A 303 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLY B 303 " --> pdb=" O GLY C 304 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL C 306 " --> pdb=" O GLY B 303 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N SER B 305 " --> pdb=" O VAL C 306 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE C 308 " --> pdb=" O SER B 305 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN B 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N TYR C 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 313 through 318 removed outlier: 6.397A pdb=" N VAL B 313 " --> pdb=" O ASP C 314 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER C 316 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU B 315 " --> pdb=" O SER C 316 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL C 318 " --> pdb=" O LEU B 315 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LYS B 317 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.733A pdb=" N LYS B 321 " --> pdb=" O CYS C 322 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.456A pdb=" N ASN B 327 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N HIS C 330 " --> pdb=" O ASN B 327 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N HIS B 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 336 through 341 removed outlier: 6.360A pdb=" N VAL B 337 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LYS A 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 339 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 344 through 346 removed outlier: 6.539A pdb=" N ASP B 345 " --> pdb=" O PHE C 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 350 through 354 removed outlier: 6.272A pdb=" N VAL B 350 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LYS A 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER B 352 " --> pdb=" O LYS A 353 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 360 through 361 removed outlier: 6.632A pdb=" N ILE B 360 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 369 through 376 removed outlier: 6.908A pdb=" N LYS B 370 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LYS A 375 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU B 376 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 371 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU B 372 " --> pdb=" O ILE C 371 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR C 373 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N HIS B 374 " --> pdb=" O THR C 373 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 144 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: 1.53 Time building geometry restraints manager: 3.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 2376 1.03 - 1.22: 6 1.22 - 1.41: 867 1.41 - 1.61: 1428 1.61 - 1.80: 6 Bond restraints: 4683 Sorted by residual: bond pdb=" CG LYS B 311 " pdb=" HG3 LYS B 311 " ideal model delta sigma weight residual 0.970 0.938 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" CG LYS C 311 " pdb=" HG3 LYS C 311 " ideal model delta sigma weight residual 0.970 0.938 0.032 2.00e-02 2.50e+03 2.62e+00 bond pdb=" CG LYS A 311 " pdb=" HG3 LYS A 311 " ideal model delta sigma weight residual 0.970 0.938 0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" CE LYS A 311 " pdb=" NZ LYS A 311 " ideal model delta sigma weight residual 1.489 1.441 0.048 3.00e-02 1.11e+03 2.58e+00 bond pdb=" CE LYS C 311 " pdb=" NZ LYS C 311 " ideal model delta sigma weight residual 1.489 1.441 0.048 3.00e-02 1.11e+03 2.54e+00 ... (remaining 4678 not shown) Histogram of bond angle deviations from ideal: 102.40 - 108.30: 1660 108.30 - 114.19: 4687 114.19 - 120.09: 801 120.09 - 125.98: 1339 125.98 - 131.88: 72 Bond angle restraints: 8559 Sorted by residual: angle pdb=" CA LYS B 281 " pdb=" CB LYS B 281 " pdb=" CG LYS B 281 " ideal model delta sigma weight residual 114.10 120.85 -6.75 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA LYS C 281 " pdb=" CB LYS C 281 " pdb=" CG LYS C 281 " ideal model delta sigma weight residual 114.10 120.84 -6.74 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA LYS A 281 " pdb=" CB LYS A 281 " pdb=" CG LYS A 281 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 angle pdb=" CB LYS B 280 " pdb=" CG LYS B 280 " pdb=" CD LYS B 280 " ideal model delta sigma weight residual 111.30 118.92 -7.62 2.30e+00 1.89e-01 1.10e+01 angle pdb=" N LYS A 281 " pdb=" CA LYS A 281 " pdb=" C LYS A 281 " ideal model delta sigma weight residual 109.23 114.36 -5.13 1.55e+00 4.16e-01 1.10e+01 ... (remaining 8554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.40: 1569 13.40 - 26.80: 138 26.80 - 40.20: 21 40.20 - 53.59: 17 53.59 - 66.99: 43 Dihedral angle restraints: 1788 sinusoidal: 885 harmonic: 903 Sorted by residual: dihedral pdb=" CA SER A 356 " pdb=" C SER A 356 " pdb=" N LEU A 357 " pdb=" CA LEU A 357 " ideal model delta harmonic sigma weight residual 180.00 155.79 24.21 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER B 356 " pdb=" C SER B 356 " pdb=" N LEU B 357 " pdb=" CA LEU B 357 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA SER C 356 " pdb=" C SER C 356 " pdb=" N LEU C 357 " pdb=" CA LEU C 357 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 ... (remaining 1785 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.049: 178 0.049 - 0.098: 128 0.098 - 