Starting phenix.real_space_refine on Wed Mar 4 04:21:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6qwl_4660/03_2026/6qwl_4660.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qwl_4660/03_2026/6qwl_4660.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6qwl_4660/03_2026/6qwl_4660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qwl_4660/03_2026/6qwl_4660.map" model { file = "/net/cci-nas-00/data/ceres_data/6qwl_4660/03_2026/6qwl_4660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qwl_4660/03_2026/6qwl_4660.cif" } resolution = 4.1 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: 5 Type Number sf(0) Gaussians P 26 5.49 5 S 74 5.16 5 C 6498 2.51 5 N 1787 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10408 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 4084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 511, 4084 Classifications: {'peptide': 511} Link IDs: {'PTRANS': 21, 'TRANS': 489} Chain: "K" Number of atoms: 4206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4206 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 514} Chain breaks: 6 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Q" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1565 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "T" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 249 Classifications: {'RNA': 12} Modifications used: {'rna2p_pyr': 4, 'rna3p_pur': 3, 'rna3p_pyr': 5} Link IDs: {'rna2p': 4, 'rna3p': 7} Chain: "W" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 304 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 4} Link IDs: {'rna2p': 2, 'rna3p': 11} Time building chain proxies: 2.40, per 1000 atoms: 0.23 Number of scatterers: 10408 At special positions: 0 Unit cell: (99.36, 104.76, 113.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 74 16.00 P 26 15.00 O 2023 8.00 N 1787 7.00 C 6498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 628.3 milliseconds 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2312 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 13 sheets defined 50.2% alpha, 7.8% beta 6 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 222 through 232 Processing helix chain 'E' and resid 239 through 246 Processing helix chain 'E' and resid 258 through 262 removed outlier: 3.846A pdb=" N ASP E 261 " --> pdb=" O LYS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 270 removed outlier: 3.584A pdb=" N ILE E 269 " --> pdb=" O GLY E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 313 removed outlier: 4.179A pdb=" N GLU E 311 " --> pdb=" O LYS E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 317 Processing helix chain 'E' and resid 332 through 345 removed outlier: 3.900A pdb=" N LEU E 336 " --> pdb=" O ASN E 332 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LYS E 338 " --> pdb=" O ASN E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 removed outlier: 3.627A pdb=" N LYS E 363 " --> pdb=" O THR E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 380 removed outlier: 3.809A pdb=" N VAL E 379 " --> pdb=" O MET E 376 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 410 Processing helix chain 'E' and resid 429 through 447 removed outlier: 3.511A pdb=" N ASN E 447 " --> pdb=" O VAL E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 472 Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.513A pdb=" N TRP E 533 " --> pdb=" O SER E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 572 removed outlier: 3.509A pdb=" N GLU E 572 " --> pdb=" O LYS E 568 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 596 removed outlier: 3.636A pdb=" N GLN E 579 " --> pdb=" O ARG E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 605 removed outlier: 3.702A pdb=" N LYS E 605 " --> pdb=" O LYS E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 628 through 646 removed outlier: 3.581A pdb=" N TYR E 644 " --> pdb=" O CYS E 640 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE E 646 " --> pdb=" O MET E 642 " (cutoff:3.500A) Processing helix chain 'E' and resid 648 through 670 removed outlier: 3.734A pdb=" N GLU E 652 " --> pdb=" O ASN E 648 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG E 660 " --> pdb=" O ALA E 656 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU E 661 " --> pdb=" O GLU E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 678 through 688 Processing helix chain 'E' and resid 693 through 714 removed outlier: 3.513A pdb=" N ILE E 697 " --> pdb=" O ASN E 693 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLN E 698 " --> pdb=" O PRO E 694 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 11 removed outlier: 3.839A pdb=" N LEU K 8 " --> pdb=" O PRO K 5 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 17 Processing helix chain 'K' and resid 37 through 48 Processing helix chain 'K' and