Starting phenix.real_space_refine on Tue Feb 11 09:49:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ttl_41610/02_2025/8ttl_41610_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ttl_41610/02_2025/8ttl_41610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ttl_41610/02_2025/8ttl_41610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ttl_41610/02_2025/8ttl_41610.map" model { file = "/net/cci-nas-00/data/ceres_data/8ttl_41610/02_2025/8ttl_41610_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ttl_41610/02_2025/8ttl_41610_neut.cif" } resolution = 2.6 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 6 5.16 5 C 1590 2.51 5 N 465 2.21 5 O 522 1.98 5 H 2607 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5190 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1322 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "B" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1322 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "C" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1322 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "D" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 408 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "E" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 408 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "F" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 408 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Time building chain proxies: 4.88, per 1000 atoms: 0.94 Number of scatterers: 5190 At special positions: 0 Unit cell: (105.457, 88.29, 35.1525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 6 16.00 O 522 8.00 N 465 7.00 C 1590 6.00 H 2607 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 351.9 milliseconds 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 13 sheets defined 0.0% alpha, 41.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 362 removed outlier: 6.909A pdb=" N ASN B 359 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ILE A 360 " --> pdb=" O ASN B 359 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR B 361 " --> pdb=" O ILE A 360 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N HIS A 362 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ASN C 359 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 360 " --> pdb=" O ASN C 359 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N THR C 361 " --> pdb=" O ILE B 360 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS B 362 " --> pdb=" O THR C 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 369 through 379 removed outlier: 6.326A pdb=" N LYS A 369 " --> pdb=" O LYS B 370 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N GLU B 372 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE A 371 " --> pdb=" O GLU B 372 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N HIS B 374 " --> pdb=" O ILE A 371 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR A 373 " --> pdb=" O HIS B 374 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N LEU B 376 " --> pdb=" O THR A 373 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LYS A 375 " --> pdb=" O LEU B 376 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N PHE B 378 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N THR A 377 " --> pdb=" O PHE B 378 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LYS B 369 " --> pdb=" O LYS C 370 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N GLU C 372 " --> pdb=" O LYS B 369 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE B 371 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N HIS C 374 " --> pdb=" O ILE B 371 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR B 373 " --> pdb=" O HIS C 374 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N LEU C 376 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 375 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE C 378 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N THR B 377 " --> pdb=" O PHE C 378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 384 through 386 removed outlier: 6.162A pdb=" N LYS A 385 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 391 through 394 removed outlier: 6.699A pdb=" N GLU B 391 " --> pdb=" O ILE C 392 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N TYR C 394 " --> pdb=" O GLU B 391 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL B 393 " --> pdb=" O TYR C 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 398 through 399 removed outlier: 6.593A pdb=" N VAL A 398 " --> pdb=" O VAL B 399 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL B 398 " --> pdb=" O VAL C 399 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 420 removed outlier: 9.161A pdb=" N ASN A 410 " --> pdb=" O VAL B 411 " (cutoff:3.500A) removed outlier: 10.120A pdb=" N SER B 413 " --> pdb=" O ASN A 410 " (cutoff:3.500A) removed outlier: 8.925A pdb=" N SER A 412 " --> pdb=" O SER B 413 " (cutoff:3.500A) removed outlier: 10.690A pdb=" N GLY B 415 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR A 414 " --> pdb=" O GLY B 415 