Starting phenix.real_space_refine on Thu Nov 14 02:46:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwm_60533/11_2024/8zwm_60533.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwm_60533/11_2024/8zwm_60533.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwm_60533/11_2024/8zwm_60533.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwm_60533/11_2024/8zwm_60533.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwm_60533/11_2024/8zwm_60533.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwm_60533/11_2024/8zwm_60533.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 2154 2.51 5 N 630 2.21 5 O 645 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3435 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "B" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 571 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "F" Number of atoms: 574 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 574 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 3.36, per 1000 atoms: 0.98 Number of scatterers: 3435 At special positions: 0 Unit cell: (133.63, 112.88, 53.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 645 8.00 N 630 7.00 C 2154 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 416.5 milliseconds 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 39.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.641A pdb=" N GLN A 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N TYR E 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.723A pdb=" N LYS A 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LYS E 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 323 removed outlier: 6.359A pdb=" N LYS A 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER E 324 " --> pdb=" O LYS A 321 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY A 323 " --> pdb=" O SER E 324 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LYS E 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N SER F 324 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLY E 323 " --> pdb=" O SER F 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 330 removed outlier: 6.542A pdb=" N ILE A 328 " --> pdb=" O HIS E 329 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 342 removed outlier: 6.719A pdb=" N GLU A 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N SER E 341 " --> pdb=" O GLU A 338 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LYS A 340 " --> pdb=" O SER E 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 350 through 351 Processing sheet with id=AA7, first strand: chain 'A' and resid 357 through 362 Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 370 removed outlier: 6.443A pdb=" N LYS A 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 376 through 378 Processing sheet with id=AB1, first strand: chain 'D' and resid 306 through 310 Processing sheet with id=AB2, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.802A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 317 through 325 removed outlier: 6.256A pdb=" N VAL B 318 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LYS C 321 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER B 320 " --> pdb=" O LYS C 321 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLY C 323 " --> pdb=" O SER B 320 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N CYS B 322 " --> pdb=" O GLY C 323 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU C 325 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER B 324 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 330 removed outlier: 6.241A pdb=" N ILE B 328 " --> pdb=" O HIS D 329 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 336 through 340 removed outlier: 6.328A pdb=" N GLN B 336 " --> pdb=" O VAL D 337 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL D 339 " --> pdb=" O GLN B 336 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 344 through 347 removed outlier: 6.364A pdb=" N LEU B 344 " --> pdb=" O ASP C 345 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LYS C 347 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE B 346 " --> pdb=" O LYS C 347 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 350 through 354 removed outlier: 6.243A pdb=" N GLN B 351 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ILE D 354 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 357 through 362 removed outlier: 6.532A pdb=" N LEU B 357 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 360 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N ASN B 359 " --> pdb=" O ILE C 360 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N HIS C 362 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N THR B 361 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 370 through 373 removed outlier: 6.380A pdb=" N ILE B 371 " --> pdb=" O GLU D 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 376 through 377 removed outlier: 6.345A pdb=" N LEU B 376 " --> pdb=" O THR C 377 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 313 through 314 removed outlier: 6.821A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 60 hydrogen bonds defined for protein. 