resid 49 through 51 No H-bonds generated for 'chain 'K' and resid 49 through 51' Processing helix chain 'K' and resid 85 through 98 Processing helix chain 'K' and resid 101 through 116 removed outlier: 3.743A pdb=" N MET K 115 " --> pdb=" O MET K 111 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N VAL K 116 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 123 removed outlier: 3.973A pdb=" N LEU K 122 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR K 123 " --> pdb=" O ASP K 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 119 through 123' Processing helix chain 'K' and resid 141 through 151 Processing helix chain 'K' and resid 152 through 154 No H-bonds generated for 'chain 'K' and resid 152 through 154' Processing helix chain 'K' and resid 162 through 172 removed outlier: 3.851A pdb=" N PHE K 166 " --> pdb=" O GLY K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 176 Processing helix chain 'K' and resid 214 through 223 removed outlier: 3.922A pdb=" N ALA K 221 " --> pdb=" O TYR K 217 " (cutoff:3.500A) Processing helix chain 'K' and resid 245 through 264 removed outlier: 4.462A pdb=" N GLY K 250 " --> pdb=" O ILE K 246 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N PHE K 251 " --> pdb=" O GLN K 247 " (cutoff:3.500A) Processing helix chain 'K' and resid 314 through 326 removed outlier: 3.751A pdb=" N PHE K 318 " --> pdb=" O ASN K 314 " (cutoff:3.500A) Processing helix chain 'K' and resid 327 through 329 No H-bonds generated for 'chain 'K' and resid 327 through 329' Processing helix chain 'K' and resid 330 through 338 removed outlier: 3.535A pdb=" N ARG K 334 " --> pdb=" O PRO K 330 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N SER K 338 " --> pdb=" O ARG K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 344 Processing helix chain 'K' and resid 377 through 381 removed outlier: 4.068A pdb=" N TYR K 381 " --> pdb=" O LEU K 378 " (cutoff:3.500A) Processing helix chain 'K' and resid 382 through 393 removed outlier: 3.636A pdb=" N ARG K 386 " --> pdb=" O ASN K 382 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS K 391 " --> pdb=" O ALA K 387 " (cutoff:3.500A) Processing helix chain 'K' and resid 394 through 396 No H-bonds generated for 'chain 'K' and resid 394 through 396' Processing helix chain 'K' and resid 413 through 426 Processing helix chain 'K' and resid 454 through 471 Processing helix chain 'K' and resid 518 through 537 removed outlier: 4.165A pdb=" N ASN K 536 " --> pdb=" O ASN K 532 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLY K 537 " --> pdb=" O MET K 533 " (cutoff:3.500A) Processing helix chain 'K' and resid 539 through 558 removed outlier: 3.680A pdb=" N GLN K 548 " --> pdb=" O GLN K 544 " (cutoff:3.500A) Processing helix chain 'K' and resid 571 through 582 removed outlier: 3.825A pdb=" N ILE K 575 " --> pdb=" O ARG K 571 " (cutoff:3.500A) Processing helix chain 'K' and resid 589 through 593 Processing helix chain 'K' and resid 607 through 612 Processing helix chain 'K' and resid 616 through 624 Processing helix chain 'Q' and resid 64 through 69 removed outlier: 3.941A pdb=" N ARG Q 69 " --> pdb=" O MET Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 105 removed outlier: 4.079A pdb=" N ASN Q 102 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY Q 105 " --> pdb=" O TRP Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 117 removed outlier: 4.133A pdb=" N TYR Q 117 " --> pdb=" O PHE Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 129 Processing helix chain 'Q' and resid 157 through 170 Processing helix chain 'Q' and resid 178 through 193 removed outlier: 5.077A pdb=" N GLU Q 186 " --> pdb=" O TRP Q 182 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N LEU Q 187 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 198 removed outlier: 4.225A pdb=" N GLY Q 197 " --> pdb=" O LYS Q 194 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N THR Q 198 " --> pdb=" O LEU Q 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 194 through 198' Processing helix chain 'Q' and resid 201 through 214 removed outlier: 3.594A pdb=" N VAL Q 214 " --> pdb=" O GLU Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 227 through 233 Processing helix chain 'Q' and resid 233 through 238 Processing sheet with id=AA1, first strand: chain 'E' and resid 373 through 374 removed outlier: 6.659A pdb=" N GLN E 373 " --> pdb=" O LYS K 365 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'E' and resid 480 through 486 removed outlier: 4.799A pdb=" N ILE E 481 " --> pdb=" O TYR E 497 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN E 483 " --> pdb=" O MET E 495 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET E 495 " --> pdb=" O ASN E 483 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 499 " --> pdb=" O PHE E 519 