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N ILE B 417 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N SER A 416 " --> pdb=" O ILE B 417 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N MET B 419 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP A 418 " --> pdb=" O MET B 419 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN B 410 " --> pdb=" O SER C 409 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 411 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N SER B 412 " --> pdb=" O VAL C 411 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER C 413 " --> pdb=" O SER B 412 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 414 " --> pdb=" O SER C 413 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLY C 415 " --> pdb=" O THR B 414 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 424 through 427 Processing sheet with id=AA8, first strand: chain 'A' and resid 435 through 439 Processing sheet with id=AA9, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.421A pdb=" N GLN D 307 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N TYR E 310 " --> pdb=" O GLN D 307 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N SER E 305 " --> pdb=" O VAL F 306 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N ILE F 308 " --> pdb=" O SER E 305 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN E 307 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N TYR F 310 " --> pdb=" O GLN E 307 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 309 " --> pdb=" O TYR F 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 313 through 314 removed outlier: 6.442A pdb=" N VAL D 313 " --> pdb=" O ASP E 314 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL E 313 " --> pdb=" O ASP F 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 317 through 319 Processing sheet with id=AB3, first strand: chain 'D' and resid 324 through 325 removed outlier: 6.540A pdb=" N SER D 324 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER E 324 " --> pdb=" O LEU F 325 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 328 through 329 32 hydrogen bonds defined for protein. 96 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.34 - 0.63: 4 0.63 - 0.93: 60 0.93 - 1.23: 2833 1.23 - 1.52: 1458 1.52 - 1.82: 871 Warning: very small bond lengths. Bond restraints: 5226 Sorted by residual: bond pdb=" OG1 THR D 319 " pdb=" HG1 THR D 319 " ideal model delta sigma weight residual 0.840 0.339 0.501 2.00e-02 2.50e+03 6.28e+02 bond pdb=" OG SER C 416 " pdb=" HG SER C 416 " ideal model delta sigma weight residual 0.840 0.369 0.471 2.00e-02 2.50e+03 5.55e+02 bond pdb=" OG SER C 352 " pdb=" HG SER C 352 " ideal model delta sigma weight residual 0.840 0.453 0.387 2.00e-02 2.50e+03 3.75e+02 bond pdb=" OG SER B 413 " pdb=" HG SER B 413 " ideal model delta sigma weight residual 0.840 0.546 0.294 2.00e-02 2.50e+03 2.15e+02 bond pdb=" OG SER B 409 " pdb=" HG SER B 409 " ideal model delta sigma weight residual 0.840 0.645 0.195 2.00e-02 2.50e+03 9.54e+01 ... (remaining 5221 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.31: 9464 8.31 - 16.61: 16 16.61 - 24.92: 2 24.92 - 33.22: 0 33.22 - 41.53: 1 Bond angle restraints: 9483 Sorted by residual: angle pdb=" CB THR D 319 " pdb=" OG1 THR D 319 " pdb=" HG1 THR D 319 " ideal model delta sigma weight residual 110.00 151.53 -41.53 3.00e+00 1.11e-01 1.92e+02 angle pdb=" CB SER C 416 " pdb=" OG SER C 416 " pdb=" HG SER C 416 " ideal model delta sigma weight residual 110.00 134.84 -24.84 3.00e+00 1.11e-01 6.85e+01 angle pdb=" CB SER B 413 " pdb=" OG SER B 413 " pdb=" HG SER B 413 " ideal model delta sigma weight residual 110.00 131.00 -21.00 3.00e+00 1.11e-01 4.90e+01 angle pdb=" CA ASP B 418 " pdb=" CB ASP B 418 " pdb=" CG ASP B 418 " ideal model delta sigma weight residual 112.60 118.77 -6.17 1.00e+00 1.00e+00 3.80e+01 angle pdb=" CA ASP C 418 " pdb=" CB ASP C 418 " pdb=" CG ASP C 418 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.13e+01 ... (remaining 9478 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.87: 2116 14.87 - 29.74: 184 29.74 - 44.61: 63 44.61 - 59.48: 67 59.48 - 74.35: 27 Dihedral angle restraints: 2457 sinusoidal: 1377 harmonic: 1080 Sorted by residual: dihedral pdb=" CA THR C 386 " pdb=" C THR C 386 " pdb=" N ASP C 387 " pdb=" CA ASP C 387 " ideal model delta harmonic sigma weight residual -180.00 -152.53 -27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA THR B 386 " pdb=" C THR B 386 " pdb=" N ASP B 387 " pdb=" CA ASP B 387 " ideal model delta harmonic sigma weight residual -180.00 -153.92 -26.08 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA THR D 319 " pdb=" C THR D 319 " pdb=" N SER D 320 " pdb=" CA SER D 320 " ideal model delta harmonic sigma weight residual -180.00 -154.31 -25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 2454 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.082: 200 0.082 - 0.162: 129 0.162 - 0.243: 63 0.243 - 0.323: 19 0.323 - 0.404: 9 Chirality restraints: 420 Sorted by residual: chirality pdb=" CA THR B 386 " pdb=" N THR B 386 " pdb=" C