Starting phenix.real_space_refine on Mon Sep 23 19:04:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/09_2024/8orf_17122.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/09_2024/8orf_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_17122/09_2024/8orf_17122.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/09_2024/8orf_17122.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/09_2024/8orf_17122.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8orf_17122/09_2024/8orf_17122.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4653 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B Time building chain proxies: 2.97, per 1000 atoms: 0.64 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 330.6 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: 0.48 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: 1.54 Time building geometry restraints manager: 1.47 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: 0.00 - 1.60: 7441 1.60 - 3.20: 937 3.20 - 4.80: 151 4.80 - 6.40: 18 6.40 - 8.01: 12 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: 1836 13.40 - 26.80: 159 26.80 - 40.20: 45 40.20 - 53.59: 46 53.59 - 66.99: 65 Dihedral angle restraints: 2151 sinusoidal: 1248 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 2148 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 2.450 nonbonded pdb=" OD2 ASP C 295 " pdb=" HZ3 LYS C 311 " model vdw 1.823 2.450 nonbonded pdb=" OD2 ASP B 295 " pdb=" HZ3 LYS B 311 " model vdw 1.823 2.450 nonbonded pdb=" OD1 ASP B 348 " pdb=" H ARG B 349 " model vdw 1.882 2.450 nonbonded pdb=" OD1 ASP C 348 " pdb=" H ARG C 349 " model vdw 1.882 2.450 ... (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 Time spend for trying shortcut: 0.00 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: 1.970 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: 0.080 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.140 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:12.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.270 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.018 0.006 HIS B 299 PHE 0.011 0.005 PHE B 346 TYR 0.015 0.009 TYR A 310 ARG 0.005 0.002 ARG B 349 *********************** 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 : 0.381 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 REVERT: B 280 LYS cc_start: 0.7089 (tptt) cc_final: 0.6757 (mtpt) REVERT: B 321 LYS cc_start: 0.7757 (mttt) cc_final: 0.7534 (tttm) REVERT: B 331 LYS cc_start: 0.8230 (mttt) cc_final: 0.7944 (mttt) REVERT: B 341 SER cc_start: 0.8365 (m) cc_final: 0.8105 (t) REVERT: A 294 LYS cc_start: 0.8630 (mttt) cc_final: 0.8257 (mttt) REVERT: A 353 LYS cc_start: 0.8472 (ttpt) cc_final: 0.8178 (ttmm) REVERT: A 358 ASP cc_start: 0.7447 (t0) cc_final: 0.7180 (t0) REVERT: A 372 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7880 (mt-10) REVERT: C 294 LYS cc_start: 0.8806 (mttt) cc_final: 0.8306 (mtpt) REVERT: C 316 SER cc_start: 0.8344 (m) cc_final: 0.8006 (p) REVERT: C 331 LYS cc_start: 0.8428 (mttt) cc_final: 0.8151 (mttp) REVERT: C 345 ASP cc_start: 0.7381 (m-30) cc_final: 0.7153 (m-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 2.2649 time to fit residues: 270.2603 Evaluate side-chains 72 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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: 0.7347 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2301 Z= 0.198 Angle : 0.606 4.947 3078 Z= 0.309 Chirality : 0.051 0.137 351 Planarity : 0.003 0.027 393 Dihedral : 6.908 18.448 306 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.03 % Allowed : 15.91 % Favored : 81.06 % 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: -3.15 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.39 (0.28), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 374 PHE 0.003 0.001 PHE C 346 TYR 0.004 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** 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 81 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.395 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: B 280 LYS cc_start: 0.7224 (tptt) cc_final: 0.6890 (mtpt) REVERT: B 296 ASN cc_start: 0.8570 (t0) cc_final: 0.8348 (t0) REVERT: B 341 SER cc_start: 0.8499 (m) cc_final: 0.8223 (t) REVERT: B 358 ASP cc_start: 0.6957 (t0) cc_final: 0.6746 (t0) REVERT: B 369 LYS cc_start: 0.6306 (mttt) cc_final: 0.5815 (ttmt) REVERT: A 316 SER cc_start: 0.8787 (m) cc_final: 0.8434 (p) REVERT: A 349 ARG cc_start: 0.8007 (mtp85) cc_final: 0.7732 (mtp180) REVERT: A 353 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8171 (ttmm) REVERT: A 369 LYS cc_start: 0.7701 (mttt) cc_final: 0.6979 (ttmt) REVERT: C 281 LYS cc_start: 0.7720 (ptpt) cc_final: 0.7452 (ptmt) REVERT: C 369 LYS cc_start: 0.6628 (mttt) cc_final: 0.6057 (ttpt) outliers start: 8 outliers final: 2 residues processed: 76 average time/residue: 1.9778 time to fit residues: 154.0151 Evaluate side-chains 69 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 67 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 352 SER 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: 5.9990 chunk 24 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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: 0.7392 moved from start: 0.5111 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= 0.224 Angle : 0.565 5.006 3078 Z= 0.289 Chirality : 0.051 0.133 351 Planarity : 0.003 0.023 393 Dihedral : 6.373 17.693 306 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.65 % Allowed : 18.56 % Favored : 78.79 % 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: -3.36 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.28), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 PHE 0.004 0.001 PHE C 346 TYR 0.004 0.001 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** 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 74 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 67 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7455 (tptt) cc_final: 0.7013 (mtpt) REVERT: B 296 ASN cc_start: 0.8605 (t0) cc_final: 0.8391 (t0) REVERT: B 341 SER cc_start: 0.8492 (m) cc_final: 0.8221 (t) REVERT: B 345 ASP cc_start: 0.7523 (OUTLIER) cc_final: 0.7292 (m-30) REVERT: B 358 ASP cc_start: 0.7047 (t0) cc_final: 0.6660 (t0) REVERT: B 369 LYS cc_start: 0.6032 (mttt) cc_final: 0.5460 (ttmt) REVERT: A 282 LEU cc_start: 0.7969 (mp) cc_final: 0.7672 (tt) REVERT: A 316 SER cc_start: 0.8920 (m) cc_final: 0.8640 (p) REVERT: A 345 ASP cc_start: 0.7584 (m-30) cc_final: 0.7381 (m-30) REVERT: A 349 ARG cc_start: 0.8073 (mtp85) cc_final: 0.7835 (mtp180) REVERT: A 353 LYS cc_start: 0.8514 (ttpt) cc_final: 0.8177 (ttmm) REVERT: A 369 LYS cc_start: 0.7723 (mttt) cc_final: 0.7042 (ttmt) REVERT: C 317 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8521 (tttp) REVERT: C 369 LYS cc_start: 0.6705 (mttt) cc_final: 0.6074 (ttpt) outliers start: 7 outliers final: 3 residues processed: 71 average time/residue: 1.9416 time to fit residues: 141.4530 Evaluate side-chains 70 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 352 SER Chi-restraints excluded: chain A residue 285 SER Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 377 THR 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: 0.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.5402 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= 0.188 Angle : 0.548 5.035 3078 Z= 0.279 Chirality : 0.051 0.131 351 Planarity : 0.004 0.023 393 Dihedral : 6.069 16.993 306 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.76 % Allowed : 20.83 % Favored : 78.41 % 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: -3.36 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.28), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.006 0.001 PHE C 346 TYR 0.004 0.001 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** 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 71 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 69 time to evaluate : 0.416 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: B 280 LYS cc_start: 0.7519 (tptt) cc_final: 0.7023 (mtpt) REVERT: B 296 ASN cc_start: 0.8551 (t0) cc_final: 0.8326 (t0) REVERT: B 336 GLN cc_start: 0.8037 (mt0) cc_final: 0.7602 (mt0) REVERT: B 341 SER cc_start: 0.8507 (m) cc_final: 0.8243 (t) REVERT: B 358 ASP cc_start: 0.6948 (t0) cc_final: 0.6603 (t0) REVERT: B 369 LYS cc_start: 0.6119 (mttt) cc_final: 0.5564 (ttmt) REVERT: A 282 LEU cc_start: 0.8036 (mp) cc_final: 0.7559 (tt) REVERT: A 316 SER cc_start: 0.8918 (m) cc_final: 0.8670 (p) REVERT: A 349 ARG cc_start: 0.8102 (mtp85) cc_final: 0.7860 (mtp180) REVERT: A 353 LYS cc_start: 0.8537 (ttpt) cc_final: 0.8210 (ttmm) REVERT: A 358 ASP cc_start: 0.6883 (t70) cc_final: 0.6508 (t0) REVERT: A 369 LYS cc_start: 