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 521 through 522 removed outlier: 3.923A pdb=" N TYR E 554 " --> pdb=" O SER E 522 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR E 537 " --> pdb=" O CYS E 557 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 521 through 522 removed outlier: 3.923A pdb=" N TYR E 554 " --> pdb=" O SER E 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 623 through 627 removed outlier: 3.859A pdb=" N GLY E 618 " --> pdb=" O VAL E 625 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLY E 627 " --> pdb=" O SER E 616 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER E 616 " --> pdb=" O GLY E 627 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN K 2 " --> pdb=" O THR E 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'K' and resid 128 through 129 Processing sheet with id=AA8, first strand: chain 'K' and resid 178 through 181 Processing sheet with id=AA9, first strand: chain 'K' and resid 435 through 437 removed outlier: 3.721A pdb=" N MET K 300 " --> pdb=" O VAL K 450 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 348 through 350 Processing sheet with id=AB2, first strand: chain 'Q' and resid 73 through 74 Processing sheet with id=AB3, first strand: chain 'Q' and resid 131 through 135 removed outlier: 5.691A pdb=" N ILE Q 245 " --> pdb=" O GLY Q 133 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 143 through 148 removed outlier: 3.845A pdb=" N ARG Q 218 " --> pdb=" O VAL Q 147 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 18 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 1.70 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2799 1.33 - 1.46: 2522 1.46 - 1.58: 5173 1.58 - 1.70: 50 1.70 - 1.83: 124 Bond restraints: 10668 Sorted by residual: bond pdb=" CB TRP E 340 " pdb=" CG TRP E 340 " ideal model delta sigma weight residual 1.498 1.428 0.070 3.10e-02 1.04e+03 5.09e+00 bond pdb=" CA ILE E 479 " pdb=" C ILE E 479 " ideal model delta sigma weight residual 1.525 1.506 0.019 8.80e-03 1.29e+04 4.60e+00 bond pdb=" CG MET E 407 " pdb=" SD MET E 407 " ideal model delta sigma weight residual 1.803 1.751 0.052 2.50e-02 1.60e+03 4.33e+00 bond pdb=" CB ASN E 560 " pdb=" CG ASN E 560 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.09e+00 bond pdb=" C ILE E 479 " pdb=" N PRO E 480 " ideal model delta sigma weight residual 1.333 1.312 0.021 1.17e-02 7.31e+03 3.27e+00 ... (remaining 10663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 13620 1.91 - 3.81: 757 3.81 - 5.72: 114 5.72 - 7.63: 23 7.63 - 9.54: 9 Bond angle restraints: 14523 Sorted by residual: angle pdb=" N ILE E 347 " pdb=" CA ILE E 347 " pdb=" C ILE E 347 " ideal model delta sigma weight residual 112.12 107.85 4.27 8.40e-01 1.42e+00 2.58e+01 angle pdb=" N LYS K 393 " pdb=" CA LYS K 393 " pdb=" C LYS K 393 " ideal model delta sigma weight residual 109.81 119.35 -9.54 2.21e+00 2.05e-01 1.86e+01 angle pdb=" C3' G T 2 " pdb=" O3' G T 2 " pdb=" P C T 3 " ideal model delta sigma weight residual 120.20 126.48 -6.28 1.50e+00 4.44e-01 1.75e+01 angle pdb=" N GLY E 367 " pdb=" CA GLY E 367 " pdb=" C GLY E 367 " ideal model delta sigma weight residual 113.18 122.07 -8.89 2.37e+00 1.78e-01 1.41e+01 angle pdb=" C ASN K 153 " pdb=" N ASP K 154 " pdb=" CA ASP K 154 " ideal model delta sigma weight residual 122.08 127.43 -5.35 1.47e+00 4.63e-01 1.32e+01 ... (remaining 14518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 6302 35.58 - 71.16: 183 71.16 - 106.74: 16 106.74 - 142.32: 1 142.32 - 177.90: 1 Dihedral angle restraints: 6503 sinusoidal: 2917 harmonic: 3586 Sorted by residual: dihedral pdb=" O4' U T 6 " pdb=" C1' U T 6 " pdb=" N1 U T 6 " pdb=" C2 U T 6 " ideal model delta sinusoidal sigma weight residual -128.00 49.90 -177.90 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA GLU K 399 " pdb=" C GLU K 399 " pdb=" N GLY K 400 " pdb=" CA GLY K 400 " ideal model delta harmonic sigma weight residual 180.00 152.97 27.03 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA THR E 366 " pdb=" C THR E 366 " pdb=" N GLY E 367 " pdb=" CA GLY E 367 " ideal model delta harmonic sigma weight residual 180.00 153.47 26.53 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 6500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1098 0.056 - 0.112: 404 0.112 - 0.168: 94 0.168 - 0.224: 27 0.224 - 0.280: 2 Chirality restraints: 1625 Sorted by residual: chirality pdb=" CB VAL K 116 " pdb=" CA VAL K 116 " pdb=" CG1 VAL K 116 " pdb=" CG2 VAL K 116 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CB THR K 401 " pdb=" CA THR K 401 " pdb=" OG1 THR K 401 " pdb=" CG2 THR K 401 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CG LEU Q 79 " pdb=" CB LEU Q 79 " pdb=" CD1 LEU Q 79 " pdb=" CD2 LEU Q 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1622 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE Q 70 