Starting phenix.real_space_refine on Thu Feb 5 03:55:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9glc_51438/02_2026/9glc_51438.cif Found real_map, /net/cci-nas-00/data/ceres_data/9glc_51438/02_2026/9glc_51438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9glc_51438/02_2026/9glc_51438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9glc_51438/02_2026/9glc_51438.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9glc_51438/02_2026/9glc_51438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9glc_51438/02_2026/9glc_51438.map" } resolution = 3.3 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 8854 2.51 5 N 2677 2.21 5 O 2794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14423 Number of models: 1 Model: "" Number of chains: 10 Chain: "BC" Number of atoms: 1910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1910 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 10, 'TRANS': 216} Chain: "BD" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1538 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "BE" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1898 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain: "BF" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1556 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain: "AC" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1535 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "AD" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1593 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 10, 'TRANS': 182} Chain: "AE" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 686 Classifications: {'peptide': 76} Link IDs: {'TRANS': 75} Chain: "CC" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 629 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Chain: "CE" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1485 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 10, 'TRANS': 170} Chain: "CF" Number of atoms: 1593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1593 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 10, 'TRANS': 182} Time building chain proxies: 3.24, per 1000 atoms: 0.22 Number of scatterers: 14423 At special positions: 0 Unit cell: (102.168, 108.79, 259.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 2794 8.00 N 2677 7.00 C 8854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.25 Conformation dependent library (CDL) restraints added in 508.9 milliseconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3336 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 65.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'BC' and resid 379 through 387 Processing helix chain 'BC' and resid 388 through 391 Processing helix chain 'BC' and resid 416 through 430 Processing helix chain 'BC' and resid 456 through 461 Processing helix chain 'BC' and resid 465 through 470 Processing helix chain 'BC' and resid 481 through 518 removed outlier: 3.895A pdb=" N ARGBC 489 " --> pdb=" O GLUBC 485 " (cutoff:3.500A) Processing helix chain 'BC' and resid 518 through 593 removed outlier: 3.675A pdb=" N ALABC 522 " --> pdb=" O GLUBC 518 " (cutoff:3.500A) Processing helix chain 'BD' and resid 160 through 168 Processing helix chain 'BD' and resid 197 through 211 removed outlier: 3.800A pdb=" N ALABD 201 " --> pdb=" O GLYBD 197 " (cutoff:3.500A) Processing helix chain 'BD' and resid 237 through 241 Processing helix chain 'BD' and resid 244 through 251 removed outlier: 3.585A pdb=" N LYSBD 249 " --> pdb=" O GLNBD 245 " (cutoff:3.500A) Processing helix chain 'BD' and resid 262 through 299 Processing helix chain 'BD' and resid 299 through 334 Processing helix chain 'BE' and resid 379 through 388 Processing helix chain 'BE' and resid 416 through 430 Processing helix chain 'BE' and resid 456 through 461 removed outlier: 3.619A pdb=" N ALABE 460 " --> pdb=" O PROBE 456 " (cutoff:3.500A) Processing helix chain 'BE' and resid 462 through 469 removed outlier: 6.042A pdb=" N METBE 465 " --> pdb=" O LYSBE 462 " (cutoff:3.500A) Processing helix chain 'BE' and resid 481 through 518 removed outlier: 4.102A pdb=" N ARGBE 489 " --> pdb=" O GLUBE 485 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLUBE 518 " --> pdb=" O LYSBE 514 " (cutoff:3.500A) Processing helix chain 'BE' and resid 518 through 592 removed outlier: 3.844A pdb=" N TYRBE 523 " --> pdb=" O METBE 519 " (cutoff:3.500A) Processing helix chain 'BF' and resid 160 through 168 Processing helix chain 'BF' and resid 197 through 211 removed outlier: 3.645A pdb=" N ALABF 201 " --> pdb=" O GLYBF 197 " (cutoff:3.500A) Processing helix chain 'BF' and resid 237 through 241 Processing helix chain 'BF' and resid 244 through 251 removed outlier: 3.532A pdb=" N HISBF 248 " --> pdb=" O ASNBF 244 " (cutoff:3.500A) Processing helix chain 'BF' and resid 262 through 299 removed outlier: 3.519A pdb=" N ARGBF 270 " --> pdb=" O GLUBF 266 " (cutoff:3.500A) Processing helix chain 'BF' and resid 299 through 336 Processing helix chain 'AC' and resid 381 through 387 removed outlier: 3.715A pdb=" N PHEAC 387 " --> pdb=" O LEUAC 383 " (cutoff:3.500A) Processing helix chain 'AC' and resid 388 through 390 No H-bonds generated for 'chain 'AC' and resid 388 through 390' Processing helix chain 'AC' and resid 416 through 430 Processing helix chain 'AC' and resid 456 through 461 Processing helix chain 'AC' and resid 463 through 468 removed outlier: 4.385A pdb=" N GLNAC 467 " --> pdb=" O ASNAC 463 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYSAC 468 " --> pdb=" O PROAC 464 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 463 through 468' Processing helix chain 'AC' and resid 481 through 518 removed outlier: 3.745A pdb=" N GLNAC 488 " --> pdb=" O TYRAC 484 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARGAC 489 " --> pdb=" O GLUAC 485 " (cutoff:3.500A) Processing helix chain 'AC' and resid 518 through 553 removed outlier: 3.763A pdb=" N TYRAC 523 " --> pdb=" O METAC 519 " (cutoff:3.500A) Processing helix chain 'AD' and resid 160 through 169 Processing helix chain 'AD' and resid 170 through 172 No H-bonds generated for 'chain 'AD' and resid 170 through 172' Processing helix chain 'AD' and resid 197 through 211 Processing helix chain 'AD' and resid 237 through 241 Processing helix chain 'AD' and resid 244 through 251 Processing helix chain 'AD' and resid 262 through 299 removed outlier: 3.610A pdb=" N GLUAD 266 " --> pdb=" O SERAD 262 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLUAD 299 " --> pdb=" O LYSAD 295 " (cutoff:3.500A) Processing helix chain 'AD' and resid 299 through 340 Processing helix chain 'AE' and resid 518 through 592 Processing helix chain 'CC' and resid 525 through 592 removed outlier: 3.689A pdb=" N ARGCC 577 " --> pdb=" O GLUCC 573 " (cutoff:3.500A) Processing helix chain 'CE' and resid 379 through 388 Processing helix chain 'CE' and resid 389 through 391 No H-bonds generated for 'chain 'CE' and resid 389 through 391' Processing helix chain 'CE' and resid 416 through 430 Processing helix chain 'CE' and resid 456 through 461 Processing helix chain 'CE' and resid 463 through 471 removed outlier: 4.645A pdb=" N GLNCE 467 " --> pdb=" O ASNCE 463 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYSCE 468 " --> pdb=" O PROCE 464 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLUCE 471 " --> pdb=" O GLNCE 467 " (cutoff:3.500A) Processing helix chain 'CE' and resid 481 through 518 removed outlier: 3.612A pdb=" N ARGCE 489 " --> pdb=" O GLUCE 485 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLUCE 518 " --> pdb=" O LYSCE 514 " (cutoff:3.500A) Processing helix chain 'CE' and resid 518 through 547 Processing helix chain 'CF' and resid 160 through 168 removed outlier: 3.913A pdb=" N LEUCF 164 " --> pdb=" O SERCF 160 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHECF 168 " --> pdb=" O LEUCF 164 " (cutoff:3.500A) Processing helix chain 'CF' and resid 169 through 171 No H-bonds generated for 'chain 'CF' and resid 169 through 171' Processing helix chain 'CF' and resid 197 through 211 Processing helix chain 'CF' and resid 237 through 241 Processing helix chain 'CF' and resid 244 through 250 removed outlier: 3.574A pdb=" N HISCF 248 " --> pdb=" O ASNCF 244 " (cutoff:3.500A) Processing helix chain 'CF' and resid 262 through 340 removed outlier: 3.606A pdb=" N ARGCF 270 " --> pdb=" O GLUCF 266 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYSCF 295 " --> pdb=" O GLUCF 291 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLUCF 301 " --> pdb=" O GLUCF 297 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALACF 302 " --> pdb=" O METCF 298 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEUCF 340 " --> pdb=" O LYSCF 336 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'BC' and resid 393 through 400 removed