0.7762 (mttt) cc_final: 0.7043 (ttmt) REVERT: C 317 LYS cc_start: 0.8765 (OUTLIER) cc_final: 0.8480 (tttp) REVERT: C 336 GLN cc_start: 0.8040 (mt0) cc_final: 0.7608 (mt0) REVERT: C 369 LYS cc_start: 0.6709 (mttt) cc_final: 0.6090 (ttpt) outliers start: 2 outliers final: 1 residues processed: 71 average time/residue: 1.7930 time to fit residues: 130.9130 Evaluate side-chains 67 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 377 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS A 286 ASN A 362 HIS C 351 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 2301 Z= 0.341 Angle : 0.587 4.874 3078 Z= 0.304 Chirality : 0.051 0.133 351 Planarity : 0.004 0.026 393 Dihedral : 6.369 17.227 306 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.27 % Allowed : 18.94 % Favored : 78.79 % 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: -3.44 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.28), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.004 0.001 PHE C 346 TYR 0.007 0.002 TYR A 310 ARG 0.002 0.000 ARG B 349 *********************** 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 74 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7282 (tptt) cc_final: 0.7074 (ttmt) REVERT: B 283 ASP cc_start: 0.7972 (t0) cc_final: 0.7554 (t0) REVERT: B 296 ASN cc_start: 0.8660 (t0) cc_final: 0.8357 (t0) REVERT: B 341 SER cc_start: 0.8511 (m) cc_final: 0.8221 (t) REVERT: B 369 LYS cc_start: 0.6103 (mttt) cc_final: 0.5536 (ttmt) REVERT: A 282 LEU cc_start: 0.8002 (mp) cc_final: 0.7634 (tt) REVERT: A 316 SER cc_start: 0.8944 (m) cc_final: 0.8701 (p) REVERT: A 349 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8034 (mtp180) REVERT: A 353 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8187 (ttmm) REVERT: A 358 ASP cc_start: 0.7017 (t70) cc_final: 0.6664 (t0) REVERT: A 369 LYS cc_start: 0.7801 (mttt) cc_final: 0.7140 (ttmt) REVERT: C 317 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8536 (tttp) REVERT: C 353 LYS cc_start: 0.8721 (ttmt) cc_final: 0.8497 (ttmm) REVERT: C 369 LYS cc_start: 0.6713 (mttt) cc_final: 0.6085 (ttmt) outliers start: 6 outliers final: 2 residues processed: 71 average time/residue: 1.9694 time to fit residues: 143.3579 Evaluate side-chains 69 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 377 THR 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: 5.9990 chunk 24 optimal weight: 0.0170 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 0.0870 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN B 336 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.5846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2301 Z= 0.138 Angle : 0.510 4.715 3078 Z= 0.261 Chirality : 0.051 0.130 351 Planarity : 0.004 0.029 393 Dihedral : 5.588 15.933 306 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 0.76 % Allowed : 20.83 % Favored : 78.41 % 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: -3.52 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.67 (0.27), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.000 PHE C 346 TYR 0.002 0.001 TYR C 310 ARG 0.001 0.000 ARG B 349 *********************** 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 74 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.391 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: B 280 LYS cc_start: 0.7292 (tptt) cc_final: 0.7039 (ttmt) REVERT: B 283 ASP cc_start: 0.7858 (t0) cc_final: 0.7607 (t0) REVERT: B 296 ASN cc_start: 0.8584 (t0) cc_final: 0.8280 (t0) REVERT: B 336 GLN cc_start: 0.8136 (mt0) cc_final: 0.7641 (mt0) REVERT: B 358 ASP cc_start: 0.6915 (t0) cc_final: 0.6563 (t0) REVERT: B 369 LYS cc_start: 0.6273 (mttt) cc_final: 0.5746 (ttmt) REVERT: A 282 LEU cc_start: 0.8022 (mp) cc_final: 0.7588 (tt) REVERT: A 349 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7916 (mtp180) REVERT: A 353 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8317 (ttmt) REVERT: A 358 ASP cc_start: 0.6630 (t0) cc_final: 0.6379 (t0) REVERT: A 359 ASN cc_start: 0.8116 (m-40) cc_final: 0.7819 (m110) REVERT: A 369 LYS cc_start: 0.7681 (mttt) cc_final: 0.7046 (ttmt) REVERT: C 317 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8365 (tttm) REVERT: C 336 GLN cc_start: 0.7970 (mt0) cc_final: 0.7511 (mt0) REVERT: C 353 LYS cc_start: 0.8699 (ttmt) cc_final: 0.8473 (ttmm) REVERT: C 369 LYS cc_start: 0.6722 (mttt) cc_final: 0.6086 (tttt) outliers start: 2 