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO Q 71 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO Q 71 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO Q 71 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE K 605 " -0.048 5.00e-02 4.00e+02 7.19e-02 8.28e+00 pdb=" N PRO K 606 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO K 606 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO K 606 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER K 405 " 0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO K 406 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO K 406 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO K 406 " 0.040 5.00e-02 4.00e+02 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1704 2.75 - 3.29: 10241 3.29 - 3.83: 18346 3.83 - 4.36: 19733 4.36 - 4.90: 32328 Nonbonded interactions: 82352 Sorted by model distance: nonbonded pdb=" O ASP K 553 " pdb=" OG1 THR K 557 " model vdw 2.214 3.040 nonbonded pdb=" O LEU K 114 " pdb=" OG1 THR K 117 " model vdw 2.244 3.040 nonbonded pdb=" O SER E 215 " pdb=" OG SER E 215 " model vdw 2.251 3.040 nonbonded pdb=" O ALA E 362 " pdb=" OG1 THR E 366 " model vdw 2.257 3.040 nonbonded pdb=" OG SER E 328 " pdb=" OE1 GLU E 329 " model vdw 2.269 3.040 ... (remaining 82347 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.870 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 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 : 0.008 0.077 10668 Z= 0.352 Angle : 1.013 9.537 14523 Z= 0.547 Chirality : 0.062 0.280 1625 Planarity : 0.008 0.075 1767 Dihedral : 17.049 177.903 4191 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.85 % Favored : 89.07 % Rotamer: Outliers : 0.93 % Allowed : 12.05 % Favored : 87.03 % 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: -4.69 (0.18), residues: 1226 helix: -2.72 (0.16), residues: 530 sheet: -3.72 (0.51), residues: 73 loop : -3.44 (0.20), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 316 TYR 0.029 0.003 TYR K 554 PHE 0.035 0.003 PHE E 604 TRP 0.018 0.003 TRP E 364 HIS 0.016 0.002 HIS K 99 Details of bonding type rmsd covalent geometry : bond 0.00772 (10668) covalent geometry : angle 1.01317 (14523) hydrogen bonds : bond 0.15055 ( 419) hydrogen bonds : angle 7.14981 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 171 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.7373 (tpp) cc_final: 0.7093 (tpp) REVERT: E 271 ASN cc_start: 0.8571 (t0) cc_final: 0.8185 (t0) REVERT: E 473 MET cc_start: 0.5167 (ttm) cc_final: 0.4879 (ttt) REVERT: E 477 LYS cc_start: 0.8610 (ptpp) cc_final: 0.8172 (ptpp) REVERT: E 483 ASN cc_start: 0.8372 (t0) cc_final: 0.8081 (t0) REVERT: E 584 MET cc_start: 0.8118 (ttp) cc_final: 0.7561 (tmm) REVERT: E 599 MET cc_start: 0.4519 (mmt) cc_final: 0.3800 (mpp) REVERT: E 659 ARG cc_start: 0.8575 (ttm110) cc_final: 0.8147 (ttm110) REVERT: K 65 MET cc_start: 0.8627 (mtt) cc_final: 0.8235 (mtm) REVERT: K 111 MET cc_start: 0.8449 (mtm) cc_final: 0.7766 (mtp) REVERT: K 114 LEU cc_start: 0.8625 (tp) cc_final: 0.8328 (tp) REVERT: K 163 LEU cc_start: 0.8817 (tt) cc_final: 0.8383 (tp) REVERT: K 174 LEU cc_start: 0.8698 (pt) cc_final: 0.8393 (pt) REVERT: K 217 TYR cc_start: 0.7725 (t80) cc_final: 0.7292 (t80) REVERT: K 300 MET cc_start: 0.7350 (mtm) cc_final: 0.6748 (mtm) REVERT: K 331 ILE cc_start: 0.8242 (mp) cc_final: 0.8036 (tp) REVERT: K 412 MET cc_start: 0.7646 (ptp) cc_final: 0.7430 (ptt) REVERT: K 459 MET cc_start: 0.8121 (mmt) cc_final: 0.7652 (mmt) REVERT: K 538 MET cc_start: 0.7336 (ttm) cc_final: 0.6566 (ttm) REVERT: Q 166 MET cc_start: 0.4454 (mtt) cc_final: 0.3921 (mmt) REVERT: Q 233 MET cc_start: 0.5615 (mmm) cc_final: 0.5024 (mmm) outliers start: 10 outliers final: 2 residues processed: 179 average time/residue: 0.1024 time to fit residues: 25.6858 Evaluate side-chains 116 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 114 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.0270 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 408 ASN E 447 ASN E 643 HIS K 261 ASN ** K 548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 184 HIS Q 235 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.119439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097037 restraints weight = 27422.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.096264 restraints weight = 26182.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097281 restraints weight = 21873.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097682 restraints weight = 17822.