THR B 386 " pdb=" CB THR B 386 " both_signs ideal model delta sigma weight residual False 2.53 2.12 0.40 2.00e-01 2.50e+01 4.08e+00 chirality pdb=" CA GLU C 380 " pdb=" N GLU C 380 " pdb=" C GLU C 380 " pdb=" CB GLU C 380 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA HIS B 388 " pdb=" N HIS B 388 " pdb=" C HIS B 388 " pdb=" CB HIS B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 417 not shown) Planarity restraints: 783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 388 " -0.140 2.00e-02 2.50e+03 7.82e-02 1.37e+02 pdb=" CG HIS A 388 " 0.114 2.00e-02 2.50e+03 pdb=" ND1 HIS A 388 " 0.050 2.00e-02 2.50e+03 pdb=" CD2 HIS A 388 " 0.091 2.00e-02 2.50e+03 pdb=" CE1 HIS A 388 " 0.017 2.00e-02 2.50e+03 pdb=" NE2 HIS A 388 " 0.030 2.00e-02 2.50e+03 pdb=" HD2 HIS A 388 " -0.021 2.00e-02 2.50e+03 pdb=" HE1 HIS A 388 " -0.065 2.00e-02 2.50e+03 pdb=" HE2 HIS A 388 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 362 " -0.102 2.00e-02 2.50e+03 5.46e-02 6.71e+01 pdb=" CG HIS C 362 " 0.096 2.00e-02 2.50e+03 pdb=" ND1 HIS C 362 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 HIS C 362 " 0.056 2.00e-02 2.50e+03 pdb=" CE1 HIS C 362 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 HIS C 362 " 0.009 2.00e-02 2.50e+03 pdb=" HD2 HIS C 362 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 HIS C 362 " -0.021 2.00e-02 2.50e+03 pdb=" HE2 HIS C 362 " -0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 359 " -0.065 2.00e-02 2.50e+03 6.67e-02 6.66e+01 pdb=" CG ASN A 359 " 0.007 2.00e-02 2.50e+03 pdb=" OD1 ASN A 359 " 0.069 2.00e-02 2.50e+03 pdb=" ND2 ASN A 359 " -0.018 2.00e-02 2.50e+03 pdb="HD21 ASN A 359 " 0.097 2.00e-02 2.50e+03 pdb="HD22 ASN A 359 " -0.089 2.00e-02 2.50e+03 ... (remaining 780 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 566 2.23 - 2.82: 9642 2.82 - 3.42: 13479 3.42 - 4.01: 18228 4.01 - 4.60: 26002 Nonbonded interactions: 67917 Sorted by model distance: nonbonded pdb=" O ALA B 382 " pdb=" HG1 THR B 427 " model vdw 1.642 2.450 nonbonded pdb=" HZ1 LYS B 395 " pdb=" OD2 ASP B 430 " model vdw 1.708 2.450 nonbonded pdb=" O ALA C 382 " pdb=" HG1 THR C 427 " model vdw 1.712 2.450 nonbonded pdb=" OE1 GLU B 431 " pdb=" HZ2 LYS B 438 " model vdw 1.727 2.450 nonbonded pdb=" HZ1 LYS A 395 " pdb=" OD2 ASP A 430 " model vdw 1.746 2.450 ... (remaining 67912 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' } ncs_group { reference = 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 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: 9.960 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: 0.090 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 17.950 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 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 : 0.013 0.074 2619 Z= 0.903 Angle : 2.136 8.399 3534 Z= 1.403 Chirality : 0.133 0.404 420 Planarity : 0.013 0.078 453 Dihedral : 13.165 74.355 963 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.88 % Allowed : 7.08 % Favored : 92.04 % Rotamer: Outliers : 1.35 % Allowed : 4.38 % Favored : 94.28 % Cbeta Deviations : 2.52 % 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: -3.09 (0.33), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.25), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.023 0.006 HIS B 388 PHE 0.057 0.020 PHE A 378 TYR 0.081 0.028 TYR D 310 ARG 0.009 0.003 ARG C 406 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 82 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 84 average time/residue: 2.3125 time to fit residues: 198.5668 Evaluate side-chains 50 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 359 ASN C 359 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.147123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.130238 restraints weight = 8617.047| |-----------------------------------------------------------------------------| r_work (start): 0.4063 rms_B_bonded: 1.58 r_work: 0.3996 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3906 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2619 Z= 0.181 Angle : 0.627 4.710 3534 Z= 0.341 Chirality : 0.051 0.137 420 Planarity : 0.004 0.056 453 Dihedral : 7.107 19.225 357 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.68 % Allowed : 16.16 % Favored : 82.15 % 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: -2.66 (0.34), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.26), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.012 0.002 PHE A 378 TYR 0.009 0.002 TYR E 310 ARG 0.007 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.440 Fit side-chains REVERT: B 369 LYS cc_start: 0.7598 (ptpt) cc_final: 0.7396 (ptpp) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 3.0391 time to fit residues: 185.9335 Evaluate side-chains 53 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 ASN E 327 ASN F 327 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.142955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.125730 restraints weight = 8689.101| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 1.63 r_work: 0.3925 