Starting phenix.real_space_refine on Thu Feb 5 04:49:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gld_51439/02_2026/9gld_51439.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gld_51439/02_2026/9gld_51439.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/9gld_51439/02_2026/9gld_51439.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gld_51439/02_2026/9gld_51439.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gld_51439/02_2026/9gld_51439.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gld_51439/02_2026/9gld_51439.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 97 5.16 5 C 8984 2.51 5 N 2717 2.21 5 O 2831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 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: 14629 Number of models: 1 Model: "" Number of chains: 10 Chain: "BA" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1564 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 10, 'TRANS': 179} Chain: "BB" 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: "BG" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1916 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain: "BH" 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: "AA" Number of atoms: 1916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1916 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain: "AB" 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: "AG" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 178, 1459 Classifications: {'peptide': 178} Link IDs: {'PTRANS': 10, 'TRANS': 167} Chain: "AH" 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: "CG" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 721 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain: "DA" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 681 Classifications: {'peptide': 75} Link IDs: {'TRANS': 74} Time building chain proxies: 3.03, per 1000 atoms: 0.21 Number of scatterers: 14629 At special positions: 0 Unit cell: (87.032, 113.52, 262.988, 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 97 16.00 O 2831 8.00 N 2717 7.00 C 8984 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: 1.24 Conformation dependent library (CDL) restraints added in 478.4 milliseconds 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3382 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 65.3% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'BA' and resid 379 through 387 removed outlier: 3.501A pdb=" N PHEBA 387 " --> pdb=" O LEUBA 383 " (cutoff:3.500A) Processing helix chain 'BA' and resid 388 through 391 Processing helix chain 'BA' and resid 416 through 429 Processing helix chain 'BA' and resid 456 through 461 Processing helix chain 'BA' and resid 463 through 471 removed outlier: 4.368A pdb=" N GLNBA 467 " --> pdb=" O ASNBA 463 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYSBA 468 " --> pdb=" O PROBA 464 " (cutoff:3.500A) Processing helix chain 'BA' and resid 481 through 518 Processing helix chain 'BA' and resid 518 through 556 removed outlier: 3.687A pdb=" N ALABA 522 " --> pdb=" O GLUBA 518 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARGBA 556 " --> pdb=" O GLUBA 552 " (cutoff:3.500A) Processing helix chain 'BB' and resid 160 through 169 Processing helix chain 'BB' and resid 197 through 211 Processing helix chain 'BB' and resid 244 through 250 Processing helix chain 'BB' and resid 262 through 299 Processing helix chain 'BB' and resid 299 through 339 Processing helix chain 'BG' and resid 379 through 387 Processing helix chain 'BG' and resid 388 through 390 No H-bonds generated for 'chain 'BG' and resid 388 through 390' Processing helix chain 'BG' and resid 416 through 430 removed outlier: 4.262A pdb=" N GLUBG 429 " --> pdb=" O GLUBG 425 " (cutoff:3.500A) Processing helix chain 'BG' and resid 456 through 461 Processing helix chain 'BG' and resid 464 through 469 removed outlier: 3.761A pdb=" N LYSBG 468 " --> pdb=" O PROBG 464 " (cutoff:3.500A) Processing helix chain 'BG' and resid 481 through 518 removed outlier: 3.810A pdb=" N GLNBG 488 " --> pdb=" O TYRBG 484 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARGBG 489 " --> pdb=" O GLUBG 485 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEUBG 493 " --> pdb=" O ARGBG 489 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VALBG 504 " --> pdb=" O GLNBG 500 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLUBG 518 " --> pdb=" O LYSBG 514 " (cutoff:3.500A) Processing helix chain 'BG' and resid 518 through 594 Processing helix chain 'BH' and resid 160 through 168 Processing helix chain 'BH' and resid 169 through 171 No H-bonds generated for 'chain 'BH' and resid 169 through 171' Processing helix chain 'BH' and resid 197 through 211 Processing helix chain 'BH' and resid 237 through 241 Processing helix chain 'BH' and resid 244 through 251 Processing helix chain 'BH' and resid 262 through 299 Processing helix chain 'BH' and resid 299 through 340 Processing helix chain 'AA' and resid 379 through 389 removed outlier: 3.982A pdb=" N GLNAA 389 " --> pdb=" O GLUAA 385 " (cutoff:3.500A) Processing helix chain 'AA' and resid 416 through 430 Processing helix chain 'AA' and resid 456 through 461 Processing helix chain 'AA' and resid 463 through 471 removed outlier: 4.439A pdb=" N GLNAA 467 " --> pdb=" O ASNAA 463 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYSAA 468 " --> pdb=" O PROAA 464 " (cutoff:3.500A) Processing helix chain 'AA' and resid 481 through 518 removed outlier: 3.580A pdb=" N GLUAA 518 " --> pdb=" O LYSAA 514 " (cutoff:3.500A) Processing helix chain 'AA' and resid 518 through 594 removed outlier: 3.567A pdb=" N ALAAA 522 " --> pdb=" O GLUAA 518 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYRAA 523 " --> pdb=" O METAA 519 " (cutoff:3.500A) Processing helix chain 'AB' and resid 160 through 168 Processing helix chain 'AB' and resid 197 through 211 Processing helix chain 'AB' and resid 244 through 250 Processing helix chain 'AB' and resid 262 through 340 removed outlier: 5.024A pdb=" N GLUAB 301 " --> pdb=" O GLUAB 297 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALAAB 302 " --> pdb=" O METAB 298 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEUAB 340 " --> pdb=" O LYSAB 336 " (cutoff:3.500A) Processing helix chain 'AG' and resid 379 through 387 Processing helix chain 'AG' and resid 388 through 391 Processing helix chain 'AG' and resid 416 through 430 removed outlier: 3.586A pdb=" N ALAAG 420 " --> pdb=" O SERAG 416 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLUAG 429 " --> pdb=" O GLUAG 425 " (cutoff:3.500A) Processing helix chain 'AG' and resid 456 through 463 removed outlier: 4.264A pdb=" N ASNAG 463 " --> pdb=" O LEUAG 459 " (cutoff:3.500A) Processing helix chain 'AG' and resid 465 through 470 Processing helix chain 'AG' and resid 481 through 518 removed outlier: 4.006A pdb=" N ARGAG 489 " --> pdb=" O GLUAG 485 " (cutoff:3.500A) Processing helix chain 'AG' and resid 518 through 544 removed outlier: 3.534A pdb=" N ALAAG 522 " --> pdb=" O GLUAG 518 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYRAG 523 " --> pdb=" O METAG 519 " (cutoff:3.500A) Processing helix chain 'AH' and resid 160 through 168 removed outlier: 3.672A pdb=" N LEUAH 164 " --> pdb=" O SERAH 160 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLUAH 165 " --> pdb=" O ASNAH 161 " (cutoff:3.500A) Processing helix chain 'AH' and resid 169 through 172 Processing helix chain 'AH' and resid 197 through 211 Processing helix chain 'AH' and resid 244 through 251 Processing helix chain 'AH' and resid 262 through 299 Processing helix chain 'AH' and resid 299 through 340 removed outlier: 3.580A pdb=" N LEUAH 340 " --> pdb=" O LYSAH 336 " (cutoff:3.500A) Processing helix chain 'CG' and resid 518 through 594 removed outlier: 3.574A pdb=" N METCG 559 " --> pdb=" O LYSCG 555 " (cutoff:3.500A) Processing helix chain 'DA' and resid 521 through 594 Processing sheet with id=AA1, first strand: chain 'BA' and resid 393 through 397 Processing sheet with id=AA2, first strand: chain 'BA' and resid 432 through 433 Processing sheet with id=AA3, first