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097853 restraints weight = 17372.630| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10668 Z= 0.167 Angle : 0.685 7.954 14523 Z= 0.359 Chirality : 0.045 0.188 1625 Planarity : 0.006 0.066 1767 Dihedral : 14.979 178.600 1738 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.21), residues: 1226 helix: -1.25 (0.20), residues: 546 sheet: -3.46 (0.50), residues: 82 loop : -3.19 (0.22), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 671 TYR 0.018 0.002 TYR K 556 PHE 0.024 0.002 PHE E 604 TRP 0.017 0.002 TRP E 533 HIS 0.006 0.001 HIS E 643 Details of bonding type rmsd covalent geometry : bond 0.00368 (10668) covalent geometry : angle 0.68491 (14523) hydrogen bonds : bond 0.04414 ( 419) hydrogen bonds : angle 5.33735 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.430 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: E 246 MET cc_start: 0.8300 (tpp) cc_final: 0.7972 (tpp) REVERT: E 473 MET cc_start: 0.6671 (ttm) cc_final: 0.5864 (ttp) REVERT: E 584 MET cc_start: 0.7173 (ttp) cc_final: 0.6841 (tmm) REVERT: K 111 MET cc_start: 0.7509 (mtm) cc_final: 0.7209 (mtp) REVERT: K 300 MET cc_start: 0.7124 (mtm) cc_final: 0.6434 (mtm) REVERT: K 392 LEU cc_start: 0.7704 (tp) cc_final: 0.7379 (tt) REVERT: K 410 MET cc_start: 0.6754 (ttm) cc_final: 0.6509 (ttt) REVERT: K 459 MET cc_start: 0.7686 (mmt) cc_final: 0.7192 (mmt) REVERT: Q 166 MET cc_start: 0.4751 (mtt) cc_final: 0.3846 (mmt) REVERT: Q 217 ARG cc_start: 0.7419 (mtt-85) cc_final: 0.6982 (mtp85) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0977 time to fit residues: 21.5417 Evaluate side-chains 121 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 98 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 43 optimal weight: 0.4980 chunk 17 optimal weight: 0.2980 chunk 52 optimal weight: 0.0370 chunk 4 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 overall best weight: 2.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 467 ASN K 429 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.118139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.096323 restraints weight = 27670.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.096386 restraints weight = 24874.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097435 restraints weight = 21497.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097624 restraints weight = 16355.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.097662 restraints weight = 16925.289| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10668 Z= 0.188 Angle : 0.671 8.205 14523 Z= 0.350 Chirality : 0.045 0.174 1625 Planarity : 0.005 0.056 1767 Dihedral : 14.794 178.307 1738 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.09 % Allowed : 4.63 % Favored : 95.27 % 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: -2.92 (0.22), residues: 1226 helix: -0.65 (0.21), residues: 549 sheet: -3.83 (0.47), residues: 85 loop : -2.96 (0.23), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 659 TYR 0.016 0.002 TYR K 556 PHE 0.023 0.002 PHE E 604 TRP 0.015 0.002 TRP E 364 HIS 0.006 0.002 HIS Q 184 Details of bonding type rmsd covalent geometry : bond 0.00420 (10668) covalent geometry : angle 0.67051 (14523) hydrogen bonds : bond 0.04293 ( 419) hydrogen bonds : angle 5.12789 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 145 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.8316 (tpp) cc_final: 0.7961 (tpp) REVERT: E 473 MET cc_start: 0.6543 (ttm) cc_final: 0.6263 (ttt) REVERT: E 599 MET cc_start: 0.4193 (mmt) cc_final: 0.3687 (tpp) REVERT: E 659 ARG cc_start: 0.7862 (ttm110) cc_final: 0.7607 (mtm180) REVERT: K 111 MET cc_start: 0.7432 (mtm) cc_final: 0.7179 (mtp) REVERT: K 392 LEU cc_start: 0.7822 (tp) cc_final: 0.7328 (tt) REVERT: K 459 MET cc_start: 0.7672 (mmt) cc_final: 0.7059 (mmt) REVERT: Q 156 MET cc_start: 0.6506 (pmm) cc_final: 0.5871 (ptp) REVERT: Q 166 MET cc_start: 0.4712 (mtt) cc_final: 0.3730 (mmt) outliers start: 1 outliers final: 0 residues processed: 146 average time/residue: 0.0910 time to fit residues: 19.1550 Evaluate side-chains 116 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 78 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 118 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 GLN E 242 ASN E 666 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.120558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.098365 restraints weight = 27801.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.098448 restraints weight = 23828.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099624 restraints weight = 20701.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.099883 restraints weight = 15605.