Starting phenix.real_space_refine on Thu Nov 14 03:01:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/11_2024/8zx6_60539.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/11_2024/8zx6_60539.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/11_2024/8zx6_60539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/11_2024/8zx6_60539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/11_2024/8zx6_60539.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zx6_60539/11_2024/8zx6_60539.cif" } resolution = 3.5 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= 0.002 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 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.73, per 1000 atoms: 0.79 Number of scatterers: 3468 At special positions: 0 Unit cell: (155.21, 83.83, 34.86, 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 648 8.00 N 642 7.00 C 2172 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: 0.76 Conformation dependent library (CDL) restraints added in 443.8 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 20 sheets defined 0.0% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 removed outlier: 6.678A pdb=" N GLN A 307 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N TYR B 310 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 309 " --> pdb=" O TYR B 310 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN B 307 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR D 310 " --> pdb=" O GLN B 307 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 removed outlier: 6.879A pdb=" N VAL A 313 " --> pdb=" O ASP B 314 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL B 313 " --> pdb=" O ASP D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.830A pdb=" N LYS A 317 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LYS B 317 " --> pdb=" O VAL D 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.356A pdb=" N LYS A 321 " --> pdb=" O CYS B 322 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LYS B 321 " --> pdb=" O CYS D 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 337 through 338 Processing sheet with id=AA6, first strand: chain 'A' and resid 345 through 346 removed outlier: 6.236A pdb=" N ASP A 345 " --> pdb=" O PHE B 346 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 345 " --> pdb=" O PHE D 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.722A pdb=" N LYS A 353 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LYS B 353 " --> pdb=" O ILE D 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 362 Processing sheet with id=AA9, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.812A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS B 369 " --> pdb=" O LYS D 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 374 through 377 Processing sheet with id=AB2, first strand: chain 'C' and resid 306 through 310 removed outlier: 6.669A pdb=" N GLN C 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N TYR E 310 " --> pdb=" O GLN C 307 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL C 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 313 through 314 removed outlier: 6.871A pdb=" N VAL C 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 317 through 318 removed outlier: 6.824A pdb=" N LYS C 317 " --> pdb=" O VAL E 318 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS E 317 " --> pdb=" O VAL F 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 321 through 322 removed outlier: 6.352A pdb=" N LYS C 321 " --> pdb=" O CYS E 322 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LYS E 321 " --> pdb=" O CYS F 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 346 removed outlier: 6.229A pdb=" N ASP C 345 " --> pdb=" O PHE E 346 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N ASP E 345 " --> pdb=" O PHE F 346 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.720A pdb=" N LYS C 353 " --> pdb=" O ILE E 354 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS E 353 " --> pdb=" O ILE F 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 359 through 362 Processing sheet with id=AC1, first strand: chain 'C' and resid 369 through 371 removed outlier: 6.806A pdb=" N LYS C 369 " --> pdb=" O LYS E 370 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS E 369 " --> pdb=" O LYS F 370 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 374 through 377 28 hydrogen bonds defined for protein. 