outlier: 3.637A pdb=" N ARGBC 395 " --> pdb=" O GLUBC 413 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LYSBC 409 " --> pdb=" O ILEBC 399 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILEBC 442 " --> pdb=" O ARGBC 372 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'BD' and resid 177 through 181 removed outlier: 5.066A pdb=" N LYSBD 190 " --> pdb=" O ILEBD 180 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VALBD 152 " --> pdb=" O GLYBD 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'BE' and resid 393 through 400 removed outlier: 3.738A pdb=" N ARGBE 395 " --> pdb=" O GLUBE 413 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYSBE 409 " --> pdb=" O ILEBE 399 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'BE' and resid 449 through 450 removed outlier: 3.792A pdb=" N VALBF 181 " --> pdb=" O ASPBE 450 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'BF' and resid 174 through 177 removed outlier: 3.809A pdb=" N VALBF 193 " --> pdb=" O LEUBF 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'AC' and resid 393 through 400 removed outlier: 4.054A pdb=" N ARGAC 395 " --> pdb=" O GLUAC 413 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILEAC 399 " --> pdb=" O LYSAC 409 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYSAC 409 " --> pdb=" O ILEAC 399 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VALAC 371 " --> pdb=" O GLYAC 410 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AC' and resid 449 through 450 removed outlier: 3.504A pdb=" N ASPAC 450 " --> pdb=" O VALAD 181 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VALAD 181 " --> pdb=" O ASPAC 450 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARGAD 176 " --> pdb=" O GLUAD 194 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N LYSAD 190 " --> pdb=" O ILEAD 180 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASPAD 182 " --> pdb=" O SERAD 188 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N SERAD 188 " --> pdb=" O ASPAD 182 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VALAD 152 " --> pdb=" O GLYAD 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'CE' and resid 393 through 397 removed outlier: 3.639A pdb=" N ARGCE 395 " --> pdb=" O GLUCE 413 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILECE 442 " --> pdb=" O ARGCE 372 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'CF' and resid 174 through 181 removed outlier: 5.301A pdb=" N LYSCF 190 " --> pdb=" O ILECF 180 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2877 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: 2.20 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2964 1.32 - 1.45: 3181 1.45 - 1.57: 8307 1.57 - 1.69: 0 1.69 - 1.82: 188 Bond restraints: 14640 Sorted by residual: bond pdb=" N VALBF 193 " pdb=" CA VALBF 193 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N PHEBF 195 " pdb=" CA PHEBF 195 " ideal model delta sigma weight residual 1.453 1.490 -0.036 1.22e-02 6.72e+03 8.81e+00 bond pdb=" N VALBE 443 " pdb=" CA VALBE 443 " ideal model delta sigma weight residual 1.458 1.491 -0.032 1.17e-02 7.31e+03 7.68e+00 bond pdb=" N TYRBE 486 " pdb=" CA TYRBE 486 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.28e-02 6.10e+03 5.96e+00 bond pdb=" N ARGBE 586 " pdb=" CA ARGBE 586 " ideal model delta sigma weight residual 1.459 1.489 -0.029 1.21e-02 6.83e+03 5.90e+00 ... (remaining 14635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 19069 2.03 - 4.06: 437 4.06 - 6.09: 45 6.09 - 8.12: 24 8.12 - 10.15: 2 Bond angle restraints: 19577 Sorted by residual: angle pdb=" N GLNCF 332 " pdb=" CA GLNCF 332 " pdb=" CB GLNCF 332 " ideal model delta sigma weight residual 110.28 116.48 -6.20 1.55e+00 4.16e-01 1.60e+01 angle pdb=" CA GLNCF 332 " pdb=" CB GLNCF 332 " pdb=" CG GLNCF 332 " ideal model delta sigma weight residual 114.10 121.81 -7.71 2.00e+00 2.50e-01 1.49e+01 angle pdb=" CB METAE 585 " pdb=" CG METAE 585 " pdb=" SD METAE 585 " ideal model delta sigma weight residual 112.70 102.55 10.15 3.00e+00 1.11e-01 1.14e+01 angle pdb=" C ASNCF 331 " pdb=" N GLNCF 332 " pdb=" CA GLNCF 332 " ideal model delta sigma weight residual 120.31 115.39 4.92 1.52e+00 4.33e-01 1.05e+01 angle pdb=" CA GLYBD 172 " pdb=" C GLYBD 172 " pdb=" N GLNBD 173 " ideal model delta sigma weight residual 114.23 117.07 -2.84 8.80e-01 1.29e+00 1.04e+01 ... (remaining 19572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 8045 17.94 - 35.87: 1033 35.87 - 53.81: 188 53.81 - 71.75: 73 71.75 - 89.69: 30 Dihedral angle restraints: 9369 sinusoidal: 4281 harmonic: 5088 Sorted by residual: dihedral pdb=" CA SERAC 379 " pdb=" C SERAC 379 " pdb=" N ASNAC 380 " pdb=" CA ASNAC 380 " ideal model delta harmonic sigma weight residual 180.00 156.43 23.57 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA PHEBE 476 " pdb=" C PHEBE 476 " pdb=" N ALABE 477 " pdb=" CA ALABE 477 " ideal model delta harmonic sigma weight residual -180.00 -161.87 -18.13 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA LYSBD 198 " pdb=" C LYSBD 198 " pdb=" N PROBD 199 " pdb=" CA PROBD 199 " ideal model delta harmonic sigma weight residual -180.00 -163.16 -16.84 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 9366 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1523 0.049 - 0.098: 400 0.098 - 0.147: 61 0.147 - 0.196: 4 0.196 - 0.245: 3 Chirality restraints: 1991 Sorted by residual: chirality pdb=" CB ILEBF 192 " pdb=" CA ILEBF 192 " pdb=" CG1 ILEBF 192 " pdb=" CG2 ILEBF 192 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA TYRBD 267 " pdb=" N TYRBD 267 " pdb=" C TYRBD 267 " pdb=" CB TYRBD 267 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VALBE 412 " pdb=" CA VALBE 412 " pdb=" CG1 VALBE 412 " pdb=" CG2 VALBE 412 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.71e-01 ... (remaining 1988 not shown) Planarity restraints: 2679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASNBC 507 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.48e+00 pdb=" C ASNBC 507 " 0.032 2.00e-02 2.50e+03 pdb=" O ASNBC 507 " -0.012 2.00e-02 2.50e+03 pdb=" N METBC 508 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLUBD 225 " 0.031 5.00e-02 4.00e+02 4.62e-02 3.41e+00 pdb=" N PROBD 226 " -0.080 5.00e-02 4.00e+02 pdb=" CA PROBD 226 " 0.022 5.00e-02 4.00e+02 pdb=" CD PROBD 226 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYRBD 267 " -0.021 2.00e-02 2.50e+03 1.28e-02 3.28e+00 pdb=" CG TYRBD 267 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYRBD 267 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TYRBD 267 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYRBD 267 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYRBD 267 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYRBD 267 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYRBD 267 " -0.007 2.00e-02 2.50e+03 ... (remaining 2676 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2020 2.75 - 3.29: 14666 3.29 - 3.83: 24122 3.83 - 4.36: 25480 4.36 - 4.90: 44895 Nonbonded interactions: 111183 Sorted by model distance: nonbonded pdb=" O GLUBC 518 " pdb=" OH TYRBD 267 " model vdw 2.213 3.040 nonbonded pdb=" OG SERAC 379 " pdb=" N GLUAC 381 " model vdw 2.217 3.120 nonbonded pdb=" O LEUAC 515 " pdb=" OH TYRAD 267 " model vdw 2.223 3.040 nonbonded pdb=" O GLUBC 425 " pdb=" OG SERBC 428 " model vdw 2.235 3.040 nonbonded pdb=" NH2 ARGBE 470 " pdb=" OE1 GLUBF 166 " model vdw 2.235 3.120 ... (remaining 111178 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 'AC' and resid 367 through 547) selection = chain 'CE' } ncs_group { reference = (chain 'AD' and resid 148 through 334) selection = chain 'BD' selection = (chain 'BF' and resid 148 through 334) selection = (chain 'CF' and resid 148 through 334) } ncs_group { reference = (chain 'AE' and resid 524 through 592) selection = chain 'CC' } ncs_group { reference = (chain 'BC' and resid 367 through 592) selection = chain 'BE' } 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: 8.