strand: chain 'BA' and resid 449 through 450 Processing sheet with id=AA4, first strand: chain 'BB' and resid 174 through 178 removed outlier: 3.502A pdb=" N ARGBB 176 " --> pdb=" O GLUBB 194 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'BG' and resid 393 through 400 removed outlier: 4.097A pdb=" N ARGBG 395 " --> pdb=" O GLUBG 413 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N LYSBG 409 " --> pdb=" O ILEBG 399 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILEBG 442 " --> pdb=" O ARGBG 372 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'BG' and resid 449 through 450 removed outlier: 3.699A pdb=" N VALBH 181 " --> pdb=" O ASPBG 450 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VALBH 174 " --> pdb=" O GLUBH 194 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLUBH 194 " --> pdb=" O VALBH 174 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARGBH 176 " --> pdb=" O ILEBH 192 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILEBH 192 " --> pdb=" O ARGBH 176 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VALBH 178 " --> pdb=" O LYSBH 190 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N LYSBH 190 " --> pdb=" O VALBH 178 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILEBH 180 " --> pdb=" O SERBH 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VALBH 152 " --> pdb=" O GLYBH 191 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'AA' and resid 393 through 400 removed outlier: 3.520A pdb=" N ARGAA 395 " --> pdb=" O GLUAA 413 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYSAA 409 " --> pdb=" O ILEAA 399 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILEAA 442 " --> pdb=" O ARGAA 372 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'AA' and resid 432 through 433 Processing sheet with id=AA9, first strand: chain 'AA' and resid 449 through 450 removed outlier: 4.088A pdb=" N VALAB 181 " --> pdb=" O ASPAA 450 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARGAB 176 " --> pdb=" O ILEAB 192 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILEAB 192 " --> pdb=" O ARGAB 176 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VALAB 178 " --> pdb=" O LYSAB 190 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LYSAB 190 " --> pdb=" O VALAB 178 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N ILEAB 180 " --> pdb=" O SERAB 188 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VALAB 152 " --> pdb=" O GLYAB 191 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'AG' and resid 393 through 400 removed outlier: 4.253A pdb=" N ARGAG 395 " --> pdb=" O GLUAG 413 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYSAG 409 " --> pdb=" O ILEAG 399 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILEAG 442 " --> pdb=" O ARGAG 372 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'AG' and resid 432 through 433 removed outlier: 3.530A pdb=" N LEUAG 433 " --> pdb=" O ARGAH 256 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'AG' and resid 449 through 450 removed outlier: 3.538A pdb=" N VALAH 181 " --> pdb=" O ASPAG 450 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VALAH 174 " --> pdb=" O GLUAH 194 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N GLUAH 194 " --> pdb=" O VALAH 174 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARGAH 176 " --> pdb=" O ILEAH 192 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ILEAH 192 " --> pdb=" O ARGAH 176 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VALAH 178 " --> pdb=" O LYSAH 190 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LYSAH 190 " --> pdb=" O VALAH 178 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILEAH 180 " --> pdb=" O SERAH 188 " (cutoff:3.500A) 1002 hydrogen bonds defined for protein. 2961 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5245 1.34 - 1.46: 1861 1.46 - 1.58: 7558 1.58 - 1.70: 0 1.70 - 1.82: 186 Bond restraints: 14850 Sorted by residual: bond pdb=" N TYRBG 486 " pdb=" CA TYRBG 486 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.27e-02 6.20e+03 6.73e+00 bond pdb=" N ASNBH 244 " pdb=" CA ASNBH 244 " ideal model delta sigma weight residual 1.456 1.486 -0.029 1.14e-02 7.69e+03 6.64e+00 bond pdb=" N ARGAH 256 " pdb=" CA ARGAH 256 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.26e-02 6.30e+03 6.61e+00 bond pdb=" N HISAH 248 " pdb=" CA HISAH 248 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.50e+00 bond pdb=" N ARGBB 325 " pdb=" CA ARGBB 325 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.84e+00 ... (remaining 14845 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 19446 2.23 - 4.47: 351 4.47 - 6.70: 39 6.70 - 8.93: 17 8.93 - 11.17: 3 Bond angle restraints: 19856 Sorted by residual: angle pdb=" CB METBG 585 " pdb=" CG METBG 585 " pdb=" SD METBG 585 " ideal model delta sigma weight residual 112.70 101.53 11.17 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CA METBG 585 " pdb=" CB METBG 585 " pdb=" CG METBG 585 " ideal model delta sigma weight residual 114.10 121.25 -7.15 2.00e+00 2.50e-01 1.28e+01 angle pdb=" N TYRBG 486 " pdb=" CA TYRBG 486 " pdb=" C TYRBG 486 " ideal model delta sigma weight residual 113.41 109.07 4.34 1.22e+00 6.72e-01 1.26e+01 angle pdb=" CA THRBB 217 " pdb=" CB THRBB 217 " pdb=" OG1 THRBB 217 " ideal model delta sigma weight residual 109.60 104.56 5.04 1.50e+00 4.44e-01 1.13e+01 angle pdb=" CB METDA 585 " pdb=" CG METDA 585 " pdb=" SD METDA 585 " ideal model delta sigma weight residual 112.70 102.84 9.86 3.00e+00 1.11e-01 1.08e+01 ... (remaining 19851 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8163 17.99 - 35.98: 1032 35.98 - 53.96: 209 53.96 - 71.95: 72 71.95 - 89.94: 26 Dihedral angle restraints: 9502 sinusoidal: 4341 harmonic: 5161 Sorted by residual: dihedral pdb=" CA VALAB 178 " pdb=" C VALAB 178 " pdb=" N VALAB 179 " pdb=" CA VALAB 179 " ideal model delta harmonic sigma weight residual 180.00 162.25 17.75 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA ASPAH 231 " pdb=" CB ASPAH 231 " pdb=" CG ASPAH 231 " pdb=" OD1 ASPAH 231 " ideal model delta sinusoidal sigma weight residual -30.00 -89.31 59.31 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA PHEBB 218 " pdb=" C PHEBB 218 " pdb=" N PROBB 219 " pdb=" CA PROBB 219 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 9499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1347 0.034 - 0.068: 456 0.068 - 0.102: 162 0.102 - 0.137: 46 0.137 - 0.171: 6 Chirality restraints: 2017 Sorted by residual: chirality pdb=" CA METAA 585 " pdb=" N METAA 585 " pdb=" C METAA 585 " pdb=" CB METAA 585 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.28e-01 chirality pdb=" CA ARGAH 256 " pdb=" N ARGAH 256 " pdb=" C ARGAH 256 " pdb=" CB ARGAH 256 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA ARGAA 570 " pdb=" N ARGAA 570 " pdb=" C ARGAA 570 " pdb=" CB ARGAA 570 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 2014 not shown) Planarity restraints: 2714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASNBG 463 " 0.043 5.00e-02 4.00e+02 6.63e-02 7.03e+00 pdb=" N PROBG 464 " -0.115 5.00e-02 4.00e+02 pdb=" CA PROBG 464 " 0.035 5.00e-02 4.00e+02 pdb=" CD PROBG 464 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEUAH 236 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PROAH 237 " -0.088 5.00e-02 4.00e+02 pdb=" CA PROAH 237 " 0.026 5.00e-02 4.00e+02 pdb=" CD PROAH 237 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THRBA 437 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PROBA 438 " 0.074 5.00e-02 4.00e+02 pdb=" CA PROBA 438 " -0.022 5.00e-02 4.00e+02 pdb=" CD PROBA 438 " -0.024 5.00e-02 4.00e+02 ... (remaining 2711 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2244 2.76 - 3.29: 14659 3.29 - 3.83: 24904 3.83 - 4.36: 25908 4.36 - 4.90: 45512 Nonbonded interactions: 113227 Sorted by model distance: nonbonded pdb=" OE2 GLUBG 582 " pdb=" NH1 ARGDA 556 " model vdw 2.220 3.120 nonbonded pdb=" OH TYRAG 486 " pdb=" O LEUAH 296 " model vdw 2.223 3.040 nonbonded pdb=" O GLNBB 259 " pdb=" OG SERBB 262 " model vdw 2.226 3.040 nonbonded pdb=" OE2 GLUAA 558 " pdb=" NH2 ARGAA 562 " model vdw 2.240 3.120 nonbonded pdb=" O LEUBA 515 " pdb=" OH TYRBB 267 " model vdw 2.247 3.040 ... (remaining 113222 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 'AA' selection = chain 'BG' } ncs_group { reference = chain 'AB' selection = chain 'AH' selection = chain 'BB' selection = chain 'BH' } ncs_group { reference = chain 'AG' selection = (chain 'BA' and resid 367 through 544) } ncs_group { reference = (chain 'CG' and resid 520 through 594) selection = chain 'DA' } 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: 8.