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3832 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2619 Z= 0.170 Angle : 0.544 4.199 3534 Z= 0.293 Chirality : 0.051 0.139 420 Planarity : 0.004 0.054 453 Dihedral : 6.324 18.863 357 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.69 % Allowed : 16.50 % Favored : 80.81 % 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: -2.48 (0.36), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.88 (0.27), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 388 PHE 0.009 0.002 PHE A 378 TYR 0.007 0.001 TYR D 310 ARG 0.010 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.416 Fit side-chains REVERT: A 370 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7825 (mmtt) REVERT: B 369 LYS cc_start: 0.7627 (ptpt) cc_final: 0.7413 (ptpp) REVERT: B 380 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8153 (mp0) outliers start: 8 outliers final: 5 residues processed: 57 average time/residue: 2.9297 time to fit residues: 170.2392 Evaluate side-chains 58 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 0.0040 chunk 25 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.145359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.128220 restraints weight = 8681.143| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.65 r_work: 0.3972 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3882 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2619 Z= 0.133 Angle : 0.498 4.006 3534 Z= 0.267 Chirality : 0.050 0.133 420 Planarity : 0.004 0.067 453 Dihedral : 5.916 18.589 357 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.69 % Allowed : 16.84 % Favored : 80.47 % 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: -2.37 (0.37), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.80 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.005 0.001 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.009 0.001 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.424 Fit side-chains REVERT: B 369 LYS cc_start: 0.7600 (ptpt) cc_final: 0.7386 (ptpp) REVERT: B 380 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8260 (mp0) outliers start: 8 outliers final: 4 residues processed: 54 average time/residue: 3.3482 time to fit residues: 184.0163 Evaluate side-chains 52 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 380 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 2 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 1 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.141064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.123814 restraints weight = 8666.090| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.63 r_work: 0.3894 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2619 Z= 0.167 Angle : 0.512 4.191 3534 Z= 0.274 Chirality : 0.050 0.134 420 Planarity : 0.005 0.067 453 Dihedral : 5.954 19.125 357 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.69 % Allowed : 17.51 % Favored : 79.80 % 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: -2.34 (0.37), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 388 PHE 0.006 0.001 PHE A 378 TYR 0.006 0.001 TYR D 310 ARG 0.010 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.448 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 3.1803 time to fit residues: 178.4076 Evaluate side-chains 56 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.143851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.126807 restraints weight = 8459.527| |-----------------------------------------------------------------------------| r_work (start): 0.4034 rms_B_bonded: 1.62 r_work: 0.3955 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3864 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.5309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2619 Z= 0.126 Angle : 0.495 3.937 3534 Z= 0.261 Chirality : 0.050 0.132 420 Planarity : 0.005 0.075 453 Dihedral : 5.694 17.988 357 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.36 % Allowed : 17.85 % Favored : 79.80 % 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: -2.30 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.003 0.001 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.011 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 351 GLN cc_start: 0.4810 (OUTLIER) cc_final: 0.2443 (tm-30) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 3.2463 time to fit residues: 185.0148 Evaluate side-chains 58 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.141949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.124851 restraints weight = 8558.690| |-----------------------------------------------------------------------------| r_work (start): 0.4013 rms_B_bonded: 1.62 r_work: 0.3933 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3839 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2619 Z= 0.163 Angle : 0.511 4.066 3534 Z= 0.271 Chirality : 0.050 0.132 420 Planarity : 0.005 0.075 453 Dihedral : 5.772 18.495 357 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.36 % Allowed : 17.17 % Favored : 80.47 % 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: -2.26 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 388 PHE 0.003 0.001 PHE A 378 TYR 0.005 0.001 TYR E 310 ARG 0.011 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 372 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7442 (mt-10) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 3.2123 time to fit residues: 176.6025 Evaluate side-chains 54 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.140293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.123004 restraints weight = 8666.371| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 1.64 r_work: 0.3905 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3813 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.5515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2619 Z= 0.178 Angle : 0.530 4.297 3534 Z= 0.279 Chirality : 0.050 0.135 420 Planarity : 0.005 0.080 453 Dihedral : 5.883 18.266 357 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.36 % Allowed : 17.17 % Favored : 80.47 % 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: -2.32 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.76 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 388 PHE 0.004 0.001 PHE A 378 TYR 0.006 0.001 TYR D 310 ARG 0.013 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.411 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7809 (mmtp) REVERT: B 372 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7460 (mt-10) outliers start: 7 outliers final: 5 residues processed: 55 average time/residue: 3.0472 time to fit residues: 170.8006 Evaluate side-chains 54 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.141434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.124420 restraints weight = 8565.906| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.60 r_work: 0.3919 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3828 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2619 Z= 0.165 Angle : 0.520 4.158 3534 Z= 0.274 Chirality : 0.050 0.131 420 Planarity : 0.005 0.080 453 Dihedral : 5.823 18.471 357 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.36 % Allowed : 17.85 % Favored : 79.80 % 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: -2.35 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.79 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.004 0.001 PHE C 378 TYR 0.006 0.001 TYR E 310 ARG 0.014 0.002 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8024 (mmmt) cc_final: 0.7811 (mmtt) REVERT: B 372 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7483 (mt-10) outliers start: 7 outliers final: 6 residues processed: 52 average time/residue: 3.1014 time to fit residues: 164.3227 Evaluate side-chains 55 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain C residue 377 THR Chi-restraints excluded: chain C residue 414 THR Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.2980 chunk 13 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.142802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.125544 restraints weight = 8657.736| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.64 r_work: 0.3942 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3850 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2619 Z= 0.131 Angle : 0.505 4.224 3534 Z= 0.263 Chirality : 0.049 0.132 420 Planarity : 0.006 0.081 453 Dihedral : 5.626 17.561 357 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.68 % Allowed : 18.52 % Favored : 79.80 % 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: -2.34 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.77 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 388 PHE 0.003 0.001 PHE C 378 TYR 0.005 0.001 TYR F 310 ARG 0.014 0.002 ARG C 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 678 Ramachandran restraints generated. 339 Oldfield, 0 Emsley, 339 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7684 (mmtp) outliers start: 5 outliers final: 4 residues processed: 54 average time/residue: 3.0716 time to fit residues: 168.9553 Evaluate side-chains 55 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain D residue 319 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain F residue 319 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.138486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.121611 restraints weight = 8876.096| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.60 r_work: 0.3887 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3796 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2619 Z= 0.213 Angle : 0.541 4.443 3534 Z= 0.286 Chirality : 0.050 0.134 420 Planarity : 0.005 0.073 453 Dihedral : 5.930 18.545 357 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.35 % Allowed : 18.18 % Favored : 80.47 % 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: -2.42 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 388 PHE 0.004 0.001 PHE A 378 TYR 0.007 0.001 TYR D 310 ARG 0.012 0.002 ARG C 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5748.51 seconds wall clock time: 101 minutes 32.19 seconds (6092.19 seconds total)