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.300 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14640 Z= 0.247 Angle : 0.731 10.148 19577 Z= 0.400 Chirality : 0.044 0.245 1991 Planarity : 0.005 0.062 2679 Dihedral : 16.970 89.687 6033 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.45 % Allowed : 0.83 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.20), residues: 1708 helix: 2.33 (0.16), residues: 1033 sheet: -0.25 (0.48), residues: 128 loop : -0.36 (0.27), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARGBE 543 TYR 0.029 0.002 TYRBF 158 PHE 0.012 0.002 PHEBD 263 TRP 0.011 0.002 TRPBD 271 HIS 0.006 0.001 HISAD 305 Details of bonding type rmsd covalent geometry : bond 0.00515 (14640) covalent geometry : angle 0.73068 (19577) hydrogen bonds : bond 0.14168 ( 979) hydrogen bonds : angle 5.60633 ( 2877) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 292 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BE 451 ASP cc_start: 0.7731 (t0) cc_final: 0.7412 (t0) REVERT: BE 586 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8383 (ttp80) REVERT: BF 232 ASP cc_start: 0.7553 (p0) cc_final: 0.7322 (p0) REVERT: BF 249 LYS cc_start: 0.9137 (tptp) cc_final: 0.8895 (tptp) REVERT: BF 306 GLU cc_start: 0.8100 (tp30) cc_final: 0.7857 (tp30) REVERT: AE 533 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7233 (tm-30) REVERT: AE 588 GLN cc_start: 0.8372 (tm-30) cc_final: 0.8138 (tm-30) REVERT: CC 588 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8206 (tm-30) REVERT: CF 253 GLN cc_start: 0.6718 (OUTLIER) cc_final: 0.5671 (pp30) REVERT: CF 328 GLU cc_start: 0.7872 (pp20) cc_final: 0.7496 (pp20) outliers start: 7 outliers final: 1 residues processed: 297 average time/residue: 0.1250 time to fit residues: 53.1006 Evaluate side-chains 243 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 240 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CF residue 253 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 0.0000 chunk 149 optimal weight: 1.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BC 461 GLN BC 539 GLN ** BD 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BF 246 GLN BF 281 GLN AC 549 HIS AD 248 HIS CC 563 GLN CE 533 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.172652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.138055 restraints weight = 22995.059| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.90 r_work: 0.3804 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14640 Z= 0.142 Angle : 0.607 9.399 19577 Z= 0.307 Chirality : 0.039 0.166 1991 Planarity : 0.004 0.039 2679 Dihedral : 4.212 47.679 1952 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.85 % Allowed : 7.54 % Favored : 90.61 % 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 are not related in a simple way. whole: 2.56 (0.21), residues: 1708 helix: 2.76 (0.15), residues: 1062 sheet: -0.48 (0.46), residues: 128 loop : 0.00 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARGBE 570 TYR 0.019 0.002 TYRCE 486 PHE 0.017 0.001 PHEBD 247 TRP 0.006 0.001 TRPBD 271 HIS 0.009 0.001 HISBD 248 Details of bonding type rmsd covalent geometry : bond 0.00305 (14640) covalent geometry : angle 0.60680 (19577) hydrogen bonds : bond 0.05189 ( 979) hydrogen bonds : angle 4.14428 ( 2877) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 254 time to evaluate : 0.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: BC 508 MET cc_start: 0.7664 (tpp) cc_final: 0.7426 (mmp) REVERT: BC 590 GLU cc_start: 0.8242 (tm-30) cc_final: 0.8025 (tm-30) REVERT: BD 227 MET cc_start: 0.7375 (tpt) cc_final: 0.6619 (tpt) REVERT: BD 248 HIS cc_start: 0.8709 (m-70) cc_final: 0.8264 (m-70) REVERT: BE 586 ARG cc_start: 0.8707 (ttp80) cc_final: 0.8385 (ttp80) REVERT: BF 306 GLU cc_start: 0.8380 (tp30) cc_final: 0.7946 (tp30) REVERT: BF 317 MET cc_start: 0.8044 (tmm) cc_final: 0.7835 (tmm) REVERT: BF 325 ARG cc_start: 0.8412 (tpp80) cc_final: 0.7889 (ttm110) REVERT: AC 429 GLU cc_start: 0.8407 (pp20) cc_final: 0.8152 (pp20) REVERT: AC 486 TYR cc_start: 0.8094 (t80) cc_final: 0.7862 (t80) REVERT: AE 533 GLN cc_start: 0.7800 (OUTLIER) cc_final: 0.7313 (tm-30) REVERT: AE 534 ASP cc_start: 0.8284 (t0) cc_final: 0.8029 (t0) REVERT: AE 581 MET cc_start: 0.8453 (tmm) cc_final: 0.8102 (tmm) REVERT: AE 588 GLN cc_start: 0.8231 (tm-30) cc_final: 0.8001 (tm-30) REVERT: CC 551 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7528 (mp10) REVERT: CC 559 MET cc_start: 0.7551 (ttm) cc_final: 0.7207 (ttm) REVERT: CC 588 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7777 (tm-30) REVERT: CE 469 GLU cc_start: 0.8063 (tp30) cc_final: 0.7746 (tp30) REVERT: CE 513 ASP cc_start: 0.9479 (OUTLIER) cc_final: 0.9272 (m-30) REVERT: CE 519 MET cc_start: 0.7486 (tpp) cc_final: 0.7196 (tpp) REVERT: CF 299 GLU cc_start: 0.8152 (tt0) cc_final: 0.7869 (tt0) outliers start: 29 outliers final: 16 residues processed: 266 average time/residue: 0.1318 time to fit residues: 49.3397 Evaluate side-chains 249 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 496 MET Chi-restraints excluded: chain BC residue 545 MET Chi-restraints excluded: chain BD residue 216 THR Chi-restraints excluded: chain BE residue 411 ILE Chi-restraints excluded: chain BE residue 476 PHE Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain BE residue 560 GLN Chi-restraints excluded: chain BF residue 277 MET Chi-restraints excluded: chain AC residue 380 ASN Chi-restraints excluded: chain AD residue 149 SER Chi-restraints excluded: chain AD residue 159 VAL Chi-restraints excluded: chain AD residue 228 ASP Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CC residue 551 GLN Chi-restraints excluded: chain CE residue 492 SER Chi-restraints excluded: chain CE residue 513 ASP Chi-restraints excluded: chain CF residue 253 GLN Chi-restraints excluded: chain CF residue 269 MET Chi-restraints excluded: chain CF residue 315 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 0.6980 chunk 118 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 106 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 81 optimal weight: 0.0980 chunk 150 optimal weight: 3.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BC 507 ASN BD 248 HIS BD 284 GLN BF 245 GLN BF 246 GLN AD 284 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.172284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.137609 restraints weight = 22899.341| |-----------------------------------------------------------------------------| r_work (start): 0.3941 rms_B_bonded: 2.91 r_work: 0.3805 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14640 Z= 0.132 Angle : 0.565 8.307 19577 Z= 0.281 Chirality : 0.039 0.175 1991 Planarity : 0.004 0.039 2679 Dihedral : 4.094 47.744 1952 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.88 % Allowed : 10.29 % Favored : 86.84 % 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 are not related in a simple way. whole: 2.84 (0.21), residues: 1708 helix: 3.03 (0.15), residues: 1062 sheet: -0.57 (0.44), residues: 128 loop : 0.08 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGBD 186 TYR 0.015 0.002 TYRCE 486 PHE 0.009 0.001 PHEBF 247 TRP 0.007 0.001 TRPCF 271 HIS 0.007 0.001 HISCC 524 Details of bonding type rmsd covalent geometry : bond 0.00287 (14640) covalent geometry : angle 0.56482 (19577) hydrogen bonds : bond 0.04738 ( 979) hydrogen bonds : angle 3.79500 ( 2877) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 590 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8009 (tm-30) REVERT: BD 227 MET cc_start: 0.7335 (tpt) cc_final: 0.6628 (tpt) REVERT: BE 450 ASP cc_start: 0.7828 (t70) cc_final: 0.7557 (t0) REVERT: BE 558 GLU cc_start: 0.8661 (pt0) cc_final: 0.8347 (pt0) REVERT: BE 564 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8120 (tm-30) REVERT: BE 568 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7830 (tpp80) REVERT: BE 586 ARG cc_start: 0.8708 (ttp80) cc_final: 0.8394 (ttp80) REVERT: BF 306 GLU cc_start: 0.8387 (tp30) cc_final: 0.8072 (tp30) REVERT: BF 317 MET cc_start: 0.7982 (tmm) cc_final: 0.7758 (tmm) REVERT: BF 325 ARG cc_start: 0.8418 (tpp80) cc_final: 0.7910 (ttm110) REVERT: AC 429 GLU cc_start: 0.8400 (pp20) cc_final: 0.8153 (pp20) REVERT: AD 239 LYS cc_start: 0.4993 (tttt) cc_final: 0.4348 (tmtt) REVERT: AD 300 MET cc_start: 0.8340 (tpp) cc_final: 0.8034 (tpp) REVERT: AE 533 GLN cc_start: 0.7840 (OUTLIER) cc_final: 0.7351 (tm-30) REVERT: AE 534 ASP cc_start: 0.8269 (t0) cc_final: 0.8029 (t0) REVERT: AE 581 MET cc_start: 0.8428 (tmm) cc_final: 0.8103 (tmm) REVERT: AE 588 GLN cc_start: 0.8233 (tm-30) cc_final: 0.8006 (tm-30) REVERT: CC 551 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: CC 553 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6519 (ptt) REVERT: CC 559 MET cc_start: 0.7679 (ttm) cc_final: 0.7314 (ttm) REVERT: CC 588 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7761 (tm-30) REVERT: CE 469 GLU cc_start: 0.8063 (tp30) cc_final: 0.7707 (tp30) REVERT: CE 533 GLN cc_start: 0.8483 (mm-40) cc_final: 0.7986 (mm110) REVERT: CF 299 GLU cc_start: 0.8132 (tt0) cc_final: 0.7880 (tt0) outliers start: 45 outliers final: 28 residues processed: 285 average time/residue: 0.1234 time to fit residues: 50.3731 Evaluate side-chains 271 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 437 THR Chi-restraints excluded: chain BC residue 496 MET Chi-restraints excluded: chain BC residue 545 MET Chi-restraints excluded: chain BD residue 216 THR Chi-restraints excluded: chain BD residue 217 THR Chi-restraints excluded: chain BE residue 411 ILE Chi-restraints excluded: chain BE residue 412 VAL Chi-restraints excluded: chain