84 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: 0.79 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1146 1.34 - 1.46: 573 1.46 - 1.57: 1797 1.57 - 1.69: 0 1.69 - 1.80: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" N LYS B 370 " pdb=" CA LYS B 370 " ideal model delta sigma weight residual 1.464 1.452 0.011 1.25e-02 6.40e+03 8.04e-01 bond pdb=" CA LYS E 370 " pdb=" C LYS E 370 " ideal model delta sigma weight residual 1.526 1.516 0.009 1.08e-02 8.57e+03 7.70e-01 bond pdb=" N LYS A 370 " pdb=" CA LYS A 370 " ideal model delta sigma weight residual 1.464 1.453 0.011 1.25e-02 6.40e+03 7.58e-01 bond pdb=" N LYS E 370 " pdb=" CA LYS E 370 " ideal model delta sigma weight residual 1.464 1.453 0.011 1.25e-02 6.40e+03 7.52e-01 bond pdb=" CA LYS F 370 " pdb=" C LYS F 370 " ideal model delta sigma weight residual 1.526 1.516 0.009 1.08e-02 8.57e+03 7.35e-01 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 4230 1.06 - 2.12: 376 2.12 - 3.19: 60 3.19 - 4.25: 29 4.25 - 5.31: 15 Bond angle restraints: 4710 Sorted by residual: angle pdb=" C ASP E 348 " pdb=" N ARG E 349 " pdb=" CA ARG E 349 " ideal model delta sigma weight residual 122.61 125.95 -3.34 1.56e+00 4.11e-01 4.59e+00 angle pdb=" C ASP C 348 " pdb=" N ARG C 349 " pdb=" CA ARG C 349 " ideal model delta sigma weight residual 122.61 125.94 -3.33 1.56e+00 4.11e-01 4.55e+00 angle pdb=" C ASP F 348 " pdb=" N ARG F 349 " pdb=" CA ARG F 349 " ideal model delta sigma weight residual 122.61 125.93 -3.32 1.56e+00 4.11e-01 4.54e+00 angle pdb=" C ASP D 348 " pdb=" N ARG D 349 " pdb=" CA ARG D 349 " ideal model delta sigma weight residual 122.61 125.91 -3.30 1.56e+00 4.11e-01 4.46e+00 angle pdb=" C ASP A 348 " pdb=" N ARG A 349 " pdb=" CA ARG A 349 " ideal model delta sigma weight residual 122.61 125.89 -3.28 1.56e+00 4.11e-01 4.42e+00 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 1932 15.10 - 30.20: 174 30.20 - 45.30: 30 45.30 - 60.40: 0 60.40 - 75.50: 6 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" CA ASP E 358 " pdb=" C ASP E 358 " pdb=" N ASN E 359 " pdb=" CA ASN E 359 " ideal model delta harmonic sigma weight residual 180.00 165.31 14.69 0 5.00e+00 4.00e-02 8.63e+00 dihedral pdb=" CA ASP D 358 " pdb=" C ASP D 358 " pdb=" N ASN D 359 " pdb=" CA ASN D 359 " ideal model delta harmonic sigma weight residual 180.00 165.32 14.68 0 5.00e+00 4.00e-02 8.62e+00 dihedral pdb=" CA ASP F 358 " pdb=" C ASP F 358 " pdb=" N ASN F 359 " pdb=" CA ASN F 359 " ideal model delta harmonic sigma weight residual 180.00 165.35 14.65 0 5.00e+00 4.00e-02 8.59e+00 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 258 0.026 - 0.051: 136 0.051 - 0.077: 35 0.077 - 0.102: 36 0.102 - 0.128: 63 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA VAL B 339 " pdb=" N VAL B 339 " pdb=" C VAL B 339 " pdb=" CB VAL B 339 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA ILE B 371 " pdb=" N ILE B 371 " pdb=" C ILE B 371 " pdb=" CB ILE B 371 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA VAL D 339 " pdb=" N VAL D 339 " pdb=" C VAL D 339 " pdb=" CB VAL D 339 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 310 " 0.008 2.00e-02 2.50e+03 5.82e-03 6.78e-01 pdb=" CG TYR E 310 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR E 310 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR E 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR E 310 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 310 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 310 " 0.008 2.00e-02 2.50e+03 5.69e-03 6.48e-01 pdb=" CG TYR F 310 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR F 310 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR F 310 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 310 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR F 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 310 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 310 " 0.008 2.00e-02 2.50e+03 5.68e-03 6.44e-01 pdb=" CG TYR C 310 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 310 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 310 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 310 " 0.001 2.00e-02 2.50e+03 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 1075 2.85 - 3.36: 2650 3.36 - 3.88: 5547 3.88 - 4.39: 5314 4.39 - 4.90: 11791 Nonbonded interactions: 26377 Sorted by model distance: nonbonded pdb=" OE1 GLU C 338 " pdb=" NZ LYS B 331 " model vdw 2.338 3.120 nonbonded pdb=" OE1 GLU E 338 " pdb=" NZ LYS D 331 " model vdw 2.341 3.120 nonbonded pdb=" OE1 GLU A 338 " pdb=" NZ LYS C 331 " model vdw 2.344 3.120 nonbonded pdb=" OE1 GLU B 338 " pdb=" NZ LYS E 331 " model vdw 2.344 3.120 nonbonded pdb=" OE1 GLU D 338 " pdb=" NZ LYS F 331 " model vdw 2.345 3.120 ... (remaining 26372 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.160 