177 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1131 1.34 - 1.45: 388 1.45 - 1.57: 1964 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 3489 Sorted by residual: bond pdb=" CA LYS D 331 " pdb=" C LYS D 331 " ideal model delta sigma weight residual 1.532 1.524 0.008 6.50e-03 2.37e+04 1.44e+00 bond pdb=" CG LEU B 325 " pdb=" CD1 LEU B 325 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.05e+00 bond pdb=" CA ASP D 348 " pdb=" C ASP D 348 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.34e-01 bond pdb=" CA ASP B 348 " pdb=" C ASP B 348 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.28e-01 bond pdb=" CA LYS E 321 " pdb=" CB LYS E 321 " ideal model delta sigma weight residual 1.526 1.512 0.014 1.53e-02 4.27e+03 8.93e-01 ... (remaining 3484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 4373 1.19 - 2.39: 233 2.39 - 3.58: 45 3.58 - 4.77: 15 4.77 - 5.96: 2 Bond angle restraints: 4668 Sorted by residual: angle pdb=" CA LYS D 331 " pdb=" C LYS D 331 " pdb=" N PRO D 332 " ideal model delta sigma weight residual 118.16 120.15 -1.99 7.00e-01 2.04e+00 8.06e+00 angle pdb=" C HIS D 330 " pdb=" N LYS D 331 " pdb=" CA LYS D 331 " ideal model delta sigma weight residual 123.10 125.50 -2.40 9.60e-01 1.09e+00 6.25e+00 angle pdb=" CA ASP D 348 " pdb=" C ASP D 348 " pdb=" N ARG D 349 " ideal model delta sigma weight residual 114.17 117.32 -3.15 1.45e+00 4.76e-01 4.72e+00 angle pdb=" CA ASP B 348 " pdb=" C ASP B 348 " pdb=" N ARG B 349 " ideal model delta sigma weight residual 114.17 117.18 -3.01 1.45e+00 4.76e-01 4.30e+00 angle pdb=" CA ASP C 348 " pdb=" C ASP C 348 " pdb=" N ARG C 349 " ideal model delta sigma weight residual 114.17 117.17 -3.00 1.45e+00 4.76e-01 4.29e+00 ... (remaining 4663 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.20: 1900 14.20 - 28.39: 166 28.39 - 42.59: 40 42.59 - 56.78: 8 56.78 - 70.98: 4 Dihedral angle restraints: 2118 sinusoidal: 879 harmonic: 1239 Sorted by residual: dihedral pdb=" CB LYS E 343 " pdb=" CG LYS E 343 " pdb=" CD LYS E 343 " pdb=" CE LYS E 343 " ideal model delta sinusoidal sigma weight residual 180.00 126.17 53.83 3 1.50e+01 4.44e-03 9.24e+00 dihedral pdb=" CA LYS C 311 " pdb=" CB LYS C 311 " pdb=" CG LYS C 311 " pdb=" CD LYS C 311 " ideal model delta sinusoidal sigma weight residual -60.00 -102.63 42.63 3 1.50e+01 4.44e-03 7.65e+00 dihedral pdb=" CA LEU F 315 " pdb=" CB LEU F 315 " pdb=" CG LEU F 315 " pdb=" CD1 LEU F 315 " ideal model delta sinusoidal sigma weight residual 60.00 101.55 -41.55 3 1.50e+01 4.44e-03 7.44e+00 ... (remaining 2115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 279 0.027 - 0.055: 139 0.055 - 0.082: 24 0.082 - 0.109: 57 0.109 - 0.136: 26 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA ILE A 371 " pdb=" N ILE A 371 " pdb=" C ILE A 371 " pdb=" CB ILE A 371 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.64e-01 chirality pdb=" CA ILE E 371 " pdb=" N ILE E 371 " pdb=" C ILE E 371 " pdb=" CB ILE E 371 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE F 371 " pdb=" N ILE F 371 " pdb=" C ILE F 371 " pdb=" CB ILE F 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 522 not shown) Planarity restraints: 594 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 363 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO E 364 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO E 364 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO E 364 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 363 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.94e+00 pdb=" N PRO D 364 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 364 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 364 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 363 " 0.022 5.00e-02 4.00e+02 3.36e-02 1.80e+00 pdb=" N PRO A 364 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 364 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 364 " 0.019 5.00e-02 4.00e+02 ... (remaining 591 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 132 2.71 - 3.26: 2840 3.26 - 3.81: 5054 3.81 - 4.35: 5898 4.35 - 4.90: 11948 Nonbonded interactions: 25872 Sorted by model distance: nonbonded