BE residue 476 PHE Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain BE residue 560 GLN Chi-restraints excluded: chain BF residue 152 VAL Chi-restraints excluded: chain AC residue 371 VAL Chi-restraints excluded: chain AC residue 380 ASN Chi-restraints excluded: chain AC residue 400 VAL Chi-restraints excluded: chain AC residue 441 VAL Chi-restraints excluded: chain AD residue 149 SER Chi-restraints excluded: chain AD residue 159 VAL Chi-restraints excluded: chain AD residue 161 ASN Chi-restraints excluded: chain AD residue 228 ASP Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CC residue 551 GLN Chi-restraints excluded: chain CC residue 553 MET Chi-restraints excluded: chain CE residue 429 GLU Chi-restraints excluded: chain CE residue 441 VAL Chi-restraints excluded: chain CE residue 492 SER Chi-restraints excluded: chain CE residue 496 MET Chi-restraints excluded: chain CE residue 508 MET Chi-restraints excluded: chain CF residue 253 GLN Chi-restraints excluded: chain CF residue 269 MET Chi-restraints excluded: chain CF residue 309 VAL Chi-restraints excluded: chain CF residue 315 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 91 optimal weight: 0.3980 chunk 139 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 151 optimal weight: 0.0870 chunk 24 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 162 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BC 507 ASN BF 245 GLN AC 524 HIS AD 248 HIS CE 524 HIS CF 332 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.172745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.139531 restraints weight = 22982.100| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 3.04 r_work: 0.3798 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14640 Z= 0.128 Angle : 0.578 10.219 19577 Z= 0.283 Chirality : 0.038 0.178 1991 Planarity : 0.004 0.038 2679 Dihedral : 4.036 46.987 1952 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.49 % Allowed : 12.46 % Favored : 85.05 % 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 are not related in a simple way. whole: 2.93 (0.21), residues: 1708 helix: 3.08 (0.15), residues: 1063 sheet: -0.60 (0.43), residues: 128 loop : 0.15 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGBD 186 TYR 0.016 0.001 TYRBD 158 PHE 0.009 0.001 PHEBF 168 TRP 0.007 0.001 TRPCF 271 HIS 0.007 0.001 HISAC 524 Details of bonding type rmsd covalent geometry : bond 0.00277 (14640) covalent geometry : angle 0.57761 (19577) hydrogen bonds : bond 0.04572 ( 979) hydrogen bonds : angle 3.69965 ( 2877) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 254 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 590 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8046 (tm-30) REVERT: BD 248 HIS cc_start: 0.8718 (m-70) cc_final: 0.8139 (m170) REVERT: BD 276 GLU cc_start: 0.8344 (mm-30) cc_final: 0.8029 (mm-30) REVERT: BD 316 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5105 (mp) REVERT: BE 382 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6716 (tt) REVERT: BE 450 ASP cc_start: 0.7835 (t70) cc_final: 0.7615 (t0) REVERT: BE 558 GLU cc_start: 0.8670 (pt0) cc_final: 0.8364 (pt0) REVERT: BE 564 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7995 (tm-30) REVERT: BE 568 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7831 (ttm-80) REVERT: BE 575 MET cc_start: 0.8281 (tpp) cc_final: 0.8045 (tpp) REVERT: BE 583 GLU cc_start: 0.8321 (tp30) cc_final: 0.7865 (tp30) REVERT: BE 586 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8333 (ttp80) REVERT: BF 306 GLU cc_start: 0.8462 (tp30) cc_final: 0.8101 (tp30) REVERT: BF 317 MET cc_start: 0.7971 (tmm) cc_final: 0.7735 (tmm) REVERT: BF 325 ARG cc_start: 0.8413 (tpp80) cc_final: 0.7887 (ttm110) REVERT: AC 518 GLU cc_start: 0.7120 (mp0) cc_final: 0.6889 (mp0) REVERT: AD 239 LYS cc_start: 0.5052 (tttt) cc_final: 0.4365 (tmtt) REVERT: AD 300 MET cc_start: 0.8362 (tpp) cc_final: 0.8057 (tpp) REVERT: AE 533 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7390 (tm-30) REVERT: AE 534 ASP cc_start: 0.8251 (t0) cc_final: 0.8004 (t0) REVERT: AE 581 MET cc_start: 0.8421 (tmm) cc_final: 0.8089 (tmm) REVERT: AE 588 GLN cc_start: 0.8269 (tm-30) cc_final: 0.8034 (tm-30) REVERT: CC 551 GLN cc_start: 0.8268 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: CC 553 MET cc_start: 0.7073 (OUTLIER) cc_final: 0.6553 (ptt) REVERT: CC 559 MET cc_start: 0.7728 (ttm) cc_final: 0.7311 (ttm) REVERT: CC 588 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7710 (tm-30) REVERT: CC 590 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8320 (mm-30) REVERT: CE 469 GLU cc_start: 0.8147 (tp30) cc_final: 0.7892 (tp30) REVERT: CF 298 MET cc_start: 0.8235 (mmp) cc_final: 0.7918 (mmt) REVERT: CF 299 GLU cc_start: 0.8087 (tt0) cc_final: 0.7798 (tt0) outliers start: 39 outliers final: 28 residues processed: 273 average time/residue: 0.1279 time to fit residues: 49.1332 Evaluate side-chains 274 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 437 THR Chi-restraints excluded: chain BC residue 496 MET Chi-restraints excluded: chain BC residue 545 MET Chi-restraints excluded: chain BD residue 216 THR Chi-restraints excluded: chain BD residue 217 THR Chi-restraints excluded: chain BD residue 316 LEU Chi-restraints excluded: chain BE residue 382 LEU Chi-restraints excluded: chain BE residue 411 ILE Chi-restraints excluded: chain BE residue 412 VAL Chi-restraints excluded: chain BE residue 476 PHE Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain BE residue 560 GLN Chi-restraints excluded: chain BF residue 245 GLN Chi-restraints excluded: chain AC residue 371 VAL Chi-restraints excluded: chain AC residue 380 ASN Chi-restraints excluded: chain AC residue 412 VAL Chi-restraints excluded: chain AC residue 441 VAL Chi-restraints excluded: chain AC residue 486 TYR Chi-restraints excluded: chain AD residue 149 SER Chi-restraints excluded: chain AD residue 159 VAL Chi-restraints excluded: chain AD residue 161 ASN Chi-restraints excluded: chain AD residue 228 ASP Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CC residue 551 GLN Chi-restraints excluded: chain CC residue 553 MET Chi-restraints excluded: chain CC residue 573 GLU Chi-restraints excluded: chain CE residue 429 GLU Chi-restraints excluded: chain CE residue 496 MET Chi-restraints excluded: chain CE residue 513 ASP Chi-restraints excluded: chain CF residue 155 LEU Chi-restraints excluded: chain CF residue 253 GLN Chi-restraints excluded: chain CF residue 269 MET Chi-restraints excluded: chain CF residue 315 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 39 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 148 optimal weight: 0.2980 chunk 121 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 0.0570 chunk 67 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.172706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.139924 restraints weight = 22928.434| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 2.96 r_work: 0.3801 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14640 Z= 0.126 Angle : 0.570 8.504 19577 Z= 0.278 Chirality : 0.038 0.181 1991 Planarity : 0.004 0.042 2679 Dihedral : 3.977 46.504 1952 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.94 % Allowed : 13.48 % Favored : 83.58 % 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 are not related in a simple way. whole: 3.01 (0.21), residues: 1708 helix: 3.17 (0.15), residues: 1061 sheet: -0.62 (0.43), residues: 128 loop : 0.17 (0.29), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGBE 543 TYR 0.016 0.001 TYRBD 267 PHE 0.008 0.001 PHEBF 168 TRP 0.006 0.001 TRPCF 271 HIS 0.007 0.001 HISCC 524 Details of bonding type rmsd covalent geometry : bond 0.00277 (14640) covalent geometry : angle 0.56974 (19577) hydrogen bonds : bond 0.04467 ( 979) hydrogen bonds : angle 3.57393 ( 2877) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 252 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 508 MET cc_start: 0.7425 (tpp) cc_final: 0.6967 (tpp) REVERT: BC 590 GLU cc_start: 0.8340 (tm-30) cc_final: 0.8044 (tm-30) REVERT: BD 248 HIS cc_start: 0.8718 (m-70) cc_final: 0.8370 (m-70) REVERT: BD 276 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8039 (mm-30) REVERT: BD 316 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5157 (mp) REVERT: BE 382 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6733 (tt) REVERT: BE 450 ASP cc_start: 0.7836 (t70) cc_final: 0.7599 (t0) REVERT: BE 558 GLU cc_start: 0.8675 (pt0) cc_final: 0.8361 (pt0) REVERT: BE 564 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7976 (tm-30) REVERT: BE 568 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7956 (ttm-80) REVERT: BE 583 GLU cc_start: 0.8450 (tp30) cc_final: 0.8177 (tp30) REVERT: BE 586 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8385 (ttp80) REVERT: BF 306 GLU cc_start: 0.8469 (tp30) cc_final: 0.8118 (tp30) REVERT: BF 317 MET cc_start: 0.8018 (tmm) cc_final: 0.7783 (tmm) REVERT: BF 325 ARG cc_start: 0.8421 (tpp80) cc_final: 0.7934 (ttm110) REVERT: AD 300 MET cc_start: 0.8325 (tpp) cc_final: 0.8017 (tpp) REVERT: AE 533 GLN cc_start: 0.7933 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: AE 534 ASP cc_start: 0.8247 (t0) cc_final: 0.8003 (t0) REVERT: AE 581 MET cc_start: 0.8409 (tmm) cc_final: 0.8072 (tmm) REVERT: AE 588 GLN cc_start: 0.8290 (tm-30) cc_final: 0.8054 (tm-30) REVERT: CC 551 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7538 (mp10) REVERT: CC 553 MET cc_start: 0.7032 (OUTLIER) cc_final: 0.6490 (ptt) REVERT: CC 559 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7508 (ttm) REVERT: CC 574 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7397 (mpp) REVERT: CC 588 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7776 (tm-30) REVERT: CE 469 GLU cc_start: 0.8110 (tp30) cc_final: 0.7833 (tp30) REVERT: CF 299 GLU cc_start: 0.8085 (tt0) cc_final: 0.7707 (tp30) outliers start: 46 outliers final: 31 residues processed: 275 average time/residue: 0.1203 time to fit residues: 47.8089 Evaluate side-chains 277 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 437 THR Chi-restraints excluded: chain BC residue 496 MET Chi-restraints excluded: chain BC residue 545 MET Chi-restraints excluded: chain BD residue 216 THR Chi-restraints excluded: chain BD residue 267 TYR Chi-restraints excluded: chain BD residue 316 LEU Chi-restraints excluded: chain BE residue 369 LEU Chi-restraints excluded: chain BE residue 382 LEU Chi-restraints excluded: chain BE residue 411 ILE Chi-restraints excluded: chain BE residue 412 VAL Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain BF residue 152 VAL Chi-restraints excluded: chain AC residue 371 VAL Chi-restraints excluded: chain AC residue 380 ASN Chi-restraints excluded: chain AC residue 400 VAL Chi-restraints excluded: chain AC residue 412 VAL Chi-restraints excluded: chain AC residue 425 GLU Chi-restraints excluded: chain AC residue 441 VAL Chi-restraints excluded: chain AC residue 486 TYR Chi-restraints excluded: chain AD residue 149 SER Chi-restraints excluded: chain AD residue 159 VAL Chi-restraints excluded: chain AD residue 161 ASN Chi-restraints excluded: chain AD residue 228 ASP Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CC residue 551 GLN Chi-restraints excluded: chain CC residue 553 MET Chi-restraints excluded: chain CC residue 559 MET Chi-restraints excluded: chain CC residue 574 MET Chi-restraints excluded: chain CE residue 429 GLU Chi-restraints excluded: chain CE residue 492 SER Chi-restraints excluded: chain CE residue 496 MET Chi-restraints excluded: chain CE residue 508 MET Chi-restraints excluded: chain CF residue 155 LEU Chi-restraints excluded: chain CF residue 253 GLN Chi-restraints excluded: chain CF residue 269 MET Chi-restraints excluded: chain CF residue 309 VAL Chi-restraints excluded: chain CF residue 312 MET Chi-restraints excluded: chain CF residue 315 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 86 optimal weight: 0.8980 chunk 129 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 132 optimal weight: 0.0020 chunk 158 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 157 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BC 507 ASN ** CF 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.171820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.137806 restraints weight = 22932.122| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.02 r_work: 0.3786 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14640 Z= 0.140 Angle : 0.579 8.366 19577 Z= 0.284 Chirality : 0.039 0.183 1991 Planarity : 0.004 0.045 2679 Dihedral : 4.024 47.263 1952 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.19 % Allowed : 14.57 % Favored : 82.24 % 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 are not related in a simple way. whole: 2.95 (0.21), residues: 1708 helix: 3.14 (0.15), residues: 1057 sheet: -0.59 (0.43), residues: 127 loop : 0.09 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGBD 186 TYR 0.015 0.001 TYRBD 267 PHE 0.009 0.001 PHEBF 195 TRP 0.007 0.001 TRPCF 271 HIS 0.007 0.001 HISCC 524 Details of bonding type rmsd covalent geometry : bond 0.00316 (14640) covalent geometry : angle 0.57941 (19577) hydrogen bonds : bond 0.04491 ( 979) hydrogen bonds : angle 3.55526 ( 2877) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 250 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 450 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6731 (p0) REVERT: BC 590 GLU cc_start: 0.8357 (tm-30) cc_final: 0.8042 (tm-30) REVERT: BD 248 HIS cc_start: 0.8758 (m-70) cc_final: 0.8385 (m-70) REVERT: BD 276 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8050 (mm-30) REVERT: BD 316 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5056 (mp) REVERT: BE 382 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6770 (tt) REVERT: BE 450 ASP cc_start: 0.7896 (t70) cc_final: 0.7542 (t0) REVERT: BE 558 GLU cc_start: 0.8727 (pt0) cc_final: 0.8408 (pt0) REVERT: BE 564 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8068 (tm-30) REVERT: BE 568 ARG cc_start: 0.8213 (tpp80) cc_final: 0.7980 (ttm-80) REVERT: BE 583 GLU cc_start: 0.8489 (tp30) cc_final: 0.8126 (tp30) REVERT: BE 586 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8331 (ttp80) REVERT: BF 249 LYS cc_start: 0.8990 (tptp) cc_final: 0.8741 (tptp) REVERT: BF 306 GLU cc_start: 0.8498 (tp30) cc_final: 0.8105 (tp30) REVERT: BF 317 MET cc_start: 0.7992 (tmm) cc_final: 0.7769 (tmm) REVERT: BF 325 ARG cc_start: 0.8430 (tpp80) cc_final: 0.7937 (ttm110) REVERT: AC 524 HIS cc_start: 0.6377 (t-90) cc_final: 0.5530 (m170) REVERT: AD 300 MET cc_start: 0.8230 (tpp) cc_final: 0.7950 (tpp) REVERT: AE 533 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: AE 534 ASP cc_start: 0.8230 (t0) cc_final: 0.7982 (t0) REVERT: AE 581 MET cc_start: 0.8383 (tmm) cc_final: 0.8047 (tmm) REVERT: AE 588 GLN cc_start: 0.8270 (tm-30) cc_final: 0.8041 (tm-30) REVERT: CC 551 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7519 (mp10) REVERT: CC 559 MET cc_start: 0.7834 (OUTLIER) cc_final: 0.7435 (ttm) REVERT: CC 574 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7382 (mpp) REVERT: CC 588 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7706 (tm-30) REVERT: CE 469 GLU cc_start: 0.8194 (tp30) cc_final: 0.7841 (tp30) REVERT: CE 519 MET cc_start: 0.7638 (ttm) cc_final: 0.7294 (ttm) REVERT: CF 266 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: CF 299 GLU cc_start: 0.8102 (tt0) cc_final: 0.7713 (tp30) outliers start: 50 outliers final: 36 residues processed: 275 average time/residue: 0.1137 time to fit residues: 44.9001 Evaluate side-chains 288 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 244 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 437 THR Chi-restraints excluded: chain BC residue 450 ASP Chi-restraints excluded: chain BC residue 496 MET Chi-restraints excluded: chain BC residue 545 MET Chi-restraints excluded: chain BD residue 216 THR Chi-restraints excluded: chain BD residue 217 THR Chi-restraints excluded: chain BD residue 267 TYR Chi-restraints excluded: chain BD residue 316 LEU Chi-restraints excluded: chain BE residue 382 LEU Chi-restraints excluded: chain BE residue 411 ILE Chi-restraints excluded: chain BE residue 412 VAL Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain BF residue 152 VAL Chi-restraints excluded: chain AC residue 371 VAL Chi-restraints excluded: chain AC residue 380 ASN Chi-restraints excluded: chain AC residue 400 VAL Chi-restraints excluded: chain AC residue 412 VAL Chi-restraints excluded: chain AC residue 425 GLU Chi-restraints excluded: chain AC residue 441 VAL Chi-restraints excluded: chain AC residue 486 TYR Chi-restraints excluded: chain AD residue 149 SER Chi-restraints excluded: chain AD residue 159 VAL Chi-restraints excluded: chain AD residue 161 ASN Chi-restraints excluded: chain AD residue 228 ASP Chi-restraints excluded: chain AE residue 530 LEU Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CC residue 551 GLN Chi-restraints excluded: chain CC residue 553 MET Chi-restraints excluded: chain CC residue 559 MET Chi-restraints excluded: chain CC residue 573 GLU Chi-restraints excluded: chain CC residue 574 MET Chi-restraints excluded: chain CE residue 429 GLU Chi-restraints excluded: chain CE residue 492 SER Chi-restraints excluded: chain CE residue 496 MET Chi-restraints excluded: chain CE residue 508 MET Chi-restraints excluded: chain CE residue 513 ASP Chi-restraints excluded: chain CE residue 514 LYS Chi-restraints excluded: chain CF residue 155 LEU Chi-restraints excluded: chain CF residue 253 