Starting phenix.real_space_refine on Fri Aug 22 15:39:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ttl_41610/08_2025/8ttl_41610_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ttl_41610/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ttl_41610/08_2025/8ttl_41610_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ttl_41610/08_2025/8ttl_41610_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ttl_41610/08_2025/8ttl_41610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ttl_41610/08_2025/8ttl_41610.map" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.21, per 1000 atoms: 0.23 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: 0.47 Conformation dependent library (CDL) restraints added in 130.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.18 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: 1.12 Time building geometry restraints manager: 0.68 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: 13.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.380 Find NCS groups from input model: 0.080 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:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.110 ------------------------------------------------------------------------------- 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= 0.864 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.003 ARG C 406 TYR 0.081 0.028 TYR D 310 PHE 0.057 0.020 PHE A 378 HIS 0.023 0.006 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.01322 ( 2619) covalent geometry : angle 2.13555 ( 3534) hydrogen bonds : bond 0.12952 ( 32) hydrogen bonds : angle 7.11432 ( 96) *********************** 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 : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 84 average time/residue: 1.0682 time to fit residues: 91.6307 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 : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4298 r_free = 0.4298 target = 0.148678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.131829 restraints weight = 8656.824| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 1.60 r_work: 0.4005 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3916 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2619 Z= 0.116 Angle : 0.620 4.607 3534 Z= 0.337 Chirality : 0.051 0.134 420 Planarity : 0.004 0.059 453 Dihedral : 7.055 19.383 357 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 1.54 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG C 379 TYR 0.008 0.002 TYR E 310 PHE 0.010 0.002 PHE A 378 HIS 0.005 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 2619) covalent geometry : angle 0.61964 ( 3534) hydrogen bonds : bond 0.01964 ( 32) hydrogen bonds : angle 4.84332 ( 96) *********************** 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 : 0.091 Fit side-chains REVERT: B 369 LYS cc_start: 0.7620 (ptpt) cc_final: 0.7413 (ptpp) outliers start: 5 outliers final: 2 residues processed: 60 average time/residue: 1.3193 time to fit residues: 80.5166 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 : 0.140 ------------------------------------------------------------------------------- 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 32 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4263 r_free = 0.4263 target = 0.146291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.129154 restraints weight = 8521.686| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.62 r_work: 0.3981 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3889 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.4561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2619 Z= 0.094 Angle : 0.527 4.113 3534 Z= 0.282 Chirality : 0.051 0.137 420 Planarity : 0.004 0.055 453 Dihedral : 6.147 18.460 357 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.68 % Allowed : 17.85 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.36), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.84 (0.27), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG C 379 TYR 0.006 0.001 TYR E 310 PHE 0.008 0.002 PHE A 378 HIS 0.005 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 2619) covalent geometry : angle 0.52683 ( 3534) hydrogen bonds : bond 0.01664 ( 32) hydrogen bonds : angle 4.36060 ( 96) *********************** 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 59 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.152 Fit side-chains REVERT: B 369 LYS cc_start: 0.7612 (ptpt) cc_final: 0.7408 (ptpp) REVERT: C 402 ASP cc_start: 0.8204 (m-30) cc_final: 0.7996 (m-30) outliers start: 5 outliers final: 4 residues processed: 56 average time/residue: 1.2190 time to fit residues: 69.5144 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 : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 25 optimal weight: 3.9990 chunk 31 optimal weight: 0.0170 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.0070 overall best weight: 0.5036 ------------------------------------------------------------------------------- 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 = 0.4290 r_free = 0.4290 target = 0.148793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.131704 restraints weight = 8551.956| |-----------------------------------------------------------------------------| r_work (start): 0.4088 rms_B_bonded: 1.63 r_work: 0.4015 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3924 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.4886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2619 Z= 0.075 Angle : 0.482 3.778 3534 Z= 0.258 Chirality : 0.050 0.134 420 Planarity : 0.004 0.063 453 Dihedral : 