pdb=" OG SER F 320 " pdb=" OD1 ASN F 368 " model vdw 2.167 3.040 nonbonded pdb=" OG SER A 320 " pdb=" OD1 ASN A 368 " model vdw 2.218 3.040 nonbonded pdb=" OG SER A 324 " pdb=" OD1 ASN A 327 " model vdw 2.297 3.040 nonbonded pdb=" O GLY A 335 " pdb=" OG SER A 356 " model vdw 2.304 3.040 nonbonded pdb=" OG SER F 324 " pdb=" OD1 ASN F 327 " model vdw 2.347 3.040 ... (remaining 25867 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' and resid 305 through 378) selection = (chain 'B' and resid 305 through 378) selection = (chain 'C' and resid 305 through 378) selection = (chain 'D' and resid 305 through 378) selection = (chain 'E' and resid 305 through 378) selection = (chain 'F' and resid 305 through 378) } 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: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 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 : 0.005 0.035 3489 Z= 0.336 Angle : 0.667 5.962 4668 Z= 0.386 Chirality : 0.049 0.136 525 Planarity : 0.004 0.036 594 Dihedral : 11.915 70.980 1332 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.27), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.20), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.009 0.001 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.002 0.001 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 311 LYS cc_start: 0.5668 (tppt) cc_final: 0.4912 (pttt) REVERT: B 340 LYS cc_start: 0.8147 (tttt) cc_final: 0.7781 (tttp) REVERT: C 340 LYS cc_start: 0.8035 (tttt) cc_final: 0.7679 (tttp) REVERT: C 345 ASP cc_start: 0.7786 (t70) cc_final: 0.7570 (t70) REVERT: C 347 LYS cc_start: 0.7628 (mtmt) cc_final: 0.6435 (mmtt) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.2822 time to fit residues: 28.5465 Evaluate side-chains 55 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN E 330 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3489 Z= 0.344 Angle : 0.577 5.656 4668 Z= 0.286 Chirality : 0.050 0.133 525 Planarity : 0.004 0.030 594 Dihedral : 4.605 13.074 462 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.78 % Allowed : 8.14 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.29), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.49 (0.22), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 330 PHE 0.008 0.001 PHE E 346 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.426 Fit side-chains REVERT: A 311 LYS cc_start: 0.5537 (tppt) cc_final: 0.4732 (pttt) REVERT: A 340 LYS cc_start: 0.8099 (mttt) cc_final: 0.7855 (mttp) REVERT: A 349 ARG cc_start: 0.8036 (mtt-85) cc_final: 0.7805 (mtt90) REVERT: B 345 ASP cc_start: 0.7582 (t0) cc_final: 0.7290 (t0) REVERT: B 347 LYS cc_start: 0.7474 (mtmm) cc_final: 0.7066 (ptpt) REVERT: B 378 PHE cc_start: 0.7053 (OUTLIER) cc_final: 0.6840 (m-80) REVERT: C 347 LYS cc_start: 0.7503 (mtmt) cc_final: 0.6274 (mmtt) REVERT: E 360 ILE cc_start: 0.9105 (mt) cc_final: 0.8895 (mp) outliers start: 7 outliers final: 2 residues processed: 55 average time/residue: 0.2371 time to fit residues: 15.2761 Evaluate side-chains 50 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 PHE Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 0.4980 chunk 37 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 19 optimal weight: 8.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- 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: 0.8642 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3489 Z= 0.149 Angle : 0.510 5.238 4668 Z= 0.247 Chirality : 0.049 0.130 525 Planarity : 0.003 0.027 594 Dihedral : 4.365 12.968 462 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.27 % Allowed : 9.67 % Favored : 89.06 % 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: -2.96 (0.30), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.23), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 374 PHE 0.006 0.001 PHE E 346 TYR 0.016 0.002 TYR B 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.314 Fit side-chains REVERT: A 311 LYS cc_start: 0.5473 (tppt) cc_final: 0.4673 (pttt) REVERT: A 340 LYS cc_start: 0.8116 (mttt) cc_final: 0.7868 (mttp) REVERT: B 345 ASP cc_start: 0.7576 (t0) cc_final: 0.7374 (t0) REVERT: C 347 LYS cc_start: 0.7524 (mtmt) cc_final: 0.6345 (mmtt) REVERT: E 360 ILE cc_start: 0.9075 (mt) cc_final: 0.8868 (mp) outliers start: 5 outliers final: 3 residues processed: 52 average time/residue: 0.2364 time to fit residues: 14.2689 Evaluate side-chains 50 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 25 optimal weight: 9.9990 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 20 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 368 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3489 