outliers final: 0 residues processed: 73 average time/residue: 1.8457 time to fit residues: 138.3675 Evaluate side-chains 68 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.5953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2301 Z= 0.145 Angle : 0.488 4.511 3078 Z= 0.251 Chirality : 0.050 0.129 351 Planarity : 0.003 0.030 393 Dihedral : 5.381 15.617 306 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.76 % Allowed : 21.59 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.27), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 362 PHE 0.003 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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 68 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7293 (tptt) cc_final: 0.7025 (ttmt) REVERT: B 283 ASP cc_start: 0.7895 (t0) cc_final: 0.7595 (t0) REVERT: B 296 ASN cc_start: 0.8620 (t0) cc_final: 0.8311 (t0) REVERT: B 358 ASP cc_start: 0.6917 (t0) cc_final: 0.6587 (t0) REVERT: B 369 LYS cc_start: 0.6371 (mttt) cc_final: 0.5810 (ttmt) REVERT: A 282 LEU cc_start: 0.7950 (mp) cc_final: 0.7560 (tt) REVERT: A 349 ARG cc_start: 0.8189 (mtp85) cc_final: 0.7956 (mtp180) REVERT: A 353 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8332 (ttmt) REVERT: A 356 SER cc_start: 0.9153 (t) cc_final: 0.8805 (p) REVERT: A 358 ASP cc_start: 0.6664 (t0) cc_final: 0.6379 (t0) REVERT: A 369 LYS cc_start: 0.7635 (mttt) cc_final: 0.7003 (ttmt) REVERT: C 317 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8407 (tttm) REVERT: C 353 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8516 (ttmm) REVERT: C 369 LYS cc_start: 0.6686 (mttt) cc_final: 0.6050 (tttt) outliers start: 2 outliers final: 0 residues processed: 67 average time/residue: 2.0012 time to fit residues: 137.5439 Evaluate side-chains 66 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 317 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.0470 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 overall best weight: 1.2060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN C 336 GLN C 351 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2301 Z= 0.170 Angle : 0.493 4.390 3078 Z= 0.257 Chirality : 0.050 0.130 351 Planarity : 0.005 0.065 393 Dihedral : 5.457 15.838 306 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.14 % Allowed : 20.83 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.28), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 362 PHE 0.002 0.001 PHE A 346 TYR 0.004 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** 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 66 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 63 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7267 (tptt) cc_final: 0.6979 (ttmt) REVERT: B 283 ASP cc_start: 0.7889 (t0) cc_final: 0.7620 (t0) REVERT: B 296 ASN cc_start: 0.8639 (t0) cc_final: 0.8330 (t0) REVERT: B 336 GLN cc_start: 0.8135 (mt0) cc_final: 0.7646 (mt0) REVERT: B 358 ASP cc_start: 0.6966 (t0) cc_final: 0.6614 (t0) REVERT: B 369 LYS cc_start: 0.6371 (mttt) cc_final: 0.5794 (ttmt) REVERT: A 282 LEU cc_start: 0.7974 (mp) cc_final: 0.7605 (tt) REVERT: A 349 ARG cc_start: 0.8246 (mtp85) cc_final: 0.8021 (mtp180) REVERT: A 353 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8293 (ttmm) REVERT: A 356 SER cc_start: 0.9177 (t) cc_final: 0.8807 (p) REVERT: A 358 ASP cc_start: 0.6639 (t0) cc_final: 0.6362 (t0) REVERT: A 369 LYS cc_start: 0.7679 (mttt) cc_final: 0.7069 (ttmt) REVERT: C 317 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8416 (tttm) REVERT: C 353 LYS cc_start: 0.8690 (ttmt) cc_final: 0.8467 (ttmm) REVERT: C 369 LYS cc_start: 0.6685 (mttt) cc_final: 0.6053 (ttpt) outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 2.0485 time to fit residues: 134.5709 Evaluate side-chains 62 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 317 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2301 Z= 0.190 Angle : 0.495 4.339 3078 Z= 0.257 Chirality : 0.050 0.130 351 Planarity : 0.004 0.057 393 Dihedral : 5.534 16.013 306 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.27 % Allowed : 19.32 % Favored : 78.41 % 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: -3.50 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.66 (0.28), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 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 65 