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 11.760 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14850 Z= 0.202 Angle : 0.719 11.167 19856 Z= 0.382 Chirality : 0.041 0.171 2017 Planarity : 0.005 0.066 2714 Dihedral : 17.059 89.939 6120 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 2.43 (0.20), residues: 1731 helix: 2.49 (0.15), residues: 1069 sheet: -0.12 (0.60), residues: 98 loop : 0.25 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARGAA 589 TYR 0.014 0.001 TYRAH 267 PHE 0.015 0.002 PHEAG 432 TRP 0.011 0.002 TRPBA 490 HIS 0.011 0.001 HISAH 305 Details of bonding type rmsd covalent geometry : bond 0.00420 (14850) covalent geometry : angle 0.71866 (19856) hydrogen bonds : bond 0.14217 ( 1002) hydrogen bonds : angle 5.38278 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BB 320 GLN cc_start: 0.8294 (tt0) cc_final: 0.8019 (tm-30) REVERT: BG 554 GLN cc_start: 0.8328 (mm110) cc_final: 0.8026 (tp40) REVERT: BG 557 LYS cc_start: 0.8934 (mtpp) cc_final: 0.8726 (mtpp) REVERT: BG 573 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7915 (tm-30) REVERT: BH 325 ARG cc_start: 0.6623 (ptp90) cc_final: 0.6411 (ptp90) REVERT: AA 465 MET cc_start: 0.8058 (ppp) cc_final: 0.7619 (pmm) REVERT: AB 277 MET cc_start: 0.8404 (tpp) cc_final: 0.8175 (tpt) REVERT: AH 266 GLU cc_start: 0.6697 (mp0) cc_final: 0.6436 (mp0) REVERT: DA 570 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7851 (ttm-80) REVERT: DA 588 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8588 (tm-30) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1250 time to fit residues: 58.8959 Evaluate side-chains 257 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BA 533 GLN BB 284 GLN AA 380 ASN AG 448 GLN ** AG 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AG 527 GLN AG 533 GLN DA 526 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.171648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.145334 restraints weight = 23709.204| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.61 r_work: 0.3822 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14850 Z= 0.181 Angle : 0.646 10.942 19856 Z= 0.328 Chirality : 0.041 0.180 2017 Planarity : 0.005 0.057 2714 Dihedral : 3.750 17.464 1974 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.45 % Allowed : 11.72 % Favored : 86.83 % 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: 2.69 (0.20), residues: 1731 helix: 2.82 (0.15), residues: 1052 sheet: -0.68 (0.59), residues: 93 loop : 0.32 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARGAA 439 TYR 0.022 0.002 TYRBG 484 PHE 0.010 0.001 PHEAG 424 TRP 0.011 0.002 TRPAA 490 HIS 0.004 0.001 HISAB 305 Details of bonding type rmsd covalent geometry : bond 0.00418 (14850) covalent geometry : angle 0.64613 (19856) hydrogen bonds : bond 0.05216 ( 1002) hydrogen bonds : angle 4.14712 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 273 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 536 MET cc_start: 0.6579 (mtp) cc_final: 0.6226 (mtm) REVERT: BB 328 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8128 (pp20) REVERT: BG 417 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.5419 (mmtt) REVERT: BG 450 ASP cc_start: 0.7166 (t0) cc_final: 0.6177 (m-30) REVERT: BG 458 LYS cc_start: 0.7416 (mmtm) cc_final: 0.6903 (mppt) REVERT: BG 573 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7913 (tm-30) REVERT: AA 508 MET cc_start: 0.6925 (ttm) cc_final: 0.6674 (tpp) REVERT: AG 485 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7933 (tm-30) REVERT: AH 149 SER cc_start: 0.8231 (p) cc_final: 0.7903 (m) REVERT: AH 227 MET cc_start: 0.8267 (tmm) cc_final: 0.7195 (tmm) REVERT: DA 560 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7810 (tm-30) REVERT: DA 570 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.7883 (ttm-80) REVERT: DA 584 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8105 (tm-30) REVERT: DA 588 GLN cc_start: 0.8813 (tm-30) cc_final: 0.8515 (tm-30) outliers start: 23 outliers final: 13 residues processed: 280 average time/residue: 0.1085 time to fit residues: 44.4843 Evaluate side-chains 269 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 255 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 504 VAL Chi-restraints excluded: chain BA residue 517 SER Chi-restraints excluded: chain BB residue 149 SER Chi-restraints excluded: chain BB residue 174 VAL Chi-restraints excluded: chain BG residue 411 ILE Chi-restraints excluded: chain BG residue 417 LYS Chi-restraints excluded: chain BH residue 285 VAL Chi-restraints excluded: chain AA residue 380 ASN Chi-restraints excluded: chain AA residue 429 GLU Chi-restraints excluded: chain AA residue 576 ILE Chi-restraints excluded: chain AG residue 411 ILE Chi-restraints excluded: chain CG residue 530 LEU Chi-restraints excluded: chain DA residue 559 MET Chi-restraints excluded: chain DA residue 572 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 164 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 168 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BG 563 GLN BH 246 GLN BH 284 GLN AA 380 ASN AG 467 GLN DA 526 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.171660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.145435 restraints weight = 23952.574| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.36 r_work: 0.3834 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14850 Z= 0.154 Angle : 0.598 9.234 19856 Z= 0.299 Chirality : 0.040 0.181 2017 Planarity : 0.004 0.050 2714 Dihedral : 3.590 14.982 1974 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.95 % Allowed : 15.56 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.91 (0.20), residues: 1731 helix: 3.03 (0.15), residues: 1055 sheet: -0.63 (0.64), residues: 81 loop : 0.29 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGAA 439 TYR 0.018 0.001 TYRBG 484 PHE 0.009 0.001 PHEBA 414 TRP 0.012 0.002 TRPAA 490 HIS 0.005 0.001 HISAH 248 Details of bonding type rmsd covalent geometry : bond 0.00353 (14850) covalent geometry : angle 0.59791 (19856) hydrogen bonds : bond 0.04666 ( 1002) hydrogen bonds : angle 3.85111 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 285 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 519 MET cc_start: 0.7292 (tpp) cc_final: 0.7058 (mmm) REVERT: BA 536 MET cc_start: 0.6413 (mtp) cc_final: 0.6141 (mtm) REVERT: BB 328 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8194 (pp20) REVERT: BG 450 ASP cc_start: 0.6998 (t0) cc_final: 0.6156 (m-30) REVERT: BG 458 LYS cc_start: 0.7420 (mmtm) cc_final: 0.6875 (pttt) REVERT: BG 573 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7881 (tm-30) REVERT: BH 277 MET cc_start: 0.8247 (ppp) cc_final: 0.8037 (ppp) REVERT: BH 324 ARG cc_start: 0.7524 (tmm160) cc_final: 0.6798 (ttp80) REVERT: AA 536 MET cc_start: 0.7965 (tpp) cc_final: 0.7700 (tpp) REVERT: AG 485 GLU cc_start: 0.8137 (tm-30) cc_final: 0.7860 (tm-30) REVERT: AH 149 SER cc_start: 0.8255 (p) cc_final: 0.7882 (m) REVERT: AH 227 MET cc_start: 0.8265 (tmm) cc_final: 0.7161 (tmm) REVERT: DA 553 MET cc_start: 0.8236 (OUTLIER) cc_final: 0.7875 (mmp) REVERT: DA 560 GLN cc_start: 0.8246 (tm-30) cc_final: 0.7932 (tm-30) REVERT: DA 570 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.7844 (ttm-80) REVERT: DA 584 GLN cc_start: 0.8498 (tm-30) cc_final: 0.8032 (tm-30) REVERT: DA 585 MET cc_start: 0.7928 (ttt) cc_final: 0.7695 (ttt) REVERT: DA 588 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8519 (tm-30) outliers start: 31 outliers final: 23 residues processed: 297 average time/residue: 0.1300 