0.147: 30 0.147 - 0.195: 11 0.195 - 0.244: 4 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA LYS A 281 " pdb=" N LYS A 281 " pdb=" C LYS A 281 " pdb=" CB LYS A 281 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LYS B 281 " pdb=" N LYS B 281 " pdb=" C LYS B 281 " pdb=" CB LYS B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA LYS C 281 " pdb=" N LYS C 281 " pdb=" C LYS C 281 " pdb=" CB LYS C 281 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 348 not shown) Planarity restraints: 681 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 359 " -0.035 2.00e-02 2.50e+03 5.29e-02 4.20e+01 pdb=" CG ASN C 359 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN C 359 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN C 359 " 0.092 2.00e-02 2.50e+03 pdb="HD21 ASN C 359 " 0.006 2.00e-02 2.50e+03 pdb="HD22 ASN C 359 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 359 " -0.035 2.00e-02 2.50e+03 5.26e-02 4.15e+01 pdb=" CG ASN B 359 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN B 359 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN B 359 " 0.092 2.00e-02 2.50e+03 pdb="HD21 ASN B 359 " 0.005 2.00e-02 2.50e+03 pdb="HD22 ASN B 359 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 359 " -0.035 2.00e-02 2.50e+03 5.25e-02 4.14e+01 pdb=" CG ASN A 359 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 359 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 359 " 0.092 2.00e-02 2.50e+03 pdb="HD21 ASN A 359 " 0.005 2.00e-02 2.50e+03 pdb="HD22 ASN A 359 " -0.082 2.00e-02 2.50e+03 ... (remaining 678 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.38: 1978 2.38 - 2.93: 10703 2.93 - 3.49: 10615 3.49 - 4.04: 16031 4.04 - 4.60: 22249 Nonbonded interactions: 61576 Sorted by model distance: nonbonded pdb=" OD2 ASP A 295 " pdb=" HZ3 LYS A 311 " model vdw 1.823 1.850 nonbonded pdb=" OD2 ASP C 295 " pdb=" HZ3 LYS C 311 " model vdw 1.823 1.850 nonbonded pdb=" OD2 ASP B 295 " pdb=" HZ3 LYS B 311 " model vdw 1.823 1.850 nonbonded pdb=" OD1 ASP B 348 " pdb=" H ARG B 349 " model vdw 1.882 1.850 nonbonded pdb=" OD1 ASP C 348 " pdb=" H ARG C 349 " model vdw 1.882 1.850 ... (remaining 61571 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.070 Extract box with map and model: 3.600 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.220 Find NCS groups from input model: 0.190 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 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 : 0.010 0.070 2301 Z= 0.663 Angle : 1.272 8.005 3078 Z= 0.672 Chirality : 0.072 0.244 351 Planarity : 0.005 0.032 393 Dihedral : 11.764 65.195 891 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % 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: -2.82 (0.38), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.14 (0.29), residues: 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 2.2850 time to fit residues: 272.7823 Evaluate side-chains 69 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 279 ASN B 286 ASN B 336 GLN C 368 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2301 Z= 0.189 Angle : 0.607 4.933 3078 Z= 0.305 Chirality : 0.051 0.136 351 Planarity : 0.003 0.021 393 Dihedral : 6.913 18.270 306 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.65 % Allowed : 18.18 % Favored : 79.17 % 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: -3.07 (0.37), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.28), residues: 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 1.8687 time to fit residues: 138.1176 Evaluate side-chains 67 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 63 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.1266 time to fit residues: 0.9966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN C 362 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2301 Z= 0.257 Angle : 0.594 5.123 3078 Z= 0.299 Chirality : 0.050 0.132 351 Planarity : 0.003 0.023 393 Dihedral : 6.450 16.807 306 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.03 % Allowed : 22.35 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.28), residues: 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 62 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 67 average time/residue: 1.6718 time to fit residues: 115.2530 Evaluate side-chains 62 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.8159 time to fit residues: 2.2948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.6305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2301 Z= 0.216 Angle : 0.573 5.118 3078 Z= 0.286 Chirality : 0.050 0.129 351 Planarity : 0.003 0.025 393 Dihedral : 6.144 15.751 306 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.03 % Allowed : 22.73 % Favored : 74.24 % 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: -3.26 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.28), residues: 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 59 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 63 average time/residue: 1.6946 time to fit residues: 109.9996 Evaluate side-chains 59 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 55 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1219 time to fit residues: 0.6187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN A 362 HIS C 336 GLN C 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2301 Z= 0.232 Angle : 0.560 