Z= 0.348 Angle : 0.560 8.215 4668 Z= 0.276 Chirality : 0.049 0.128 525 Planarity : 0.004 0.029 594 Dihedral : 4.484 14.292 462 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.04 % Allowed : 10.69 % Favored : 87.28 % 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: -2.86 (0.31), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 330 PHE 0.008 0.001 PHE E 346 TYR 0.014 0.003 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.398 Fit side-chains REVERT: A 311 LYS cc_start: 0.5574 (tppt) cc_final: 0.4650 (pttt) REVERT: A 340 LYS cc_start: 0.8098 (mttt) cc_final: 0.7845 (mttp) REVERT: B 315 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9154 (mt) REVERT: B 345 ASP cc_start: 0.7606 (t0) cc_final: 0.7339 (t0) REVERT: D 321 LYS cc_start: 0.8838 (mttt) cc_final: 0.8574 (mttp) REVERT: C 347 LYS cc_start: 0.7422 (mtmt) cc_final: 0.6225 (mmtt) outliers start: 8 outliers final: 5 residues processed: 55 average time/residue: 0.2663 time to fit residues: 16.8269 Evaluate side-chains 50 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain D residue 345 ASP Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 0 optimal weight: 0.7980 chunk 20 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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: 0.8662 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3489 Z= 0.268 Angle : 0.532 8.316 4668 Z= 0.260 Chirality : 0.049 0.130 525 Planarity : 0.004 0.035 594 Dihedral : 4.401 14.584 462 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.53 % Allowed : 12.98 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.31), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 329 PHE 0.007 0.001 PHE E 346 TYR 0.013 0.003 TYR B 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.308 Fit side-chains REVERT: A 311 LYS cc_start: 0.5290 (tppt) cc_final: 0.4396 (pttt) REVERT: A 340 LYS cc_start: 0.8118 (mttt) cc_final: 0.7863 (mttp) REVERT: C 347 LYS cc_start: 0.7357 (mtmt) cc_final: 0.6178 (mmtt) REVERT: E 360 ILE cc_start: 0.9071 (mt) cc_final: 0.8866 (mp) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.2051 time to fit residues: 12.0465 Evaluate side-chains 48 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 44 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.0050 chunk 40 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 21 optimal weight: 0.0870 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 0.4980 chunk 29 optimal weight: 9.9990 overall best weight: 1.0974 ------------------------------------------------------------------------------- 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: 0.8635 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3489 Z= 0.151 Angle : 0.488 7.409 4668 Z= 0.234 Chirality : 0.049 0.124 525 Planarity : 0.004 0.042 594 Dihedral : 4.115 13.911 462 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.02 % Allowed : 14.50 % Favored : 84.48 % 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: -2.58 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 362 PHE 0.005 0.001 PHE E 346 TYR 0.015 0.002 TYR B 310 ARG 0.000 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.427 Fit side-chains REVERT: A 311 LYS cc_start: 0.5163 (tppt) cc_final: 0.4302 (pttt) REVERT: A 340 LYS cc_start: 0.8130 (mttt) cc_final: 0.7875 (mttp) REVERT: B 310 TYR cc_start: 0.8855 (t80) cc_final: 0.8586 (t80) REVERT: C 347 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6085 (mmtt) REVERT: E 360 ILE cc_start: 0.9074 (mt) cc_final: 0.8858 (mp) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.2133 time to fit residues: 12.2383 Evaluate side-chains 47 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 378 PHE Chi-restraints excluded: chain C residue 325 LEU Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 20 optimal weight: 0.0970 overall best weight: 6.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN F 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 3489 Z= 0.617 Angle : 0.649 7.475 4668 Z= 0.330 Chirality : 0.052 0.130 525 Planarity : 0.004 0.039 594 Dihedral : 4.656 14.521 462 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.02 % Allowed : 15.27 % Favored : 83.72 % 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: -2.72 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.06 (0.24), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 329 PHE 0.012 0.002 PHE F 346 TYR 0.022 0.005 TYR A 310 ARG 0.002 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.417 Fit side-chains REVERT: A 311 LYS cc_start: 0.5424 (tppt) cc_final: 0.4357 (ptpt) REVERT: A 340 LYS cc_start: 0.8086 (mttt) cc_final: 0.7816 (mttp) REVERT: B 310 