time to fit residues: 55.7320 Evaluate side-chains 280 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 400 VAL Chi-restraints excluded: chain BA residue 411 ILE Chi-restraints excluded: chain BA residue 412 VAL Chi-restraints excluded: chain BA residue 504 VAL Chi-restraints excluded: chain BA residue 517 SER Chi-restraints excluded: chain BB residue 149 SER Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 380 ASN Chi-restraints excluded: chain BG residue 411 ILE Chi-restraints excluded: chain BG residue 443 VAL Chi-restraints excluded: chain BG residue 575 MET Chi-restraints excluded: chain BG residue 576 ILE Chi-restraints excluded: chain BH residue 285 VAL Chi-restraints excluded: chain AA residue 429 GLU Chi-restraints excluded: chain AA residue 576 ILE Chi-restraints excluded: chain AB residue 294 GLU Chi-restraints excluded: chain AG residue 380 ASN Chi-restraints excluded: chain AG residue 411 ILE Chi-restraints excluded: chain AG residue 508 MET Chi-restraints excluded: chain AH residue 159 VAL Chi-restraints excluded: chain AH residue 181 VAL Chi-restraints excluded: chain CG residue 530 LEU Chi-restraints excluded: chain DA residue 553 MET Chi-restraints excluded: chain DA residue 572 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 95 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 154 optimal weight: 0.9990 chunk 104 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 78 optimal weight: 6.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA 533 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.169799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.143417 restraints weight = 23764.336| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.41 r_work: 0.3798 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14850 Z= 0.178 Angle : 0.616 9.307 19856 Z= 0.310 Chirality : 0.041 0.182 2017 Planarity : 0.005 0.047 2714 Dihedral : 3.691 16.841 1974 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.59 % Allowed : 15.69 % Favored : 80.72 % 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: 2.76 (0.20), residues: 1731 helix: 2.99 (0.15), residues: 1055 sheet: -0.93 (0.63), residues: 81 loop : 0.08 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGDA 569 TYR 0.018 0.002 TYRAB 158 PHE 0.011 0.001 PHEBA 414 TRP 0.015 0.002 TRPAA 490 HIS 0.006 0.001 HISAH 248 Details of bonding type rmsd covalent geometry : bond 0.00416 (14850) covalent geometry : angle 0.61640 (19856) hydrogen bonds : bond 0.04720 ( 1002) hydrogen bonds : angle 3.78170 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 271 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 428 SER cc_start: 0.7788 (t) cc_final: 0.7508 (p) REVERT: BB 328 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8119 (pp20) REVERT: BG 450 ASP cc_start: 0.6835 (t0) cc_final: 0.6208 (m-30) REVERT: BG 458 LYS cc_start: 0.7391 (mmtm) cc_final: 0.7011 (pttt) REVERT: BG 573 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7587 (tp30) REVERT: BH 251 ARG cc_start: 0.7967 (tpm170) cc_final: 0.7706 (tpm170) REVERT: BH 324 ARG cc_start: 0.7625 (tmm160) cc_final: 0.6970 (ttp80) REVERT: AG 374 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7196 (pp) REVERT: AH 149 SER cc_start: 0.8245 (p) cc_final: 0.7809 (m) REVERT: AH 227 MET cc_start: 0.8337 (tmm) cc_final: 0.7089 (tmm) REVERT: AH 253 GLN cc_start: 0.6898 (OUTLIER) cc_final: 0.6378 (pp30) REVERT: CG 588 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7740 (tm-30) REVERT: DA 553 MET cc_start: 0.8311 (OUTLIER) cc_final: 0.7818 (mmp) REVERT: DA 560 GLN cc_start: 0.8342 (tm-30) cc_final: 0.8019 (tm-30) REVERT: DA 563 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.8036 (mm-40) REVERT: DA 584 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8031 (tm-30) REVERT: DA 585 MET cc_start: 0.8146 (ttt) cc_final: 0.7851 (ttt) REVERT: DA 588 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8604 (tm-30) outliers start: 57 outliers final: 37 residues processed: 306 average time/residue: 0.1177 time to fit residues: 52.5920 Evaluate side-chains 299 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 258 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 393 ILE Chi-restraints excluded: chain BA residue 400 VAL Chi-restraints excluded: chain BA residue 411 ILE Chi-restraints excluded: chain BA residue 451 ASP Chi-restraints excluded: chain BA residue 504 VAL Chi-restraints excluded: chain BA residue 517 SER Chi-restraints excluded: chain BB residue 149 SER Chi-restraints excluded: chain BB residue 161 ASN Chi-restraints excluded: chain BB residue 217 THR Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 380 ASN Chi-restraints excluded: chain BG residue 411 ILE Chi-restraints excluded: chain BG residue 435 THR Chi-restraints excluded: chain BG residue 443 VAL Chi-restraints excluded: chain BG residue 476 PHE Chi-restraints excluded: chain BG residue 555 LYS Chi-restraints excluded: chain BG residue 575 MET Chi-restraints excluded: chain BG residue 576 ILE Chi-restraints excluded: chain BH residue 216 THR Chi-restraints excluded: chain BH residue 285 VAL Chi-restraints excluded: chain AA residue 429 GLU Chi-restraints excluded: chain AA residue 476 PHE Chi-restraints excluded: chain AA residue 576 ILE Chi-restraints excluded: chain AB residue 294 GLU Chi-restraints excluded: chain AG residue 374 LEU Chi-restraints excluded: chain AG residue 380 ASN Chi-restraints excluded: chain AG residue 398 VAL Chi-restraints excluded: chain AG residue 411 ILE Chi-restraints excluded: chain AG residue 412 VAL Chi-restraints excluded: chain AG residue 508 MET Chi-restraints excluded: chain AG residue 515 LEU Chi-restraints excluded: chain AH residue 159 VAL Chi-restraints excluded: chain AH residue 166 GLU Chi-restraints excluded: chain AH residue 181 VAL Chi-restraints excluded: chain AH residue 216 THR Chi-restraints excluded: chain AH residue 253 GLN Chi-restraints excluded: chain AH residue 315 ASP Chi-restraints excluded: chain CG residue 530 LEU Chi-restraints excluded: chain DA residue 553 MET Chi-restraints excluded: chain DA residue 563 GLN Chi-restraints excluded: chain DA residue 572 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 114 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: AH 332 GLN DA 526 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.168804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.142450 restraints weight = 23758.778| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 3.58 r_work: 0.3785 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14850 Z= 0.196 Angle : 0.652 9.952 19856 Z= 0.325 Chirality : 0.042 0.188 2017 Planarity : 0.005 0.048 2714 Dihedral : 3.744 15.815 1974 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.84 % Allowed : 17.14 % Favored : 79.02 % 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: 2.64 (0.20), residues: 1731 helix: 2.94 (0.15), residues: 1055 sheet: -1.19 (0.62), residues: 81 loop : -0.01 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARGCG 579 TYR 0.016 0.001 TYRBA 466 PHE 0.010 0.001 PHEAG 432 TRP 0.014 0.002 TRPAA 490 HIS 0.006 0.001 HISAH 248 Details of bonding type rmsd covalent geometry : bond 0.00459 (14850) covalent geometry : angle 0.65156 (19856) hydrogen bonds : bond 0.04765 ( 1002) hydrogen bonds : angle 3.81635 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 265 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 428 SER cc_start: 0.7798 (t) cc_final: 0.7496 (p) REVERT: BA 486 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.7208 (t80) REVERT: BB 328 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8135 (pp20) REVERT: BG 450 ASP cc_start: 0.6870 (t0) cc_final: 0.6267 (m-30) REVERT: BG 573 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7773 (tm-30) REVERT: BG 583 GLU cc_start: 0.8747 (tp30) cc_final: 0.8461 (tp30) REVERT: BH 324 ARG cc_start: 0.7644 (tmm160) cc_final: 0.7003 (ttp80) REVERT: AA 536 MET cc_start: 0.7866 (tpp) cc_final: 0.7611 (tpp) REVERT: AB 324 ARG cc_start: 0.7134 (tmm160) cc_final: 0.6700 (ttt180) REVERT: AG 374 