4.940 3078 Z= 0.282 Chirality : 0.050 0.128 351 Planarity : 0.003 0.029 393 Dihedral : 6.034 16.053 306 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.65 % Allowed : 23.11 % Favored : 74.24 % 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: -3.28 (0.37), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.28), residues: 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 1.7815 time to fit residues: 106.3793 Evaluate side-chains 58 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1292 time to fit residues: 0.8328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 336 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2301 Z= 0.193 Angle : 0.527 3.628 3078 Z= 0.266 Chirality : 0.050 0.128 351 Planarity : 0.003 0.028 393 Dihedral : 5.801 15.734 306 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.89 % Allowed : 24.24 % Favored : 73.86 % 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: -3.28 (0.37), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.28), residues: 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 60 average time/residue: 1.6279 time to fit residues: 100.7750 Evaluate side-chains 58 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1252 time to fit residues: 0.6426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 14 optimal weight: 4.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.6711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2301 Z= 0.202 Angle : 0.523 3.750 3078 Z= 0.266 Chirality : 0.050 0.127 351 Planarity : 0.004 0.029 393 Dihedral : 5.777 16.178 306 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.27 % Allowed : 23.11 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.37), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.28), residues: 297 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 1.7146 time to fit residues: 107.8094 Evaluate side-chains 58 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1252 time to fit residues: 0.6599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.6756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2301 Z= 0.295 Angle : 0.553 4.342 3078 Z= 0.284 Chirality : 0.049 0.129 351 Planarity : 0.004 0.029 393 Dihedral : 6.049 17.277 306 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.27 % Allowed : 24.24 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.31 (0.37), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.28), residues: 297 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 1.6792 time to fit residues: 100.4763 Evaluate side-chains 59 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.398 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.1299 time to fit residues: 0.8504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 25 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.6824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2301 Z= 0.180 Angle : 0.516 4.682 3078 Z= 0.262 Chirality : 0.050 0.126 351 Planarity : 0.003 0.030 393 Dihedral : 5.705 16.074 306 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.89 % Allowed : 25.38 % Favored : 72.73 % 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: -3.29 (0.37), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.50 (0.28), residues: 297 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 57 average time/residue: 1.7026 time to fit residues: 100.0445 Evaluate side-chains 58 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 53 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 1 average time/residue: 0.1299 time to fit residues: 0.6239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.2980 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.6916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2301 Z= 0.147 Angle : 0.504 4.975 3078 Z= 0.255 Chirality : 0.050 0.127 351 Planarity : 0.003 0.030 393 Dihedral : 5.488 17.004 306 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.52 % Allowed : 25.38 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.38), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.44 (0.29), residues: 297 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 594 Ramachandran restraints generated. 297 Oldfield, 0 Emsley, 297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 60 average time/residue: 1.7239 time to fit residues: 106.5718 Evaluate side-chains 58 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 54 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 1 average time/residue: 0.1337 time to fit residues: 0.6673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.136768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.123788 restraints weight = 8698.284| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 1.74 r_work: 0.3918 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.6857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2301 Z= 0.269 Angle : 0.552 5.144 3078 Z= 0.282 Chirality : 0.049 0.129 351 Planarity : 0.004 0.031 393 Dihedral : 5.871 18.558 306 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.52 % Allowed : 26.89 % Favored : 71.59 % 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: -3.23 (0.38), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.29), residues: 297 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3713.54 seconds wall clock time: 65 minutes 11.96 seconds (3911.96 seconds total)