5.726 17.932 357 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.69 % Allowed : 18.18 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.29 (0.37), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.28), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.002 ARG C 379 TYR 0.005 0.001 TYR E 310 PHE 0.003 0.001 PHE C 378 HIS 0.004 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00166 ( 2619) covalent geometry : angle 0.48234 ( 3534) hydrogen bonds : bond 0.01388 ( 32) hydrogen bonds : angle 3.98549 ( 96) *********************** 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 63 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.111 Fit side-chains revert: symmetry clash REVERT: B 369 LYS cc_start: 0.7621 (ptpt) cc_final: 0.7420 (ptpp) REVERT: B 380 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8243 (mp0) REVERT: C 402 ASP cc_start: 0.8218 (m-30) cc_final: 0.7985 (m-30) outliers start: 8 outliers final: 4 residues processed: 58 average time/residue: 1.5738 time to fit residues: 92.7457 Evaluate side-chains 56 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 353 LYS Chi-restraints excluded: chain B residue 380 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4259 r_free = 0.4259 target = 0.146563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.129429 restraints weight = 8688.907| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 1.65 r_work: 0.3971 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3879 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.5096 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= 0.081 Angle : 0.483 4.068 3534 Z= 0.257 Chirality : 0.050 0.135 420 Planarity : 0.004 0.070 453 Dihedral : 5.625 16.982 357 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.69 % Allowed : 19.19 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.37), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 379 TYR 0.005 0.001 TYR E 310 PHE 0.004 0.001 PHE A 378 HIS 0.004 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00185 ( 2619) covalent geometry : angle 0.48320 ( 3534) hydrogen bonds : bond 0.01430 ( 32) hydrogen bonds : angle 3.96901 ( 96) *********************** 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 : 0.178 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 1.4809 time to fit residues: 82.8461 Evaluate side-chains 55 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.103 ------------------------------------------------------------------------------- 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 386 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 11 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 27 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- 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 = 0.4262 r_free = 0.4262 target = 0.146335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.129109 restraints weight = 8554.447| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 1.66 r_work: 0.3980 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3888 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.5228 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= 0.086 Angle : 0.492 3.884 3534 Z= 0.260 Chirality : 0.050 0.134 420 Planarity : 0.005 0.076 453 Dihedral : 5.563 17.549 357 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.69 % Allowed : 20.20 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.20 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG C 379 TYR 0.005 0.001 TYR E 310 PHE 0.004 0.001 PHE A 378 HIS 0.004 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00196 ( 2619) covalent geometry : angle 0.49182 ( 3534) hydrogen bonds : bond 0.01387 ( 32) hydrogen bonds : angle 3.87490 ( 96) *********************** 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: 8 poor density : 51 time to evaluate : 0.156 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 1.5222 time to fit residues: 86.6952 Evaluate side-chains 56 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.152 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 3 optimal weight: 0.0270 chunk 7 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 overall best weight: 0.5838 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.146853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.129762 restraints weight = 8541.983| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.65 r_work: 0.3974 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3880 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.5423 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= 0.080 Angle : 0.480 3.994 3534 Z= 0.254 Chirality : 0.049 0.133 420 Planarity : 0.005 0.079 453 Dihedral : 5.437 17.219 357 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.35 % Allowed : 20.20 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG C 379 TYR 0.004 0.001 TYR E 310 PHE 0.002 0.001 PHE B 378 HIS 0.003 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00183 ( 2619) covalent geometry : angle 0.48047 ( 3534) hydrogen bonds : bond 0.01380 ( 32) hydrogen bonds : angle 3.67234 ( 96) *********************** 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 55 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.153 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 1.5024 time to fit residues: 80.9609 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 : 0.141 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.3980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.143075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.125975 restraints weight = 8642.836| |-----------------------------------------------------------------------------| r_work (start): 0.4017 rms_B_bonded: 1.64 r_work: 0.3942 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3849 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.5489 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= 0.100 Angle : 0.501 4.331 3534 Z= 0.265 Chirality : 0.050 0.133 420 Planarity : 0.005 0.077 453 Dihedral : 5.577 17.602 357 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.69 % Allowed : 18.86 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 379 TYR 0.005 0.001 TYR E 310 PHE 0.004 0.001 PHE A 378 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 2619) covalent geometry : angle 0.50065 ( 3534) hydrogen bonds : bond 0.01441 ( 32) hydrogen bonds : angle 3.76674 ( 96) *********************** 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: 8 poor density : 51 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 351 GLN cc_start: 0.4688 (OUTLIER) cc_final: 0.2425 (tm-30) outliers start: 8 outliers final: 5 residues processed: 56 average time/residue: 1.5584 time to fit residues: 88.7162 Evaluate side-chains 55 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 GLN Chi-restraints excluded: chain A residue 428 LEU Chi-restraints excluded: chain C residue 386 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: 2.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 27 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 GLN A 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.142120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.125012 restraints weight = 8625.937| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 1.64 r_work: 0.3941 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2619 Z= 0.103 Angle : 0.511 4.380 3534 Z= 0.269 Chirality : 0.050 0.133 420 Planarity : 0.005 0.081 453 Dihedral : 5.621 17.524 357 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.36 % Allowed : 18.86 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.38), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 379 TYR 0.006 0.001 TYR E 310 PHE 0.003 0.001 PHE A 378 HIS 0.004 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 2619) covalent geometry : angle 0.51128 ( 3534) hydrogen bonds : bond 0.01467 ( 32) hydrogen bonds : angle 3.74590 ( 96) *********************** 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 57 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8001 (mmmt) cc_final: 0.7767 (mmtp) REVERT: B 372 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7536 (mt-10) outliers start: 7 outliers final: 5 residues processed: 54 average time/residue: 1.3863 time to fit residues: 76.2166 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 : 0.130 ------------------------------------------------------------------------------- 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 386 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 3 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 17 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: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.145426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.128499 restraints weight = 8588.775| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.61 r_work: 0.3967 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.5720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2619 Z= 0.087 Angle : 0.496 4.157 3534 Z= 0.260 Chirality : 0.049 0.131 420 Planarity : 0.005 0.081 453 Dihedral : 5.471 17.093 357 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.35 % Allowed : 20.54 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.39), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.29), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG C 379 TYR 0.005 0.001 TYR E 310 PHE 0.002 0.001 PHE A 378 HIS 0.004 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00201 ( 2619) covalent geometry : angle 0.49586 ( 3534) hydrogen bonds : bond 0.01366 ( 32) hydrogen bonds : angle 3.62932 ( 96) ********************** 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 53 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.138 Fit side-chains revert: symmetry clash REVERT: A 370 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7822 (mmtt) outliers start: 4 outliers final: 4 residues processed: 51 average time/residue: 1.4016 time to fit residues: 72.7163 Evaluate side-chains 53 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.091 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 32 optimal weight: 0.3980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.145432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.128419 restraints weight = 8639.971| |-----------------------------------------------------------------------------| r_work (start): 0.4043 rms_B_bonded: 1.64 r_work: 0.3966 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3874 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2619 Z= 0.085 Angle : 0.492 4.231 3534 Z= 0.257 Chirality : 0.049 0.132 420 Planarity : 0.005 0.079 453 Dihedral : 5.398 16.766 357 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.68 % Allowed : 19.87 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.39), residues: 339 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.002 ARG C 379 TYR 0.004 0.001 TYR F 310 PHE 0.003 0.001 PHE C 378 HIS 0.004 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 2619) covalent geometry : angle 0.49179 ( 3534) hydrogen bonds : bond 0.01351 ( 32) hydrogen bonds : angle 3.57410 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.12 seconds wall clock time: 49 minutes 47.66 seconds (2987.66 seconds total)