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100787 restraints weight = 15252.523| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10668 Z= 0.122 Angle : 0.612 8.874 14523 Z= 0.313 Chirality : 0.042 0.164 1625 Planarity : 0.005 0.051 1767 Dihedral : 14.566 177.645 1738 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.09 % Allowed : 4.73 % Favored : 95.18 % 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: -2.34 (0.23), residues: 1226 helix: -0.07 (0.22), residues: 543 sheet: -3.61 (0.55), residues: 72 loop : -2.77 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 327 TYR 0.011 0.001 TYR K 556 PHE 0.022 0.001 PHE E 604 TRP 0.019 0.001 TRP E 533 HIS 0.006 0.001 HIS K 99 Details of bonding type rmsd covalent geometry : bond 0.00268 (10668) covalent geometry : angle 0.61157 (14523) hydrogen bonds : bond 0.03674 ( 419) hydrogen bonds : angle 4.70530 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.8287 (tpp) cc_final: 0.7882 (tpp) REVERT: E 473 MET cc_start: 0.6675 (ttm) cc_final: 0.6375 (ttt) REVERT: E 483 ASN cc_start: 0.8223 (t0) cc_final: 0.7959 (t0) REVERT: E 599 MET cc_start: 0.4011 (mmt) cc_final: 0.3542 (tpp) REVERT: E 659 ARG cc_start: 0.7874 (ttm110) cc_final: 0.7654 (mtp180) REVERT: K 111 MET cc_start: 0.7444 (mtm) cc_final: 0.7188 (mtp) REVERT: K 243 THR cc_start: 0.7847 (p) cc_final: 0.7452 (t) REVERT: K 247 GLN cc_start: 0.8525 (mp10) cc_final: 0.8294 (mm-40) REVERT: K 300 MET cc_start: 0.6997 (mtp) cc_final: 0.6680 (mtp) REVERT: K 392 LEU cc_start: 0.7606 (tp) cc_final: 0.7312 (tt) REVERT: K 459 MET cc_start: 0.7518 (mmt) cc_final: 0.7023 (mmt) REVERT: Q 163 ASN cc_start: 0.7639 (t0) cc_final: 0.7123 (t0) REVERT: Q 166 MET cc_start: 0.4760 (mtt) cc_final: 0.3820 (mmt) REVERT: Q 211 ARG cc_start: 0.6979 (tpt90) cc_final: 0.6639 (tpt90) REVERT: Q 217 ARG cc_start: 0.7001 (mtp85) cc_final: 0.6518 (mtp85) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.0880 time to fit residues: 20.8735 Evaluate side-chains 129 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 61 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 103 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 GLN E 704 ASN K 47 HIS K 663 HIS Q 150 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.117085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094738 restraints weight = 27740.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.094753 restraints weight = 23465.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.095720 restraints weight = 20078.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.095982 restraints weight = 16242.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096180 restraints weight = 14799.269| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10668 Z= 0.240 Angle : 0.732 9.843 14523 Z= 0.380 Chirality : 0.047 0.183 1625 Planarity : 0.005 0.053 1767 Dihedral : 14.664 177.671 1738 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.09 % Allowed : 4.45 % Favored : 95.46 % 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: -2.57 (0.23), residues: 1226 helix: -0.25 (0.22), residues: 548 sheet: -3.80 (0.49), residues: 85 loop : -2.87 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 659 TYR 0.021 0.002 TYR E 229 PHE 0.024 0.002 PHE E 604 TRP 0.015 0.002 TRP E 364 HIS 0.005 0.002 HIS Q 235 Details of bonding type rmsd covalent geometry : bond 0.00537 (10668) covalent geometry : angle 0.73244 (14523) hydrogen bonds : bond 0.04391 ( 419) hydrogen bonds : angle 5.06165 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.407 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: E 246 MET cc_start: 0.8234 (tpp) cc_final: 0.7862 (tpp) REVERT: E 279 TYR cc_start: 0.8021 (t80) cc_final: 0.7415 (t80) REVERT: E 483 ASN cc_start: 0.8397 (t0) cc_final: 0.8126 (t0) REVERT: E 659 ARG cc_start: 0.7963 (ttm110) cc_final: 0.7694 (mtp180) REVERT: K 247 GLN cc_start: 0.8593 (mp10) cc_final: 0.8306 (mm-40) REVERT: K 300 MET cc_start: 0.7160 (mtp) cc_final: 0.6925 (mtp) REVERT: K 459 MET cc_start: 0.7532 (mmt) cc_final: 0.7178 (mmt) REVERT: Q 150 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.6036 (p0) REVERT: Q 156 MET cc_start: 0.6762 (pmm) cc_final: 0.6211 (ptp) REVERT: Q 163 ASN cc_start: 0.7752 (t0) cc_final: 0.7421 (t0) REVERT: Q 166 MET cc_start: 0.4711 (mtt) cc_final: 0.3743 (mmt) outliers start: 1 outliers final: 0 residues processed: 144 average time/residue: 0.0915 time to fit residues: 19.2150 Evaluate side-chains 119 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 7 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 467 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.121086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.098859 restraints weight = 27592.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098598 restraints weight = 22889.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099717 restraints weight = 19885.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.100018 restraints weight = 15865.