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.7209 (pp) REVERT: AG 432 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.6585 (t80) REVERT: AH 149 SER cc_start: 0.8237 (p) cc_final: 0.7802 (m) REVERT: AH 227 MET cc_start: 0.8383 (tmm) cc_final: 0.7218 (tmm) REVERT: AH 253 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6409 (pp30) REVERT: CG 552 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: DA 553 MET cc_start: 0.8331 (OUTLIER) cc_final: 0.7877 (mmp) REVERT: DA 560 GLN cc_start: 0.8366 (tm-30) cc_final: 0.8038 (tm-30) REVERT: DA 563 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.8034 (mm-40) REVERT: DA 584 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8031 (tm-30) REVERT: DA 585 MET cc_start: 0.8173 (ttt) cc_final: 0.7905 (ttt) REVERT: DA 588 GLN cc_start: 0.8824 (tm-30) cc_final: 0.8595 (tm-30) outliers start: 61 outliers final: 41 residues processed: 303 average time/residue: 0.1128 time to fit residues: 49.8828 Evaluate side-chains 302 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 254 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 393 ILE Chi-restraints excluded: chain BA residue 400 VAL Chi-restraints excluded: chain BA residue 411 ILE Chi-restraints excluded: chain BA residue 412 VAL Chi-restraints excluded: chain BA residue 451 ASP Chi-restraints excluded: chain BA residue 486 TYR Chi-restraints excluded: chain BA residue 504 VAL Chi-restraints excluded: chain BA residue 517 SER Chi-restraints excluded: chain BB residue 149 SER Chi-restraints excluded: chain BB residue 161 ASN Chi-restraints excluded: chain BB residue 174 VAL Chi-restraints excluded: chain BB residue 178 VAL Chi-restraints excluded: chain BB residue 217 THR Chi-restraints excluded: chain BB residue 241 VAL Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 380 ASN Chi-restraints excluded: chain BG residue 411 ILE Chi-restraints excluded: chain BG residue 435 THR Chi-restraints excluded: chain BG residue 443 VAL Chi-restraints excluded: chain BG residue 476 PHE Chi-restraints excluded: chain BG residue 576 ILE Chi-restraints excluded: chain BH residue 216 THR Chi-restraints excluded: chain BH residue 285 VAL Chi-restraints excluded: chain AA residue 429 GLU Chi-restraints excluded: chain AA residue 476 PHE Chi-restraints excluded: chain AA residue 504 VAL Chi-restraints excluded: chain AA residue 576 ILE Chi-restraints excluded: chain AB residue 294 GLU Chi-restraints excluded: chain AG residue 374 LEU Chi-restraints excluded: chain AG residue 380 ASN Chi-restraints excluded: chain AG residue 398 VAL Chi-restraints excluded: chain AG residue 412 VAL Chi-restraints excluded: chain AG residue 432 PHE Chi-restraints excluded: chain AG residue 472 THR Chi-restraints excluded: chain AG residue 508 MET Chi-restraints excluded: chain AG residue 515 LEU Chi-restraints excluded: chain AH residue 159 VAL Chi-restraints excluded: chain AH residue 166 GLU Chi-restraints excluded: chain AH residue 181 VAL Chi-restraints excluded: chain AH residue 216 THR Chi-restraints excluded: chain AH residue 253 GLN Chi-restraints excluded: chain AH residue 277 MET Chi-restraints excluded: chain AH residue 315 ASP Chi-restraints excluded: chain CG residue 530 LEU Chi-restraints excluded: chain CG residue 552 GLU Chi-restraints excluded: chain DA residue 553 MET Chi-restraints excluded: chain DA residue 563 GLN Chi-restraints excluded: chain DA residue 572 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 9 optimal weight: 0.9980 chunk 110 optimal weight: 0.0370 chunk 91 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 67 optimal weight: 0.3980 chunk 114 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 117 optimal weight: 1.9990 chunk 108 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- 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 = 0.4373 r_free = 0.4373 target = 0.172490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.146240 restraints weight = 23663.845| |-----------------------------------------------------------------------------| r_work (start): 0.4089 rms_B_bonded: 3.36 r_work: 0.3828 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14850 Z= 0.129 Angle : 0.607 13.003 19856 Z= 0.294 Chirality : 0.039 0.186 2017 Planarity : 0.004 0.043 2714 Dihedral : 3.520 16.364 1974 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.71 % Allowed : 18.40 % Favored : 78.89 % 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: 2.94 (0.20), residues: 1731 helix: 3.16 (0.15), residues: 1052 sheet: -1.26 (0.60), residues: 81 loop : 0.19 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGDA 569 TYR 0.018 0.001 TYRAA 486 PHE 0.008 0.001 PHEAB 247 TRP 0.014 0.002 TRPAA 490 HIS 0.007 0.001 HISAH 248 Details of bonding type rmsd covalent geometry : bond 0.00291 (14850) covalent geometry : angle 0.60746 (19856) hydrogen bonds : bond 0.04322 ( 1002) hydrogen bonds : angle 3.55985 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 273 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 428 SER cc_start: 0.7761 (t) cc_final: 0.7481 (p) REVERT: BA 486 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7102 (t80) REVERT: BB 328 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8096 (pp20) REVERT: BG 450 ASP cc_start: 0.6663 (t0) cc_final: 0.6258 (m-30) REVERT: BG 469 GLU cc_start: 0.8303 (tp30) cc_final: 0.8076 (tp30) REVERT: BG 573 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7717 (tp30) REVERT: BG 583 GLU cc_start: 0.8775 (tp30) cc_final: 0.8512 (tp30) REVERT: BH 251 ARG cc_start: 0.7753 (tpm170) cc_final: 0.7425 (tpm170) REVERT: BH 324 ARG cc_start: 0.7659 (tmm160) cc_final: 0.6944 (ttp80) REVERT: AA 536 MET cc_start: 0.7837 (tpp) cc_final: 0.7535 (tpp) REVERT: AB 256 ARG cc_start: 0.6854 (ppt170) cc_final: 0.6559 (ppt170) REVERT: AB 294 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7243 (mm-30) REVERT: AB 324 ARG cc_start: 0.6988 (tmm160) cc_final: 0.6549 (ttt180) REVERT: AG 432 PHE cc_start: 0.7549 (OUTLIER) cc_final: 0.6528 (t80) REVERT: AH 149 SER cc_start: 0.8241 (p) cc_final: 0.7852 (m) REVERT: AH 227 MET cc_start: 0.8325 (tmm) cc_final: 0.7125 (tmm) REVERT: AH 253 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.6346 (pp30) REVERT: AH 328 GLU cc_start: 0.8032 (pt0) cc_final: 0.7692 (pt0) REVERT: CG 588 GLN cc_start: 0.8264 (tm-30) cc_final: 0.7823 (tm-30) REVERT: DA 536 MET cc_start: 0.6182 (mmp) cc_final: 0.5968 (mmp) REVERT: DA 553 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7784 (mmp) REVERT: DA 560 GLN cc_start: 0.8365 (tm-30) cc_final: 0.8047 (tm-30) REVERT: DA 584 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8032 (tm-30) outliers start: 43 outliers final: 29 residues processed: 299 average time/residue: 0.1284 time to fit residues: 55.7214 Evaluate side-chains 287 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 381 GLU Chi-restraints excluded: chain BA residue 393 ILE Chi-restraints excluded: chain BA residue 411 ILE Chi-restraints excluded: chain BA residue 412 VAL Chi-restraints excluded: chain BA residue 425 GLU Chi-restraints excluded: chain BA residue 486 TYR Chi-restraints excluded: chain BA residue 517 SER Chi-restraints excluded: chain BB residue 149 SER Chi-restraints excluded: chain BB residue 178 VAL Chi-restraints excluded: chain BB residue 217 THR Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 380 ASN Chi-restraints excluded: chain BG residue 411 ILE Chi-restraints excluded: chain BG residue 443 VAL Chi-restraints excluded: chain BG residue 476 PHE Chi-restraints excluded: chain BG residue 563 GLN Chi-restraints excluded: chain BG residue 575 MET Chi-restraints excluded: chain BG residue 576 ILE Chi-restraints excluded: chain AA residue 429 GLU Chi-restraints excluded: chain AB residue 294 GLU Chi-restraints excluded: chain AG residue 380 ASN Chi-restraints excluded: chain AG residue 398 VAL Chi-restraints excluded: chain AG residue 411 ILE Chi-restraints excluded: chain AG residue 432 PHE Chi-restraints excluded: chain AG residue 508 MET Chi-restraints excluded: chain AH residue 159 VAL Chi-restraints excluded: chain AH residue 181 VAL