TYR cc_start: 0.8888 (t80) cc_final: 0.8640 (t80) REVERT: D 340 LYS cc_start: 0.8300 (tttt) cc_final: 0.7896 (tttp) REVERT: C 347 LYS cc_start: 0.7422 (mtmt) cc_final: 0.6236 (mmtt) outliers start: 4 outliers final: 3 residues processed: 57 average time/residue: 0.2405 time to fit residues: 15.9826 Evaluate side-chains 51 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3489 Z= 0.312 Angle : 0.551 6.651 4668 Z= 0.273 Chirality : 0.049 0.126 525 Planarity : 0.004 0.042 594 Dihedral : 4.517 15.920 462 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.76 % Allowed : 16.03 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.32), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.03 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.007 0.001 PHE E 346 TYR 0.013 0.003 TYR B 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.383 Fit side-chains REVERT: A 311 LYS cc_start: 0.5378 (tppt) cc_final: 0.4396 (ptmt) REVERT: A 340 LYS cc_start: 0.8076 (mttt) cc_final: 0.7805 (mttp) REVERT: B 310 TYR cc_start: 0.8876 (t80) cc_final: 0.8661 (t80) REVERT: C 347 LYS cc_start: 0.7416 (mtmt) cc_final: 0.6223 (mmtt) REVERT: E 360 ILE cc_start: 0.9073 (mt) cc_final: 0.8858 (mp) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.2574 time to fit residues: 15.1648 Evaluate side-chains 49 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 0.0570 chunk 24 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 overall best weight: 3.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3489 Z= 0.330 Angle : 0.548 6.312 4668 Z= 0.273 Chirality : 0.049 0.124 525 Planarity : 0.004 0.045 594 Dihedral : 4.487 15.313 462 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.02 % Allowed : 15.27 % Favored : 83.72 % 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: -2.62 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 362 PHE 0.007 0.001 PHE E 346 TYR 0.013 0.003 TYR A 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.415 Fit side-chains REVERT: A 311 LYS cc_start: 0.5298 (tppt) cc_final: 0.4305 (ptmt) REVERT: A 340 LYS cc_start: 0.8085 (mttt) cc_final: 0.7817 (mttp) REVERT: C 340 LYS cc_start: 0.7892 (tttt) cc_final: 0.7584 (tttp) REVERT: C 347 LYS cc_start: 0.7435 (mtmt) cc_final: 0.6306 (mmtt) REVERT: E 360 ILE cc_start: 0.9085 (mt) cc_final: 0.8865 (mp) outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 0.2559 time to fit residues: 15.1719 Evaluate side-chains 50 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3489 Z= 0.268 Angle : 0.549 8.295 4668 Z= 0.269 Chirality : 0.049 0.126 525 Planarity : 0.004 0.049 594 Dihedral : 4.425 15.464 462 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.02 % Allowed : 15.27 % Favored : 83.72 % 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: -2.60 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.97 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 362 PHE 0.006 0.001 PHE E 346 TYR 0.011 0.002 TYR A 310 ARG 0.001 0.000 ARG E 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 882 Ramachandran restraints generated. 441 Oldfield, 0 Emsley, 441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.448 Fit side-chains REVERT: A 311 LYS cc_start: 0.5234 (tppt) cc_final: 0.4161 (ptmm) REVERT: A 340 LYS cc_start: 0.8100 (mttt) cc_final: 0.7833 (mttp) REVERT: C 340 LYS cc_start: 0.7879 (tttt) cc_final: 0.7572 (tttp) REVERT: C 347 LYS cc_start: 0.7436 (mtmt) cc_final: 0.6288 (mmtt) REVERT: E 360 ILE cc_start: 0.9082 (mt) cc_final: 0.8866 (mp) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 0.2460 time to fit residues: 15.2738 Evaluate side-chains 51 residues out of total 393 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain E residue 341 SER Chi-restraints excluded: chain F residue 341 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.102879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089303 restraints weight = 4993.570| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.20 r_work: 0.3176 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3489 Z= 0.271 Angle : 0.541 8.253 4668 Z= 0.264 Chirality : 0.049 0.125 525 Planarity : 0.004 0.051 594 Dihedral : 4.376 15.247 462 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.02 % Allowed : 15.27 % Favored : 83.72 % 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: -2.56 (0.33), residues: 441 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.25), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 362 PHE 0.006 0.001 PHE E 346 TYR 0.012 0.002 TYR C 310 ARG 0.001 0.000 ARG E 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1297.51 seconds wall clock time: 24 minutes 39.13 seconds (1479.13 seconds total)