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.100147 restraints weight = 14836.083| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10668 Z= 0.118 Angle : 0.610 8.169 14523 Z= 0.312 Chirality : 0.042 0.195 1625 Planarity : 0.005 0.055 1767 Dihedral : 14.472 177.094 1738 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % 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: -2.13 (0.23), residues: 1226 helix: 0.23 (0.23), residues: 537 sheet: -3.76 (0.46), residues: 93 loop : -2.66 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 216 TYR 0.013 0.001 TYR E 229 PHE 0.020 0.001 PHE E 604 TRP 0.016 0.001 TRP E 533 HIS 0.003 0.001 HIS E 506 Details of bonding type rmsd covalent geometry : bond 0.00263 (10668) covalent geometry : angle 0.61012 (14523) hydrogen bonds : bond 0.03566 ( 419) hydrogen bonds : angle 4.56573 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.388 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: E 246 MET cc_start: 0.8125 (tpp) cc_final: 0.7785 (tpp) REVERT: E 599 MET cc_start: 0.3888 (mmt) cc_final: 0.3524 (tpp) REVERT: K 572 MET cc_start: 0.8234 (mmm) cc_final: 0.7783 (tpp) REVERT: Q 163 ASN cc_start: 0.8012 (t0) cc_final: 0.7601 (t0) REVERT: Q 166 MET cc_start: 0.4479 (mtt) cc_final: 0.3590 (mmt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0915 time to fit residues: 20.3419 Evaluate side-chains 124 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 0 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 119 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.120438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.098477 restraints weight = 27450.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098278 restraints weight = 24621.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099350 restraints weight = 21320.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.099645 restraints weight = 17029.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.099779 restraints weight = 16222.929| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10668 Z= 0.139 Angle : 0.631 8.858 14523 Z= 0.324 Chirality : 0.043 0.185 1625 Planarity : 0.004 0.054 1767 Dihedral : 14.384 177.007 1738 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % 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: -2.05 (0.23), residues: 1226 helix: 0.21 (0.22), residues: 540 sheet: -3.67 (0.46), residues: 93 loop : -2.55 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 575 TYR 0.019 0.002 TYR E 644 PHE 0.022 0.002 PHE E 604 TRP 0.025 0.002 TRP K 131 HIS 0.003 0.001 HIS K 47 Details of bonding type rmsd covalent geometry : bond 0.00315 (10668) covalent geometry : angle 0.63110 (14523) hydrogen bonds : bond 0.03771 ( 419) hydrogen bonds : angle 4.56709 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.412 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: E 246 MET cc_start: 0.8149 (tpp) cc_final: 0.7809 (tpp) REVERT: E 465 LEU cc_start: 0.8755 (tp) cc_final: 0.8446 (tp) REVERT: E 599 MET cc_start: 0.3883 (mmt) cc_final: 0.3457 (tpp) REVERT: K 336 PHE cc_start: 0.6908 (t80) cc_final: 0.6692 (m-80) REVERT: K 572 MET cc_start: 0.8199 (mmm) cc_final: 0.7809 (tpp) REVERT: Q 156 MET cc_start: 0.6772 (pmm) cc_final: 0.6171 (ptp) REVERT: Q 163 ASN cc_start: 0.7964 (t0) cc_final: 0.7578 (t0) REVERT: Q 166 MET cc_start: 0.4520 (mtt) cc_final: 0.3607 (mmt) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0979 time to fit residues: 21.7608 Evaluate side-chains 127 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 55 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 65 optimal weight: 0.0870 chunk 78 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.0138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.121804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.099647 restraints weight = 27146.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100038 restraints weight = 20805.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101028 restraints weight = 19047.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.101325 restraints weight = 14361.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101452 restraints weight = 14232.529| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10668 Z= 0.118 Angle : 0.614 9.287 14523 Z= 0.312 Chirality : 0.042 0.177 1625 Planarity : 0.004 0.053 1767 Dihedral : 14.295 176.843 1738 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.09 % Allowed : 0.83 % Favored : 99.07 % 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: -1.89 (0.23), residues: 1226 helix: 0.27 (0.22), residues: 544 sheet: -3.36 (0.51), residues: 81 loop : -2.47 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 216 TYR 0.025 0.001 TYR E 361 PHE 0.020 0.001 PHE E 604 TRP 0.026 0.002 TRP K 131 HIS 0.004 0.001 HIS E 506 Details of bonding type rmsd covalent geometry : bond 0.00265 (10668) covalent geometry : angle 0.61357 (14523) hydrogen bonds : bond 0.03466 ( 419) hydrogen bonds : angle 4.46329 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 151 time to evaluate : 0.347 