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.910 Find NCS groups from input model: 0.150 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3522 Z= 0.292 Angle : 0.769 5.310 4710 Z= 0.429 Chirality : 0.052 0.128 528 Planarity : 0.002 0.014 600 Dihedral : 12.489 75.495 1350 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % 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: -4.38 (0.26), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 362 PHE 0.005 0.001 PHE E 378 TYR 0.014 0.003 TYR E 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.420 Fit side-chains REVERT: D 342 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7409 (pm20) outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.4679 time to fit residues: 16.0231 Evaluate side-chains 23 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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: 0.0070 chunk 31 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- 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: 0.7752 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3522 Z= 0.162 Angle : 0.564 5.547 4710 Z= 0.279 Chirality : 0.050 0.115 528 Planarity : 0.002 0.026 600 Dihedral : 5.144 13.633 468 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.25 % Allowed : 5.81 % Favored : 93.94 % 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: -3.68 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.80 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 362 PHE 0.003 0.001 PHE E 378 TYR 0.013 0.003 TYR D 310 ARG 0.003 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.361 Fit side-chains REVERT: D 325 LEU cc_start: 0.8688 (mt) cc_final: 0.8320 (mp) REVERT: D 375 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7047 (tttp) REVERT: F 325 LEU cc_start: 0.8648 (mt) cc_final: 0.8261 (mp) REVERT: F 342 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7458 (pm20) REVERT: F 375 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7344 (mtpp) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.4414 time to fit residues: 16.0725 Evaluate side-chains 26 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 41 optimal weight: 0.0030 chunk 34 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- 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: 0.7790 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3522 Z= 0.284 Angle : 0.623 4.685 4710 Z= 0.320 Chirality : 0.052 0.119 528 Planarity : 0.004 0.030 600 Dihedral : 5.284 14.047 468 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.02 % Allowed : 6.31 % Favored : 91.67 % 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: -3.48 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 362 PHE 0.007 0.002 PHE F 378 TYR 0.024 0.006 TYR C 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.387 Fit side-chains REVERT: D 325 LEU cc_start: 0.8685 (mt) cc_final: 0.8390 (mp) REVERT: D 342 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7465 (pm20) REVERT: D 375 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7043 (tmtt) REVERT: F 325 LEU cc_start: 0.8637 (mt) cc_final: 0.8326 (mp) REVERT: F 342 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7401 (pm20) REVERT: F 375 LYS cc_start: 0.7919 (ttmt) cc_final: 0.7432 (mtpp) outliers start: 8 outliers final: 4 residues processed: 29 average time/residue: 0.3682 time to fit residues: 12.1852 Evaluate side-chains 26 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- 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: 0.7830 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 3522 Z= 0.401 Angle : 0.712 4.987 4710 Z= 0.368 Chirality : 0.054 0.121 528 Planarity : 0.004 0.030 600 Dihedral : 5.626 15.369 468 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 1.52 % Allowed : 6.82 % Favored : 91.67 % 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: -3.62 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS E 362 PHE 0.009 0.003 PHE F 378 TYR 0.030 0.008 TYR C 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.393 Fit side-chains REVERT: B 378 PHE cc_start: 0.8195 (t80) cc_final: 0.7965 (t80) REVERT: D 325 LEU cc_start: 0.8709 (mt) cc_final: 0.8469 (mp) REVERT: D 342 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7532 (pm20) REVERT: D 375 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7090 (tmtt) REVERT: F 325 LEU cc_start: 0.8591 (mt) cc_final: 0.8338 (mp) REVERT: F 342 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7556 (pm20) REVERT: F 375 LYS cc_start: 0.7933 (ttmt) cc_final: 0.6946 (tmtt) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 0.3021 time to fit residues: 12.8530 Evaluate side-chains 33 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP 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: 3.