GLN Chi-restraints excluded: chain CF residue 266 GLU Chi-restraints excluded: chain CF residue 269 MET Chi-restraints excluded: chain CF residue 309 VAL Chi-restraints excluded: chain CF residue 312 MET Chi-restraints excluded: chain CF residue 315 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 0.6980 chunk 159 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 129 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 162 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 8 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AD 248 HIS ** CF 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.171620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.136839 restraints weight = 22916.481| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 2.91 r_work: 0.3796 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14640 Z= 0.136 Angle : 0.593 9.997 19577 Z= 0.287 Chirality : 0.038 0.189 1991 Planarity : 0.004 0.046 2679 Dihedral : 4.020 47.561 1952 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.13 % Allowed : 15.46 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.21), residues: 1708 helix: 3.15 (0.15), residues: 1057 sheet: -0.60 (0.43), residues: 127 loop : 0.14 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGBE 543 TYR 0.014 0.001 TYRBD 158 PHE 0.008 0.001 PHEBF 195 TRP 0.006 0.001 TRPBF 271 HIS 0.007 0.001 HISCC 524 Details of bonding type rmsd covalent geometry : bond 0.00309 (14640) covalent geometry : angle 0.59298 (19577) hydrogen bonds : bond 0.04439 ( 979) hydrogen bonds : angle 3.51119 ( 2877) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 450 ASP cc_start: 0.7344 (OUTLIER) cc_final: 0.6759 (p0) REVERT: BC 590 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8039 (tm-30) REVERT: BD 248 HIS cc_start: 0.8746 (m-70) cc_final: 0.8327 (m-70) REVERT: BD 276 GLU cc_start: 0.8342 (mm-30) cc_final: 0.8031 (mm-30) REVERT: BD 316 LEU cc_start: 0.5970 (OUTLIER) cc_final: 0.5249 (mp) REVERT: BE 382 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6716 (tt) REVERT: BE 450 ASP cc_start: 0.7930 (t70) cc_final: 0.7599 (t0) REVERT: BE 558 GLU cc_start: 0.8728 (pt0) cc_final: 0.8404 (pt0) REVERT: BE 564 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8019 (tm-30) REVERT: BE 568 ARG cc_start: 0.8213 (ttp80) cc_final: 0.8011 (ttm-80) REVERT: BE 583 GLU cc_start: 0.8495 (tp30) cc_final: 0.8133 (tp30) REVERT: BE 586 ARG cc_start: 0.8606 (ttp80) cc_final: 0.8307 (ttp80) REVERT: BF 249 LYS cc_start: 0.8964 (tptp) cc_final: 0.8718 (tptp) REVERT: BF 306 GLU cc_start: 0.8478 (tp30) cc_final: 0.8024 (tp30) REVERT: BF 317 MET cc_start: 0.7985 (tmm) cc_final: 0.7767 (tmm) REVERT: BF 325 ARG cc_start: 0.8429 (tpp80) cc_final: 0.7955 (ttm110) REVERT: AC 524 HIS cc_start: 0.6394 (t-90) cc_final: 0.5553 (m170) REVERT: AD 300 MET cc_start: 0.8211 (tpp) cc_final: 0.7908 (tpp) REVERT: AE 533 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7397 (tm-30) REVERT: AE 534 ASP cc_start: 0.8260 (t0) cc_final: 0.8015 (t0) REVERT: AE 581 MET cc_start: 0.8396 (tmm) cc_final: 0.8057 (tmm) REVERT: AE 588 GLN cc_start: 0.8295 (tm-30) cc_final: 0.8071 (tm-30) REVERT: CC 551 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: CC 559 MET cc_start: 0.7861 (OUTLIER) cc_final: 0.7442 (ttm) REVERT: CC 574 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7360 (mpp) REVERT: CC 588 GLN cc_start: 0.8042 (tm-30) cc_final: 0.7786 (tm-30) REVERT: CC 590 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8292 (mm-30) REVERT: CE 476 PHE cc_start: 0.7561 (m-80) cc_final: 0.7299 (m-80) REVERT: CF 266 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6777 (mp0) REVERT: CF 299 GLU cc_start: 0.8092 (tt0) cc_final: 0.7708 (tp30) outliers start: 49 outliers final: 36 residues processed: 277 average time/residue: 0.1067 time to fit residues: 42.9936 Evaluate side-chains 283 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 437 THR Chi-restraints excluded: chain BC residue 450 ASP Chi-restraints excluded: chain BC residue 496 MET Chi-restraints excluded: chain BC residue 545 MET Chi-restraints excluded: chain BD residue 216 THR Chi-restraints excluded: chain BD residue 217 THR Chi-restraints excluded: chain BD residue 267 TYR Chi-restraints excluded: chain BD residue 316 LEU Chi-restraints excluded: chain BE residue 382 LEU Chi-restraints excluded: chain BE residue 411 ILE Chi-restraints excluded: chain BE residue 412 VAL Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain BF residue 152 VAL Chi-restraints excluded: chain BF residue 192 ILE Chi-restraints excluded: chain AC residue 371 VAL Chi-restraints excluded: chain AC residue 380 ASN Chi-restraints excluded: chain AC residue 400 VAL Chi-restraints excluded: chain AC residue 412 VAL Chi-restraints excluded: chain AC residue 441 VAL Chi-restraints excluded: chain AC residue 486 TYR Chi-restraints excluded: chain AD residue 149 SER Chi-restraints excluded: chain AD residue 159 VAL Chi-restraints excluded: chain AD residue 161 ASN Chi-restraints excluded: chain AD residue 228 ASP Chi-restraints excluded: chain AE residue 519 MET Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CC residue 551 GLN Chi-restraints excluded: chain CC residue 553 MET Chi-restraints excluded: chain CC residue 559 MET Chi-restraints excluded: chain CC residue 573 GLU Chi-restraints excluded: chain CC residue 574 MET Chi-restraints excluded: chain CE residue 429 GLU Chi-restraints excluded: chain CE residue 492 SER Chi-restraints excluded: chain CE residue 496 MET Chi-restraints excluded: chain CE residue 508 MET Chi-restraints excluded: chain CE residue 513 ASP Chi-restraints excluded: chain CE residue 514 LYS Chi-restraints excluded: chain CF residue 155 LEU Chi-restraints excluded: chain CF residue 253 GLN Chi-restraints excluded: chain CF residue 266 GLU Chi-restraints excluded: chain CF residue 269 MET Chi-restraints excluded: chain CF residue 309 VAL Chi-restraints excluded: chain CF residue 312 MET Chi-restraints excluded: chain CF residue 315 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 110 optimal weight: 0.8980 chunk 50 optimal weight: 0.0030 chunk 121 optimal weight: 0.8980 chunk 158 optimal weight: 0.0370 chunk 138 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 117 optimal weight: 0.1980 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 163 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.4068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** CF 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.172383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.137912 restraints weight = 22601.439| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.88 r_work: 0.3810 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14640 Z= 0.123 Angle : 0.592 9.845 19577 Z= 0.286 Chirality : 0.038 0.188 1991 Planarity : 0.004 0.042 2679 Dihedral : 3.980 46.846 1952 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 3.13 % Allowed : 15.91 % Favored : 80.96 % 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 are not related in a simple way. whole: 3.13 (0.21), residues: 1708 helix: 3.27 (0.15), residues: 1050 sheet: -0.57 (0.45), residues: 122 loop : 0.27 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARGBD 186 TYR 0.013 0.001 TYRBD 158 PHE 0.009 0.001 PHECF 247 TRP 0.005 0.001 TRPCF 271 HIS 0.007 0.001 HISCC 524 Details of bonding type rmsd covalent geometry : bond 0.00272 (14640) covalent geometry : angle 0.59237 (19577) hydrogen bonds : bond 0.04301 ( 979) hydrogen bonds : angle 3.43468 ( 2877) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 450 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6755 (p0) REVERT: BC 590 GLU cc_start: 0.8370 (tm-30) cc_final: 0.8050 (tm-30) REVERT: BD 248 HIS cc_start: 0.8766 (m-70) cc_final: 0.8347 (m-70) REVERT: BD 276 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8049 (mm-30) REVERT: BD 316 LEU cc_start: 0.5926 (OUTLIER) cc_final: 0.5416 (mp) REVERT: BE 450 ASP cc_start: 0.7912 (t70) cc_final: 0.7603 (t0) REVERT: BE 558 GLU cc_start: 0.8720 (pt0) cc_final: 0.8395 (pt0) REVERT: BE 564 GLU cc_start: 0.8490 (tm-30) cc_final: 0.7507 (tm-30) REVERT: BE 568 ARG cc_start: 0.8211 (ttp80) cc_final: 0.7564 (tpp80) REVERT: BE 583 GLU cc_start: 0.8527 (tp30) cc_final: 0.8174 (tp30) REVERT: BE 586 ARG cc_start: 0.8603 (ttp80) cc_final: 0.8310 (ttp80) REVERT: BF 306 GLU cc_start: 0.8452 (tp30) cc_final: 0.8000 (tp30) REVERT: BF 317 MET cc_start: 0.7979 (tmm) cc_final: 0.7757 (tmm) REVERT: BF 325 ARG cc_start: 0.8393 (tpp80) cc_final: 0.7936 (ttm110) REVERT: AC 524 HIS cc_start: 0.6324 (t-90) cc_final: 0.5519 (m170) REVERT: AD 300 MET cc_start: 0.8231 (tpp) cc_final: 0.7925 (tpp) REVERT: AE 533 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: AE 534 ASP cc_start: 0.8242 (t0) cc_final: 