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7228 (tptt) cc_final: 0.6951 (ttmt) REVERT: B 283 ASP cc_start: 0.7899 (t0) cc_final: 0.7672 (t0) REVERT: B 296 ASN cc_start: 0.8653 (t0) cc_final: 0.8342 (t0) REVERT: B 345 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: B 358 ASP cc_start: 0.6794 (t0) cc_final: 0.6491 (t0) REVERT: B 369 LYS cc_start: 0.6504 (mttt) cc_final: 0.5938 (ttmt) REVERT: A 281 LYS cc_start: 0.8453 (ptmt) cc_final: 0.8250 (ptmm) REVERT: A 282 LEU cc_start: 0.7957 (mp) cc_final: 0.7597 (tt) REVERT: A 349 ARG cc_start: 0.8255 (mtp85) cc_final: 0.8028 (mtp180) REVERT: A 353 LYS cc_start: 0.8564 (ttpt) cc_final: 0.8287 (ttmm) REVERT: A 358 ASP cc_start: 0.6712 (t0) cc_final: 0.6416 (t0) REVERT: A 369 LYS cc_start: 0.7698 (mttt) cc_final: 0.7079 (ttmt) REVERT: C 317 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8438 (tttm) REVERT: C 336 GLN cc_start: 0.8174 (tt0) cc_final: 0.7937 (tt0) REVERT: C 353 LYS cc_start: 0.8693 (ttmt) cc_final: 0.8475 (ttmm) REVERT: C 369 LYS cc_start: 0.6674 (mttt) cc_final: 0.6030 (ttpt) outliers start: 6 outliers final: 2 residues processed: 62 average time/residue: 2.2215 time to fit residues: 141.4492 Evaluate side-chains 63 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASP Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 377 THR 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: 6.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 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 336 GLN C 351 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.6044 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= 0.187 Angle : 0.506 4.334 3078 Z= 0.261 Chirality : 0.050 0.129 351 Planarity : 0.004 0.056 393 Dihedral : 5.549 16.091 306 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.89 % Allowed : 20.08 % Favored : 78.03 % 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: -3.53 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.28), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 299 PHE 0.002 0.001 PHE A 346 TYR 0.005 0.001 TYR A 310 ARG 0.001 0.000 ARG B 349 ********************** 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 64 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 280 LYS cc_start: 0.7231 (tptt) cc_final: 0.6953 (ttmt) REVERT: B 283 ASP cc_start: 0.7830 (t0) cc_final: 0.7615 (t0) REVERT: B 296 ASN cc_start: 0.8643 (t0) cc_final: 0.8329 (t0) REVERT: B 336 GLN cc_start: 0.8171 (mt0) cc_final: 0.7706 (mt0) REVERT: B 358 ASP cc_start: 0.6845 (t0) cc_final: 0.6520 (t0) REVERT: B 369 LYS cc_start: 0.6510 (mttt) cc_final: 0.5955 (ttmt) REVERT: A 282 LEU cc_start: 0.7983 (mp) cc_final: 0.7670 (tt) REVERT: A 349 ARG cc_start: 0.8256 (mtp85) cc_final: 0.8010 (mtp180) REVERT: A 353 LYS cc_start: 0.8568 (ttpt) cc_final: 0.8291 (ttmm) REVERT: A 358 ASP cc_start: 0.6672 (t0) cc_final: 0.6368 (t0) REVERT: A 369 LYS cc_start: 0.7704 (mttt) cc_final: 0.7078 (ttmt) REVERT: C 317 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8420 (tttm) REVERT: C 353 LYS cc_start: 0.8692 (ttmt) cc_final: 0.8476 (ttmm) REVERT: C 369 LYS cc_start: 0.6680 (mttt) cc_final: 0.6033 (ttpt) outliers start: 5 outliers final: 3 residues processed: 62 average time/residue: 2.1585 time to fit residues: 137.0813 Evaluate side-chains 62 residues out of total 264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain C residue 317 LYS Chi-restraints excluded: chain C residue 377 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.136624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.122647 restraints weight = 8484.120| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.79 r_work: 0.3895 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.6045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2301 Z= 0.303 Angle : 0.550 4.350 3078 Z= 0.286 Chirality : 0.050 0.131 351 Planarity : 0.004 0.053 393 Dihedral : 5.922 16.728 306 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.89 % Allowed : 20.83 % Favored : 77.27 % 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: -3.53 (0.36), residues: 297 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.28), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 299 PHE 0.003 0.001 PHE C 346 TYR 0.007 0.002 TYR A 310 ARG 0.001 0.000 ARG B 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4019.70 seconds wall clock time: 70 minutes 24.47 seconds (4224.47 seconds total)