Chi-restraints excluded: chain AH residue 216 THR Chi-restraints excluded: chain AH residue 244 ASN Chi-restraints excluded: chain AH residue 253 GLN Chi-restraints excluded: chain AH residue 277 MET Chi-restraints excluded: chain AH residue 315 ASP Chi-restraints excluded: chain DA residue 553 MET Chi-restraints excluded: chain DA residue 572 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 146 optimal weight: 0.2980 chunk 121 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 526 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.170749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.144074 restraints weight = 23601.306| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 3.48 r_work: 0.3810 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14850 Z= 0.158 Angle : 0.639 11.733 19856 Z= 0.313 Chirality : 0.040 0.181 2017 Planarity : 0.004 0.043 2714 Dihedral : 3.551 14.374 1974 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.78 % Allowed : 18.27 % Favored : 77.95 % 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: 2.87 (0.20), residues: 1731 helix: 3.12 (0.15), residues: 1051 sheet: -1.37 (0.60), residues: 85 loop : 0.17 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGDA 569 TYR 0.017 0.001 TYRBA 466 PHE 0.008 0.001 PHEAB 168 TRP 0.011 0.002 TRPAA 490 HIS 0.003 0.001 HISAB 305 Details of bonding type rmsd covalent geometry : bond 0.00366 (14850) covalent geometry : angle 0.63912 (19856) hydrogen bonds : bond 0.04466 ( 1002) hydrogen bonds : angle 3.59792 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 261 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 428 SER cc_start: 0.7774 (t) cc_final: 0.7488 (p) REVERT: BA 486 TYR cc_start: 0.7536 (OUTLIER) cc_final: 0.7027 (t80) REVERT: BA 554 GLN cc_start: 0.7787 (pp30) cc_final: 0.7296 (pm20) REVERT: BB 328 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8177 (tm-30) REVERT: BG 450 ASP cc_start: 0.6749 (t0) cc_final: 0.6299 (m-30) REVERT: BG 573 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7790 (tm-30) REVERT: BG 583 GLU cc_start: 0.8782 (tp30) cc_final: 0.8532 (tp30) REVERT: BH 251 ARG cc_start: 0.7898 (tpm170) cc_final: 0.7552 (tpm170) REVERT: BH 321 GLU cc_start: 0.8098 (tp30) cc_final: 0.7468 (tp30) REVERT: BH 324 ARG cc_start: 0.7707 (tmm160) cc_final: 0.6978 (ttp80) REVERT: AA 536 MET cc_start: 0.7862 (tpp) cc_final: 0.7546 (tpp) REVERT: AB 294 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7503 (mm-30) REVERT: AB 324 ARG cc_start: 0.7050 (tmm160) cc_final: 0.6543 (ttt180) REVERT: AG 432 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.6481 (t80) REVERT: AG 525 GLU cc_start: 0.7163 (pp20) cc_final: 0.6535 (tm-30) REVERT: AH 149 SER cc_start: 0.8255 (p) cc_final: 0.7844 (m) REVERT: AH 227 MET cc_start: 0.8365 (tmm) cc_final: 0.7194 (tmm) REVERT: AH 253 GLN cc_start: 0.6759 (OUTLIER) cc_final: 0.6474 (pp30) REVERT: CG 552 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: DA 553 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7815 (mmp) REVERT: DA 560 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8089 (tm-30) REVERT: DA 584 GLN cc_start: 0.8501 (tm-30) cc_final: 0.8156 (tm-30) outliers start: 60 outliers final: 39 residues processed: 299 average time/residue: 0.1215 time to fit residues: 53.3275 Evaluate side-chains 293 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 248 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 381 GLU Chi-restraints excluded: chain BA residue 400 VAL Chi-restraints excluded: chain BA residue 411 ILE Chi-restraints excluded: chain BA residue 412 VAL Chi-restraints excluded: chain BA residue 425 GLU Chi-restraints excluded: chain BA residue 429 GLU Chi-restraints excluded: chain BA residue 486 TYR Chi-restraints excluded: chain BA residue 517 SER Chi-restraints excluded: chain BB residue 149 SER Chi-restraints excluded: chain BB residue 161 ASN Chi-restraints excluded: chain BB residue 178 VAL Chi-restraints excluded: chain BB residue 217 THR Chi-restraints excluded: chain BB residue 241 VAL Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 380 ASN Chi-restraints excluded: chain BG residue 411 ILE Chi-restraints excluded: chain BG residue 435 THR Chi-restraints excluded: chain BG residue 443 VAL Chi-restraints excluded: chain BG residue 476 PHE Chi-restraints excluded: chain BG residue 563 GLN Chi-restraints excluded: chain BG residue 576 ILE Chi-restraints excluded: chain BH residue 216 THR Chi-restraints excluded: chain AA residue 375 SER Chi-restraints excluded: chain AA residue 429 GLU Chi-restraints excluded: chain AA residue 476 PHE Chi-restraints excluded: chain AA residue 576 ILE Chi-restraints excluded: chain AB residue 294 GLU Chi-restraints excluded: chain AG residue 380 ASN Chi-restraints excluded: chain AG residue 398 VAL Chi-restraints excluded: chain AG residue 432 PHE Chi-restraints excluded: chain AG residue 508 MET Chi-restraints excluded: chain AG residue 515 LEU Chi-restraints excluded: chain AH residue 152 VAL Chi-restraints excluded: chain AH residue 159 VAL Chi-restraints excluded: chain AH residue 166 GLU Chi-restraints excluded: chain AH residue 181 VAL Chi-restraints excluded: chain AH residue 216 THR Chi-restraints excluded: chain AH residue 244 ASN Chi-restraints excluded: chain AH residue 253 GLN Chi-restraints excluded: chain AH residue 277 MET Chi-restraints excluded: chain AH residue 315 ASP Chi-restraints excluded: chain CG residue 530 LEU Chi-restraints excluded: chain CG residue 552 GLU Chi-restraints excluded: chain DA residue 553 MET Chi-restraints excluded: chain DA residue 572 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 112 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 60 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 380 ASN ** 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 = 0.4339 r_free = 0.4339 target = 0.169381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.142843 restraints weight = 23871.455| |-----------------------------------------------------------------------------| r_work (start): 0.4050 rms_B_bonded: 3.63 r_work: 0.3793 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14850 Z= 0.167 Angle : 0.652 11.306 19856 Z= 0.320 Chirality : 0.041 0.189 2017 Planarity : 0.004 0.043 2714 Dihedral : 3.623 15.826 1974 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.28 % Allowed : 18.65 % Favored : 78.07 % 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: 2.80 (0.20), residues: 1731 helix: 3.05 (0.15), residues: 1067 sheet: -1.44 (0.59), residues: 85 loop : 0.08 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGDA 569 TYR 0.017 0.001 TYRBA 466 PHE 0.008 0.001 PHEBA 414 TRP 0.012 0.002 TRPAA 490 HIS 0.005 0.001 HISAH 248 Details of bonding type rmsd covalent geometry : bond 0.00391 (14850) covalent geometry : angle 0.65198 (19856) hydrogen bonds : bond 0.04490 ( 1002) hydrogen bonds : angle 3.61914 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 428 SER cc_start: 0.7805 (t) cc_final: 0.7249 (p) REVERT: BA 429 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6498 (pm20) REVERT: BA 486 TYR cc_start: 0.7575 (OUTLIER) cc_final: 0.7063 (t80) REVERT: BA 554 GLN cc_start: 0.7709 (pp30) cc_final: 0.7121 (pt0) REVERT: BB 328 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8188 (tm-30) REVERT: BG 450 ASP cc_start: 0.6671 (t0) cc_final: 0.6355 (m-30) REVERT: BG 476 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8154 (t80) REVERT: BG 583 GLU cc_start: 0.8792 (tp30) cc_final: 0.8557 (tp30) REVERT: BH 321 GLU cc_start: 0.8111 (tp30) cc_final: 0.7469 (tp30) REVERT: BH 324 ARG cc_start: 0.7711 (tmm160) cc_final: 0.6948 (ttp80) REVERT: AA 536 MET cc_start: 0.7908 (tpp) cc_final: 0.7580 (tpp) REVERT: AB 294 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7539 (mm-30) REVERT: AB 324 ARG cc_start: 0.7119 (tmm160) cc_final: 0.6548 (ttt180) REVERT: AG 432 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6682 (t80) REVERT: AH 149 SER cc_start: 0.8260 (p) cc_final: 0.7839 (m) REVERT: AH 227 MET cc_start: 0.8358 (tmm) cc_final: 0.7228 (tmm) REVERT: AH 253 