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.1980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 13 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.7765 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 3522 Z= 0.154 Angle : 0.567 9.062 4710 Z= 0.282 Chirality : 0.050 0.117 528 Planarity : 0.004 0.033 600 Dihedral : 4.884 13.534 468 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.26 % Allowed : 7.58 % Favored : 91.16 % 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: -3.32 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.52 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 362 PHE 0.003 0.000 PHE F 378 TYR 0.011 0.003 TYR E 310 ARG 0.001 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.408 Fit side-chains REVERT: D 325 LEU cc_start: 0.8643 (mt) cc_final: 0.8389 (mp) REVERT: D 342 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7446 (pm20) REVERT: D 375 LYS cc_start: 0.8046 (ttmt) cc_final: 0.7045 (tmtt) REVERT: F 325 LEU cc_start: 0.8612 (mt) cc_final: 0.8320 (mp) REVERT: F 342 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7421 (pm20) REVERT: F 375 LYS cc_start: 0.7904 (ttmt) cc_final: 0.7430 (mtpp) outliers start: 5 outliers final: 3 residues processed: 28 average time/residue: 0.3622 time to fit residues: 11.5847 Evaluate side-chains 25 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 21 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.1164 ------------------------------------------------------------------------------- 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: 0.7770 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 3522 Z= 0.191 Angle : 0.569 7.733 4710 Z= 0.287 Chirality : 0.050 0.117 528 Planarity : 0.004 0.029 600 Dihedral : 4.823 13.413 468 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.27 % Allowed : 6.31 % Favored : 91.41 % 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: -3.25 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.004 0.001 PHE F 378 TYR 0.016 0.004 TYR C 310 ARG 0.000 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 23 time to evaluate : 0.404 Fit side-chains REVERT: D 325 LEU cc_start: 0.8665 (mt) cc_final: 0.8419 (mp) REVERT: D 342 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7353 (pm20) REVERT: D 375 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7048 (tmtt) REVERT: F 325 LEU cc_start: 0.8567 (mt) cc_final: 0.8300 (mp) REVERT: F 342 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7481 (pm20) REVERT: F 375 LYS cc_start: 0.7896 (ttmt) cc_final: 0.7431 (mtpp) outliers start: 9 outliers final: 6 residues processed: 27 average time/residue: 0.3492 time to fit residues: 10.8291 Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 10.0000 chunk 34 optimal weight: 0.0010 chunk 40 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 20 optimal weight: 1.9990 overall best weight: 3.9994 ------------------------------------------------------------------------------- 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: 0.7812 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3522 Z= 0.336 Angle : 0.658 5.822 4710 Z= 0.338 Chirality : 0.052 0.121 528 Planarity : 0.004 0.035 600 Dihedral : 5.262 14.215 468 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 1.52 % Allowed : 7.58 % Favored : 90.91 % 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 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 362 PHE 0.008 0.002 PHE F 378 TYR 0.026 0.006 TYR C 310 ARG 0.001 0.000 ARG E 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.422 Fit side-chains REVERT: A 328 ILE cc_start: 0.9090 (mt) cc_final: 0.8713 (mp) REVERT: D 325 LEU cc_start: 0.8673 (mt) cc_final: 0.8445 (mp) REVERT: D 342 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7427 (pm20) REVERT: D 375 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7090 (tmtt) REVERT: F 325 LEU cc_start: 0.8570 (mt) cc_final: 0.8312 (mp) REVERT: F 342 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7454 (pm20) REVERT: F 375 LYS cc_start: 0.7929 (ttmt) cc_final: 0.6928 (tmtt) outliers start: 6 outliers final: 6 residues processed: 27 average time/residue: 0.3603 time to fit residues: 11.0975 Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.7785 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 3522 Z= 0.205 Angle : 0.580 5.375 4710 Z= 0.294 Chirality : 0.050 0.119 528 Planarity : 0.004 0.032 600 Dihedral : 4.933 13.846 468 