0.7999 (t0) REVERT: AE 581 MET cc_start: 0.8375 (tmm) cc_final: 0.8030 (tmm) REVERT: AE 588 GLN cc_start: 0.8303 (tm-30) cc_final: 0.8070 (tm-30) REVERT: CC 551 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7973 (mt0) REVERT: CC 559 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7416 (ttm) REVERT: CC 574 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7301 (mpp) REVERT: CC 588 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7775 (tm-30) REVERT: CC 590 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8316 (mm-30) REVERT: CE 427 CYS cc_start: 0.4933 (m) cc_final: 0.4680 (m) REVERT: CE 469 GLU cc_start: 0.8077 (tp30) cc_final: 0.7774 (tp30) REVERT: CE 476 PHE cc_start: 0.7483 (m-80) cc_final: 0.7234 (m-80) REVERT: CF 154 ASN cc_start: 0.8302 (t0) cc_final: 0.7816 (t0) REVERT: CF 266 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6712 (mp0) REVERT: CF 298 MET cc_start: 0.8286 (mmp) cc_final: 0.7958 (mmt) REVERT: CF 299 GLU cc_start: 0.8133 (tt0) cc_final: 0.7788 (tp30) REVERT: CF 325 ARG cc_start: 0.8399 (tpt90) cc_final: 0.8116 (tpp-160) outliers start: 49 outliers final: 36 residues processed: 274 average time/residue: 0.1118 time to fit residues: 44.2539 Evaluate side-chains 290 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 450 ASP Chi-restraints excluded: chain BC residue 496 MET Chi-restraints excluded: chain BC residue 545 MET Chi-restraints excluded: chain BD residue 216 THR Chi-restraints excluded: chain BD residue 217 THR Chi-restraints excluded: chain BD residue 267 TYR Chi-restraints excluded: chain BD residue 316 LEU Chi-restraints excluded: chain BE residue 411 ILE Chi-restraints excluded: chain BE residue 412 VAL Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain BF residue 152 VAL Chi-restraints excluded: chain BF residue 192 ILE Chi-restraints excluded: chain AC residue 371 VAL Chi-restraints excluded: chain AC residue 380 ASN Chi-restraints excluded: chain AC residue 400 VAL Chi-restraints excluded: chain AC residue 412 VAL Chi-restraints excluded: chain AC residue 425 GLU Chi-restraints excluded: chain AC residue 441 VAL Chi-restraints excluded: chain AC residue 486 TYR Chi-restraints excluded: chain AD residue 149 SER Chi-restraints excluded: chain AD residue 159 VAL Chi-restraints excluded: chain AD residue 161 ASN Chi-restraints excluded: chain AD residue 228 ASP Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CC residue 551 GLN Chi-restraints excluded: chain CC residue 553 MET Chi-restraints excluded: chain CC residue 559 MET Chi-restraints excluded: chain CC residue 573 GLU Chi-restraints excluded: chain CC residue 574 MET Chi-restraints excluded: chain CE residue 429 GLU Chi-restraints excluded: chain CE residue 492 SER Chi-restraints excluded: chain CE residue 496 MET Chi-restraints excluded: chain CE residue 508 MET Chi-restraints excluded: chain CE residue 513 ASP Chi-restraints excluded: chain CE residue 514 LYS Chi-restraints excluded: chain CF residue 155 LEU Chi-restraints excluded: chain CF residue 159 VAL Chi-restraints excluded: chain CF residue 253 GLN Chi-restraints excluded: chain CF residue 266 GLU Chi-restraints excluded: chain CF residue 269 MET Chi-restraints excluded: chain CF residue 309 VAL Chi-restraints excluded: chain CF residue 312 MET Chi-restraints excluded: chain CF residue 315 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 131 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 chunk 60 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 164 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.170862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.137659 restraints weight = 22902.445| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 3.01 r_work: 0.3774 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14640 Z= 0.151 Angle : 0.630 11.999 19577 Z= 0.305 Chirality : 0.039 0.188 1991 Planarity : 0.004 0.051 2679 Dihedral : 4.064 48.554 1952 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.99 % Favored : 97.95 % Rotamer: Outliers : 2.94 % Allowed : 16.29 % Favored : 80.77 % 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 are not related in a simple way. whole: 3.01 (0.21), residues: 1708 helix: 3.19 (0.15), residues: 1051 sheet: -0.63 (0.45), residues: 122 loop : 0.19 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARGBE 570 TYR 0.014 0.002 TYRBD 158 PHE 0.009 0.001 PHEBF 195 TRP 0.008 0.001 TRPBF 271 HIS 0.008 0.001 HISCC 524 Details of bonding type rmsd covalent geometry : bond 0.00347 (14640) covalent geometry : angle 0.62990 (19577) hydrogen bonds : bond 0.04430 ( 979) hydrogen bonds : angle 3.49281 ( 2877) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 253 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 450 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.6718 (p0) REVERT: BC 590 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8060 (tm-30) REVERT: BD 248 HIS cc_start: 0.8781 (m-70) cc_final: 0.8327 (m-70) REVERT: BD 276 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8078 (mm-30) REVERT: BD 316 LEU cc_start: 0.6044 (OUTLIER) cc_final: 0.5556 (mp) REVERT: BE 450 ASP cc_start: 0.8039 (t70) cc_final: 0.7653 (t0) REVERT: BE 558 GLU cc_start: 0.8716 (pt0) cc_final: 0.8393 (pt0) REVERT: BE 564 GLU cc_start: 0.8486 (tm-30) cc_final: 0.7485 (tm-30) REVERT: BE 568 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7489 (tpp80) REVERT: BE 583 GLU cc_start: 0.8532 (tp30) cc_final: 0.8159 (tp30) REVERT: BE 586 ARG cc_start: 0.8575 (ttp80) cc_final: 0.8273 (ttp80) REVERT: BF 249 LYS cc_start: 0.8964 (tptp) cc_final: 0.8700 (tptp) REVERT: BF 306 GLU cc_start: 0.8511 (tp30) cc_final: 0.8033 (tp30) REVERT: BF 317 MET cc_start: 0.7990 (tmm) cc_final: 0.7764 (tmm) REVERT: BF 325 ARG cc_start: 0.8405 (tpp80) cc_final: 0.7926 (ttm110) REVERT: AC 524 HIS cc_start: 0.6324 (t-90) cc_final: 0.5520 (m170) REVERT: AD 300 MET cc_start: 0.8267 (tpp) cc_final: 0.7920 (tpp) REVERT: AE 533 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7348 (tm-30) REVERT: AE 534 ASP cc_start: 0.8249 (t0) cc_final: 0.8002 (t0) REVERT: AE 581 MET cc_start: 0.8377 (tmm) cc_final: 0.8042 (tmm) REVERT: AE 588 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8104 (tm-30) REVERT: CC 536 MET cc_start: 0.7634 (mmt) cc_final: 0.6975 (mtt) REVERT: CC 551 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7981 (mt0) REVERT: CC 559 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7453 (ttm) REVERT: CC 574 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7244 (mpp) REVERT: CC 588 GLN cc_start: 0.8004 (tm-30) cc_final: 0.7759 (tm-30) REVERT: CC 590 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8324 (mm-30) REVERT: CE 427 CYS cc_start: 0.4951 (m) cc_final: 0.4705 (m) REVERT: CE 469 GLU cc_start: 0.8094 (tp30) cc_final: 0.7858 (tp30) REVERT: CE 476 PHE cc_start: 0.7566 (m-80) cc_final: 0.7315 (m-80) REVERT: CE 508 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6265 (tpp) REVERT: CF 154 ASN cc_start: 0.8345 (t0) cc_final: 0.7920 (t0) REVERT: CF 266 GLU cc_start: 0.7209 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: CF 298 MET cc_start: 0.8319 (mmp) cc_final: 0.8011 (mmt) REVERT: CF 299 GLU cc_start: 0.8165 (tt0) cc_final: 0.7752 (tp30) REVERT: CF 325 ARG cc_start: 0.8394 (tpt90) cc_final: 0.8101 (tpp-160) outliers start: 46 outliers final: 35 residues processed: 276 average time/residue: 0.1247 time to fit residues: 49.0357 Evaluate side-chains 286 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 243 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 450 ASP Chi-restraints excluded: chain BC residue 465 MET Chi-restraints excluded: chain BC residue 496 MET Chi-restraints excluded: chain BC residue 545 MET Chi-restraints excluded: chain BD residue 217 THR Chi-restraints excluded: chain BD residue 267 TYR Chi-restraints excluded: chain BD residue 316 LEU Chi-restraints excluded: chain BE residue 411 ILE Chi-restraints excluded: chain BE residue 412 VAL Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain BF residue 152 VAL Chi-restraints excluded: chain BF residue 192 ILE Chi-restraints excluded: chain AC residue 371 VAL Chi-restraints excluded: chain AC residue 380 ASN Chi-restraints excluded: chain AC residue 400 VAL Chi-restraints excluded: chain AC residue 412 VAL Chi-restraints excluded: chain AC residue 425 GLU Chi-restraints excluded: chain AC residue 441 VAL Chi-restraints excluded: chain AC residue 486 TYR Chi-restraints excluded: chain AD residue 149 SER Chi-restraints excluded: chain AD residue 159 VAL Chi-restraints excluded: chain AD residue 161 ASN Chi-restraints excluded: chain AD residue 228 ASP Chi-restraints excluded: chain AE residue 519 MET Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CC residue 551 GLN Chi-restraints excluded: chain CC residue 553 MET Chi-restraints excluded: chain CC residue 559 MET Chi-restraints excluded: chain CC residue 573 GLU Chi-restraints excluded: chain CC residue 574 MET Chi-restraints excluded: chain CE residue 429 GLU Chi-restraints excluded: chain CE residue 492 SER Chi-restraints excluded: chain CE residue 496 MET Chi-restraints excluded: chain CE residue 508 MET Chi-restraints excluded: chain CE residue 513 ASP Chi-restraints excluded: chain CE residue 514 LYS Chi-restraints excluded: chain CF residue 159 VAL Chi-restraints excluded: chain CF residue 253 GLN Chi-restraints excluded: chain CF residue 266 GLU Chi-restraints excluded: chain CF residue 269 MET Chi-restraints excluded: chain CF residue 309 VAL Chi-restraints excluded: chain CF residue 312 MET Chi-restraints excluded: chain CF residue 315 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 28 optimal weight: 0.5980 chunk 148 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 152 optimal weight: 0.8980 chunk 158 optimal weight: 0.0570 chunk 9 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 165 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 150 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BC 467 GLN ** AD 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.172273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.137730 restraints weight = 22699.749| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.90 r_work: 0.3810 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14640 Z= 0.127 Angle : 0.625 11.034 19577 Z= 0.303 Chirality : 0.038 0.191 1991 Planarity : 0.004 0.063 2679 Dihedral : 4.023 47.571 1952 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.11 % Favored : 98.83 % Rotamer: Outliers : 2.68 % Allowed : 16.55 % Favored : 80.77 % 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 are not related in a simple way. whole: 3.16 (0.21), residues: 1708 helix: 3.27 (0.15), residues: 1051 sheet: -0.51 (0.45), residues: 122 loop : 0.31 (0.29), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARGBD 186 TYR 0.016 0.001 TYRBD 158 PHE 0.010 0.001 PHECF 247 TRP 0.005 0.001 TRPBE 490 HIS 0.008 0.001 HISCC 524 Details of bonding type rmsd covalent geometry : bond 0.00283 (14640) covalent geometry : angle 0.62489 (19577) hydrogen bonds : bond 0.04260 ( 979) hydrogen bonds : angle 3.43101 ( 2877) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BC 450 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.6735 (p0) REVERT: BC 590 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8052 (tm-30) REVERT: BD 248 HIS cc_start: 0.8794 (m-70) cc_final: 0.8349 (m-70) REVERT: BD 276 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8056 (mm-30) REVERT: BD 316 LEU cc_start: 0.5951 (OUTLIER) cc_final: 0.5462 (mp) REVERT: BE 450 ASP cc_start: 0.7979 (t70) cc_final: 0.7663 (t0) REVERT: BE 465 MET cc_start: 0.7030 (tmm) cc_final: 0.6741 (tmm) REVERT: BE 547 GLU cc_start: 0.8254 (mm-30) cc_final: 0.7938 (tp30) REVERT: BE 558 GLU cc_start: 0.8712 (pt0) cc_final: 0.8387 (pt0) REVERT: BE 564 GLU cc_start: 0.8439 (tm-30) cc_final: 0.7463 (tm-30) REVERT: BE 568 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7560 (tpp80) REVERT: BE 583 GLU cc_start: 0.8544 (tp30) cc_final: 0.8245 (tp30) REVERT: BE 586 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8287 (ttp80) REVERT: BF 183 ASP cc_start: 0.6170 (p0) cc_final: 0.5877 (p0) REVERT: BF 249 LYS cc_start: 0.8967 (tptp) cc_final: 0.8725 (tptp) REVERT: BF 306 GLU cc_start: 0.8467 (tp30) cc_final: 0.7989 (tp30) REVERT: BF 317 MET cc_start: 0.7986 (tmm) cc_final: 0.7763 (tmm) REVERT: BF 325 ARG cc_start: 0.8375 (tpp80) cc_final: 0.7930 (ttm110) REVERT: AC 518 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: AC 524 HIS cc_start: 0.6313 (t-90) cc_final: 0.5512 (m170) REVERT: AD 300 MET cc_start: 0.8191 (tpp) cc_final: 0.7861 (tpp) REVERT: AE 533 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: AE 534 ASP cc_start: 0.8238 (t0) cc_final: 0.8001 (t0) REVERT: AE 581 MET cc_start: 0.8389 (tmm) cc_final: 0.8042 (tmm) REVERT: AE 588 GLN cc_start: 0.8309 (tm-30) cc_final: 0.8081 (tm-30) REVERT: CC 536 MET cc_start: 0.7659 (mmt) cc_final: 0.7016 (mtt) REVERT: CC 551 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.8006 (mt0) REVERT: CC 559 MET cc_start: 0.7864 (OUTLIER) cc_final: 0.7420 (ttm) REVERT: CC 574 MET cc_start: 0.8118 (OUTLIER) cc_final: 0.7766 (mtm) REVERT: CC 588 GLN cc_start: 0.8049 (tm-30) cc_final: 0.7790 (tm-30) REVERT: CC 590 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8288 (mm-30) REVERT: CE 427 CYS cc_start: 0.4726 (m) cc_final: 0.4481 (m) REVERT: CE 476 PHE cc_start: 0.7482 (m-80) cc_final: 0.7250 (m-80) REVERT: CF 154 ASN cc_start: 0.8350 (t0) cc_final: 0.8005 (t0) REVERT: CF 266 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6663 (mp0) REVERT: CF 298 MET cc_start: 0.8310 (mmp) cc_final: 0.8083 (mmt) REVERT: CF 299 GLU cc_start: 0.8159 (tt0) cc_final: 0.7796 (tt0) REVERT: CF 325 ARG cc_start: 0.8388 (tpt90) cc_final: 0.8104 (tpp-160) outliers start: 42 outliers final: 33 residues processed: 280 average time/residue: 0.1226 time to fit residues: 49.1847 Evaluate side-chains 290 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BC residue 450 ASP Chi-restraints excluded: chain BC residue 465 MET Chi-restraints excluded: chain BC residue 496 MET Chi-restraints excluded: chain BC residue 545 MET Chi-restraints excluded: chain BD residue 216 THR Chi-restraints excluded: chain BD residue 217 THR Chi-restraints excluded: chain BD residue 267 TYR Chi-restraints excluded: chain BD residue 316 LEU Chi-restraints excluded: chain BE residue 411 ILE Chi-restraints excluded: chain BE residue 412 VAL Chi-restraints excluded: chain BE residue 486 TYR Chi-restraints excluded: chain BF residue 152 VAL Chi-restraints excluded: chain BF residue 192 ILE Chi-restraints excluded: chain AC residue 371 VAL Chi-restraints excluded: chain AC residue 380 ASN Chi-restraints excluded: chain AC residue 412 VAL Chi-restraints excluded: chain AC residue 425 GLU Chi-restraints excluded: chain AC residue 441 VAL Chi-restraints excluded: chain AC residue 486 TYR Chi-restraints excluded: chain AC residue 518 GLU Chi-restraints excluded: chain AD residue 159 VAL Chi-restraints excluded: chain AD residue 161 ASN Chi-restraints excluded: chain AD residue 228 ASP Chi-restraints excluded: chain AE residue 530 LEU Chi-restraints excluded: chain AE residue 533 GLN Chi-restraints excluded: chain CC residue 551 GLN Chi-restraints excluded: chain CC residue 553 MET Chi-restraints excluded: chain CC residue 559 MET Chi-restraints excluded: chain CC residue 573 GLU Chi-restraints excluded: chain CC residue 574 MET Chi-restraints excluded: chain CE residue 429 GLU Chi-restraints excluded: chain CE residue 492 SER Chi-restraints excluded: chain CE residue 508 MET Chi-restraints excluded: chain CE residue 514 LYS Chi-restraints excluded: chain CF residue 159 VAL Chi-restraints excluded: chain CF residue 253 GLN Chi-restraints excluded: chain CF residue 266 GLU Chi-restraints excluded: chain CF residue 269 MET Chi-restraints excluded: chain CF residue 309 VAL Chi-restraints excluded: chain CF residue 312 MET Chi-restraints excluded: chain CF residue 315 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 145 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 135 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 157 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** AD 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** CF 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.169454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.135178 restraints weight = 22947.916| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.99 r_work: 0.3756 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14640 Z= 0.181 Angle : 0.678 12.227 19577 Z= 0.332 Chirality : 0.041 0.188 1991 Planarity : 0.005 0.099 2679 Dihedral : 4.205 50.030 1952 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.28 % Favored : 97.66 % Rotamer: Outliers : 2.68 % Allowed : 16.55 % Favored : 80.77 % 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 are not related in a simple way. whole: 2.97 (0.21), residues: 1708 helix: 3.17 (0.15), residues: 1046 sheet: -0.65 (0.46), residues: 122 loop : 0.17 (0.29), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARGBE 570 TYR 0.012 0.002 TYRBC 593 PHE 0.010 0.001 PHEBF 195 TRP 0.010 0.002 TRPBF 271 HIS 0.008 0.001 HISCC 524 Details of bonding type rmsd covalent geometry : bond 0.00420 (14640) covalent geometry : angle 0.67755 (19577) hydrogen bonds : bond 0.04600 ( 979) hydrogen bonds : angle 3.56856 ( 2877) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3660.96 seconds wall clock time: 63 minutes 21.21 seconds (3801.21 seconds total)