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6217 (pm20) REVERT: AH 328 GLU cc_start: 0.7980 (pt0) cc_final: 0.7696 (pt0) REVERT: CG 552 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: CG 555 LYS cc_start: 0.8763 (ttpp) cc_final: 0.8539 (ttpp) REVERT: CG 588 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7810 (tm-30) REVERT: DA 536 MET cc_start: 0.6235 (mmp) cc_final: 0.6019 (mmt) REVERT: DA 553 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.7857 (mmp) REVERT: DA 560 GLN cc_start: 0.8442 (tm-30) cc_final: 0.8139 (tm-30) REVERT: DA 584 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8080 (tm-30) outliers start: 52 outliers final: 41 residues processed: 289 average time/residue: 0.1237 time to fit residues: 52.8102 Evaluate side-chains 301 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 381 GLU Chi-restraints excluded: chain BA residue 400 VAL Chi-restraints excluded: chain BA residue 411 ILE Chi-restraints excluded: chain BA residue 412 VAL Chi-restraints excluded: chain BA residue 425 GLU Chi-restraints excluded: chain BA residue 429 GLU Chi-restraints excluded: chain BA residue 451 ASP Chi-restraints excluded: chain BA residue 486 TYR Chi-restraints excluded: chain BA residue 517 SER Chi-restraints excluded: chain BB residue 149 SER Chi-restraints excluded: chain BB residue 161 ASN Chi-restraints excluded: chain BB residue 178 VAL Chi-restraints excluded: chain BB residue 217 THR Chi-restraints excluded: chain BB residue 241 VAL Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 380 ASN Chi-restraints excluded: chain BG residue 411 ILE Chi-restraints excluded: chain BG residue 435 THR Chi-restraints excluded: chain BG residue 443 VAL Chi-restraints excluded: chain BG residue 476 PHE Chi-restraints excluded: chain BG residue 486 TYR Chi-restraints excluded: chain BG residue 563 GLN Chi-restraints excluded: chain BH residue 216 THR Chi-restraints excluded: chain BH residue 298 MET Chi-restraints excluded: chain AA residue 378 VAL Chi-restraints excluded: chain AA residue 429 GLU Chi-restraints excluded: chain AA residue 476 PHE Chi-restraints excluded: chain AA residue 576 ILE Chi-restraints excluded: chain AB residue 294 GLU Chi-restraints excluded: chain AB residue 296 LEU Chi-restraints excluded: chain AG residue 380 ASN Chi-restraints excluded: chain AG residue 398 VAL Chi-restraints excluded: chain AG residue 411 ILE Chi-restraints excluded: chain AG residue 432 PHE Chi-restraints excluded: chain AG residue 508 MET Chi-restraints excluded: chain AG residue 515 LEU Chi-restraints excluded: chain AH residue 152 VAL Chi-restraints excluded: chain AH residue 159 VAL Chi-restraints excluded: chain AH residue 166 GLU Chi-restraints excluded: chain AH residue 181 VAL Chi-restraints excluded: chain AH residue 216 THR Chi-restraints excluded: chain AH residue 253 GLN Chi-restraints excluded: chain AH residue 277 MET Chi-restraints excluded: chain AH residue 309 VAL Chi-restraints excluded: chain AH residue 315 ASP Chi-restraints excluded: chain CG residue 530 LEU Chi-restraints excluded: chain CG residue 552 GLU Chi-restraints excluded: chain DA residue 553 MET Chi-restraints excluded: chain DA residue 572 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 30 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 150 optimal weight: 0.8980 chunk 104 optimal weight: 0.3980 chunk 153 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 526 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.170019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.143489 restraints weight = 23843.870| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.61 r_work: 0.3799 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14850 Z= 0.154 Angle : 0.654 11.733 19856 Z= 0.319 Chirality : 0.040 0.190 2017 Planarity : 0.004 0.042 2714 Dihedral : 3.579 17.148 1974 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.47 % Allowed : 18.59 % Favored : 77.95 % 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: 2.86 (0.20), residues: 1731 helix: 3.09 (0.15), residues: 1067 sheet: -1.11 (0.56), residues: 96 loop : 0.08 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARGAG 537 TYR 0.015 0.001 TYRAA 486 PHE 0.008 0.001 PHEBA 414 TRP 0.012 0.002 TRPAA 490 HIS 0.006 0.001 HISAH 248 Details of bonding type rmsd covalent geometry : bond 0.00360 (14850) covalent geometry : angle 0.65385 (19856) hydrogen bonds : bond 0.04391 ( 1002) hydrogen bonds : angle 3.57964 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 261 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 428 SER cc_start: 0.7791 (t) cc_final: 0.7249 (p) REVERT: BA 429 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6538 (pm20) REVERT: BA 486 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.6951 (t80) REVERT: BA 554 GLN cc_start: 0.7649 (pp30) cc_final: 0.7243 (pt0) REVERT: BB 328 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8159 (tm-30) REVERT: BG 450 ASP cc_start: 0.6628 (t0) cc_final: 0.6366 (m-30) REVERT: BG 476 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8174 (t80) REVERT: BG 583 GLU cc_start: 0.8773 (tp30) cc_final: 0.8539 (tp30) REVERT: BH 321 GLU cc_start: 0.8115 (tp30) cc_final: 0.7473 (tp30) REVERT: BH 324 ARG cc_start: 0.7727 (tmm160) cc_final: 0.7038 (ttp80) REVERT: AA 536 MET cc_start: 0.7895 (tpp) cc_final: 0.7563 (tpp) REVERT: AB 294 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7505 (mm-30) REVERT: AB 324 ARG cc_start: 0.7060 (tmm160) cc_final: 0.6489 (ttt180) REVERT: AG 432 PHE cc_start: 0.7703 (OUTLIER) cc_final: 0.6736 (t80) REVERT: AG 468 LYS cc_start: 0.8864 (ptmm) cc_final: 0.8658 (pptt) REVERT: AG 525 GLU cc_start: 0.7006 (pp20) cc_final: 0.6434 (tm-30) REVERT: AH 149 SER cc_start: 0.8257 (p) cc_final: 0.7834 (m) REVERT: AH 227 MET cc_start: 0.8349 (tmm) cc_final: 0.7285 (tmm) REVERT: AH 253 GLN cc_start: 0.6723 (OUTLIER) cc_final: 0.6290 (pm20) REVERT: AH 269 MET cc_start: 0.7895 (mmt) cc_final: 0.7688 (mmt) REVERT: AH 328 GLU cc_start: 0.8019 (pt0) cc_final: 0.7706 (pt0) REVERT: CG 552 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: CG 555 LYS cc_start: 0.8742 (ttpp) cc_final: 0.8506 (ttpp) REVERT: CG 588 GLN cc_start: 0.8221 (tm-30) cc_final: 0.7789 (tm-30) REVERT: DA 553 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7828 (mmp) REVERT: DA 560 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8152 (tm-30) outliers start: 55 outliers final: 40 residues processed: 294 average time/residue: 0.1217 time to fit residues: 52.4548 Evaluate side-chains 305 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 257 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 381 GLU Chi-restraints excluded: chain BA residue 400 VAL Chi-restraints excluded: chain BA residue 411 ILE Chi-restraints excluded: chain BA residue 412 VAL Chi-restraints excluded: chain BA residue 425 GLU Chi-restraints excluded: chain BA residue 429 GLU Chi-restraints excluded: chain BA residue 486 TYR Chi-restraints excluded: chain BA residue 517 SER Chi-restraints excluded: chain BB residue 149 SER Chi-restraints excluded: chain BB residue 161 ASN Chi-restraints excluded: chain BB residue 178 VAL Chi-restraints excluded: chain BB residue 217 THR Chi-restraints excluded: chain BB residue 241 VAL Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 380 ASN Chi-restraints excluded: chain BG residue 411 ILE Chi-restraints excluded: chain BG residue 443 VAL Chi-restraints excluded: chain BG residue 476 PHE Chi-restraints excluded: chain BG residue 486 TYR Chi-restraints excluded: chain BG residue 563 GLN Chi-restraints excluded: chain BH residue 216 THR Chi-restraints excluded: chain AA residue 375 SER Chi-restraints excluded: chain AA residue 429 GLU Chi-restraints excluded: chain AA residue 476 PHE Chi-restraints excluded: chain AA residue 576 ILE Chi-restraints excluded: chain AB residue 294 GLU Chi-restraints excluded: chain AB residue 296 LEU Chi-restraints excluded: chain AG residue 380 ASN Chi-restraints excluded: chain AG residue 398 VAL Chi-restraints excluded: chain AG residue 411 ILE Chi-restraints excluded: chain AG residue 432 PHE Chi-restraints excluded: chain AG residue 508 MET Chi-restraints excluded: chain AG residue 515 LEU Chi-restraints excluded: chain AH residue 152 VAL Chi-restraints excluded: chain AH residue 159 VAL Chi-restraints excluded: chain AH residue 181 VAL Chi-restraints excluded: chain AH residue 216 THR Chi-restraints excluded: chain AH residue 253 GLN Chi-restraints excluded: chain AH residue 277 MET Chi-restraints excluded: chain AH residue 309 VAL Chi-restraints excluded: chain AH residue 315 ASP Chi-restraints excluded: chain CG residue 530 LEU Chi-restraints excluded: chain CG residue 535 LEU Chi-restraints excluded: chain CG residue 552 GLU Chi-restraints excluded: chain DA residue 526 HIS Chi-restraints excluded: chain DA residue 553 MET Chi-restraints excluded: chain DA residue 572 GLU Chi-restraints excluded: chain DA residue 580 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 168 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 0.0030 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** BG 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** DA 526 HIS DA 563 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.170835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.144524 restraints weight = 23884.088| |-----------------------------------------------------------------------------| r_work (start): 0.4067 rms_B_bonded: 3.36 r_work: 0.3815 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14850 Z= 0.148 Angle : 0.663 11.675 19856 Z= 0.322 Chirality : 0.040 0.188 2017 Planarity : 0.004 0.045 2714 Dihedral : 3.556 18.190 1974 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.15 % Allowed : 19.16 % Favored : 77.69 % 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: 2.88 (0.21), residues: 1731 helix: 3.10 (0.15), residues: 1067 sheet: -1.23 (0.54), residues: 100 loop : 0.15 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGDA 569 TYR 0.014 0.001 TYRAA 486 PHE 0.009 0.001 PHEAB 195 TRP 0.012 0.002 TRPAA 490 HIS 0.013 0.001 HISDA 526 Details of bonding type rmsd covalent geometry : bond 0.00345 (14850) covalent geometry : angle 0.66350 (19856) hydrogen bonds : bond 0.04326 ( 1002) hydrogen bonds : angle 3.55416 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3462 Ramachandran restraints generated. 1731 Oldfield, 0 Emsley, 1731 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: BA 428 SER cc_start: 0.7743 (t) cc_final: 0.7198 (p) REVERT: BA 429 GLU cc_start: 0.6970 (OUTLIER) cc_final: 0.6550 (pm20) REVERT: BA 486 TYR cc_start: 0.7632 (OUTLIER) cc_final: 0.6949 (t80) REVERT: BA 554 GLN cc_start: 0.7504 (pp30) cc_final: 0.7101 (pt0) REVERT: BB 328 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8162 (tm-30) REVERT: BG 450 ASP cc_start: 0.6604 (t0) cc_final: 0.6381 (m-30) REVERT: BG 476 PHE cc_start: 0.8800 (OUTLIER) cc_final: 0.8190 (t80) REVERT: BG 583 GLU cc_start: 0.8818 (tp30) cc_final: 0.8581 (tp30) REVERT: BH 321 GLU cc_start: 0.8105 (tp30) cc_final: 0.7459 (tp30) REVERT: BH 324 ARG cc_start: 0.7767 (tmm160) cc_final: 0.7081 (ttp80) REVERT: AA 536 MET cc_start: 0.7846 (tpp) cc_final: 0.7520 (tpp) REVERT: AB 298 MET cc_start: 0.8110 (mmm) cc_final: 0.7538 (mmt) REVERT: AB 324 ARG cc_start: 0.7132 (tmm160) cc_final: 0.6535 (ttt180) REVERT: AG 432 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.6724 (t80) REVERT: AG 525 GLU cc_start: 0.7030 (pp20) cc_final: 0.6482 (tm-30) REVERT: AH 149 SER cc_start: 0.8196 (p) cc_final: 0.7792 (m) REVERT: AH 227 MET cc_start: 0.8395 (tmm) cc_final: 0.7288 (tmm) REVERT: AH 253 GLN cc_start: 0.6673 (OUTLIER) cc_final: 0.6383 (pp30) REVERT: CG 552 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: CG 555 LYS cc_start: 0.8733 (ttpp) cc_final: 0.8501 (ttpp) REVERT: CG 588 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7785 (tm-30) REVERT: DA 553 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7801 (mmp) REVERT: DA 560 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8112 (tm-30) outliers start: 50 outliers final: 41 residues processed: 292 average time/residue: 0.1238 time to fit residues: 52.8209 Evaluate side-chains 304 residues out of total 1587 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 256 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain BA residue 381 GLU Chi-restraints excluded: chain BA residue 400 VAL Chi-restraints excluded: chain BA residue 411 ILE Chi-restraints excluded: chain BA residue 412 VAL Chi-restraints excluded: chain BA residue 425 GLU Chi-restraints excluded: chain BA residue 429 GLU Chi-restraints excluded: chain BA residue 486 TYR Chi-restraints excluded: chain BA residue 504 VAL Chi-restraints excluded: chain BA residue 517 SER Chi-restraints excluded: chain BB residue 149 SER Chi-restraints excluded: chain BB residue 178 VAL Chi-restraints excluded: chain BB residue 217 THR Chi-restraints excluded: chain BG residue 369 LEU Chi-restraints excluded: chain BG residue 380 ASN Chi-restraints excluded: chain BG residue 411 ILE Chi-restraints excluded: chain BG residue 443 VAL Chi-restraints excluded: chain BG residue 476 PHE Chi-restraints excluded: chain BG residue 486 TYR Chi-restraints excluded: chain BG residue 563 GLN Chi-restraints excluded: chain BH residue 216 THR Chi-restraints excluded: chain AA residue 375 SER Chi-restraints excluded: chain AA residue 378 VAL Chi-restraints excluded: chain AA residue 429 GLU Chi-restraints excluded: chain AA residue 476 PHE Chi-restraints excluded: chain AA residue 576 ILE Chi-restraints excluded: chain AB residue 296 LEU Chi-restraints excluded: chain AG residue 380 ASN Chi-restraints excluded: chain AG residue 398 VAL Chi-restraints excluded: chain AG residue 411 ILE Chi-restraints excluded: chain AG residue 432 PHE Chi-restraints excluded: chain AG residue 472 THR Chi-restraints excluded: chain AG residue 508 MET Chi-restraints excluded: chain AG residue 515 LEU Chi-restraints excluded: chain AH residue 152 VAL Chi-restraints excluded: chain AH residue 159 VAL Chi-restraints excluded: chain AH residue 181 VAL Chi-restraints excluded: chain AH residue 193 VAL Chi-restraints excluded: chain AH residue 216 THR Chi-restraints excluded: chain AH residue 253 GLN Chi-restraints excluded: chain AH residue 277 MET Chi-restraints excluded: chain AH residue 309 VAL Chi-restraints excluded: chain AH residue 315 ASP Chi-restraints excluded: chain CG residue 530 LEU Chi-restraints excluded: chain CG residue 535 LEU Chi-restraints excluded: chain CG residue 552 GLU Chi-restraints excluded: chain DA residue 553 MET Chi-restraints excluded: chain DA residue 572 GLU Chi-restraints excluded: chain DA residue 580 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 18 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 128 optimal weight: 0.0570 chunk 168 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 156 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: BG 380 ASN DA 526 HIS DA 533 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.170038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.143563 restraints weight = 23865.942| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.26 r_work: 0.3815 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14850 Z= 0.157 Angle : 0.679 11.673 19856 Z= 0.331 Chirality : 0.040 0.186 2017 Planarity : 0.004 0.046 2714 Dihedral : 3.562 16.351 1974 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.40 % Allowed : 18.84 % Favored : 77.76 % 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: 2.82 (0.21), residues: 1731 helix: 3.05 (0.15), residues: 1067 sheet: -1.25 (0.54), residues: 100 loop : 0.13 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARGDA 569 TYR 0.015 0.001 TYRAH 267 PHE 0.009 0.001 PHEAB 195 TRP 0.012 0.002 TRPAA 490 HIS 0.007 0.001 HISAH 248 Details of bonding type rmsd covalent geometry : bond 0.00368 (14850) covalent geometry : angle 0.67930 (19856) hydrogen bonds : bond 0.04350 ( 1002) hydrogen bonds : angle 3.57352 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3632.19 seconds wall clock time: 63 minutes 5.94 seconds (3785.94 seconds total)