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.52 % Allowed : 8.08 % Favored : 90.40 % 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: -3.19 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 362 PHE 0.005 0.001 PHE F 378 TYR 0.018 0.004 TYR C 310 ARG 0.001 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.412 Fit side-chains REVERT: D 325 LEU cc_start: 0.8657 (mt) cc_final: 0.8422 (mp) REVERT: D 342 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7348 (pm20) REVERT: D 375 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7047 (tmtt) REVERT: F 325 LEU cc_start: 0.8563 (mt) cc_final: 0.8323 (mp) REVERT: F 342 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7380 (pm20) REVERT: F 375 LYS cc_start: 0.7914 (ttmt) cc_final: 0.6926 (tmtt) outliers start: 6 outliers final: 6 residues processed: 25 average time/residue: 0.3952 time to fit residues: 11.2729 Evaluate side-chains 30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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: 0.7811 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3522 Z= 0.300 Angle : 0.626 5.560 4710 Z= 0.323 Chirality : 0.052 0.120 528 Planarity : 0.004 0.032 600 Dihedral : 5.166 14.294 468 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.02 % Allowed : 7.58 % Favored : 90.40 % 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 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.007 0.002 PHE F 378 TYR 0.023 0.006 TYR C 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.376 Fit side-chains REVERT: A 328 ILE cc_start: 0.9090 (mt) cc_final: 0.8714 (mp) REVERT: D 325 LEU cc_start: 0.8669 (mt) cc_final: 0.8446 (mp) REVERT: D 342 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7411 (pm20) REVERT: D 375 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7045 (tmtt) REVERT: F 325 LEU cc_start: 0.8573 (mt) cc_final: 0.8325 (mp) REVERT: F 342 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7479 (pm20) REVERT: F 375 LYS cc_start: 0.7932 (ttmt) cc_final: 0.6939 (tmtt) outliers start: 8 outliers final: 6 residues processed: 27 average time/residue: 0.3417 time to fit residues: 10.6523 Evaluate side-chains 28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 34 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- 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: 0.7807 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3522 Z= 0.279 Angle : 0.628 5.467 4710 Z= 0.321 Chirality : 0.052 0.121 528 Planarity : 0.004 0.031 600 Dihedral : 5.164 14.318 468 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.52 % Allowed : 7.83 % Favored : 90.66 % 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 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.007 0.002 PHE F 378 TYR 0.022 0.005 TYR C 310 ARG 0.001 0.000 ARG F 349 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.385 Fit side-chains REVERT: A 328 ILE cc_start: 0.9099 (mt) cc_final: 0.8725 (mp) REVERT: D 325 LEU cc_start: 0.8661 (mt) cc_final: 0.8436 (mp) REVERT: D 342 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7402 (pm20) REVERT: D 375 LYS cc_start: 0.7997 (ttmt) cc_final: 0.7012 (tmtt) REVERT: F 325 LEU cc_start: 0.8573 (mt) cc_final: 0.8327 (mp) REVERT: F 342 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7476 (pm20) REVERT: F 375 LYS cc_start: 0.7931 (ttmt) cc_final: 0.6935 (tmtt) outliers start: 6 outliers final: 6 residues processed: 25 average time/residue: 0.3624 time to fit residues: 10.4371 Evaluate side-chains 28 residues out of total 396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain F residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.120025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.101563 restraints weight = 4762.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.103919 restraints weight = 2453.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.105423 restraints weight = 1658.850| |-----------------------------------------------------------------------------| r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3522 Z= 0.331 Angle : 0.660 6.416 4710 Z= 0.341 Chirality : 0.053 0.123 528 Planarity : 0.004 0.031 600 Dihedral : 5.307 14.606 468 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 1.52 % Allowed : 7.32 % Favored : 91.16 % 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: -3.33 (0.32), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.008 0.002 PHE F 378 TYR 0.025 0.006 TYR C 310 ARG 0.001 0.000 ARG B 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1099.48 seconds wall clock time: 21 minutes 12.86 seconds (1272.86 seconds total)