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: E 246 MET cc_start: 0.8114 (tpp) cc_final: 0.7745 (tpp) REVERT: E 599 MET cc_start: 0.3884 (mmt) cc_final: 0.3464 (tpp) REVERT: K 243 THR cc_start: 0.7813 (p) cc_final: 0.7451 (t) REVERT: K 336 PHE cc_start: 0.6840 (t80) cc_final: 0.6627 (m-80) REVERT: K 572 MET cc_start: 0.8096 (mmm) cc_final: 0.7474 (tpp) REVERT: Q 156 MET cc_start: 0.6969 (pmm) cc_final: 0.6433 (ptp) REVERT: Q 163 ASN cc_start: 0.7888 (t0) cc_final: 0.7417 (t0) REVERT: Q 166 MET cc_start: 0.4503 (mtt) cc_final: 0.3591 (mmt) REVERT: Q 208 MET cc_start: 0.3472 (tpt) cc_final: 0.2654 (tpt) outliers start: 1 outliers final: 0 residues processed: 152 average time/residue: 0.0923 time to fit residues: 20.3375 Evaluate side-chains 128 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 128 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 244 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.119671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.097925 restraints weight = 27441.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.097598 restraints weight = 23747.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098649 restraints weight = 21287.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.098976 restraints weight = 16885.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.099113 restraints weight = 16041.333| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10668 Z= 0.166 Angle : 0.666 12.972 14523 Z= 0.339 Chirality : 0.044 0.182 1625 Planarity : 0.005 0.054 1767 Dihedral : 14.317 176.753 1738 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: -1.92 (0.23), residues: 1226 helix: 0.23 (0.22), residues: 550 sheet: -3.44 (0.48), residues: 84 loop : -2.48 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 575 TYR 0.026 0.002 TYR K 482 PHE 0.022 0.002 PHE E 604 TRP 0.028 0.002 TRP K 131 HIS 0.005 0.001 HIS K 604 Details of bonding type rmsd covalent geometry : bond 0.00378 (10668) covalent geometry : angle 0.66609 (14523) hydrogen bonds : bond 0.03774 ( 419) hydrogen bonds : angle 4.60182 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.324 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: E 246 MET cc_start: 0.8160 (tpp) cc_final: 0.7799 (tpp) REVERT: E 483 ASN cc_start: 0.8224 (t0) cc_final: 0.7920 (t0) REVERT: E 599 MET cc_start: 0.3928 (mmt) cc_final: 0.3537 (tpp) REVERT: K 243 THR cc_start: 0.7856 (p) cc_final: 0.7549 (t) REVERT: K 572 MET cc_start: 0.8159 (mmm) cc_final: 0.7584 (tpp) REVERT: Q 78 GLN cc_start: 0.7731 (mp10) cc_final: 0.7461 (mp10) REVERT: Q 163 ASN cc_start: 0.7860 (t0) cc_final: 0.7319 (t0) REVERT: Q 166 MET cc_start: 0.4483 (mtt) cc_final: 0.3579 (mmt) outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.0869 time to fit residues: 19.6542 Evaluate side-chains 125 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 47 optimal weight: 1.9990 chunk 55 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 32 optimal weight: 8.9990 chunk 1 optimal weight: 0.4980 chunk 121 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 120 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 429 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 = 0.3880 r_free = 0.3880 target = 0.118980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097306 restraints weight = 27861.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.097246 restraints weight = 24187.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.098209 restraints weight = 20971.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098495 restraints weight = 16627.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.098728 restraints weight = 15277.447| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10668 Z= 0.194 Angle : 0.710 12.507 14523 Z= 0.363 Chirality : 0.046 0.184 1625 Planarity : 0.005 0.054 1767 Dihedral : 14.440 176.315 1738 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.08 (0.23), residues: 1226 helix: 0.07 (0.22), residues: 551 sheet: -3.71 (0.47), residues: 83 loop : -2.50 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 227 TYR 0.026 0.002 TYR E 497 PHE 0.022 0.002 PHE E 604 TRP 0.030 0.002 TRP K 131 HIS 0.006 0.001 HIS K 47 Details of bonding type rmsd covalent geometry : bond 0.00444 (10668) covalent geometry : angle 0.71003 (14523) hydrogen bonds : bond 0.03986 ( 419) hydrogen bonds : angle 4.83130 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2452 Ramachandran restraints generated. 1226 Oldfield, 0 Emsley, 1226 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.8186 (tpp) cc_final: 0.7880 (tpp) REVERT: E 376 MET cc_start: 0.7382 (pmm) cc_final: 0.6854 (pmm) REVERT: E 483 ASN cc_start: 0.8348 (t0) cc_final: 0.8122 (t0) REVERT: E 599 MET cc_start: 0.3820 (mmt) cc_final: 0.3475 (tpp) REVERT: K 392 LEU cc_start: 0.7228 (tp) cc_final: 0.6927 (tt) REVERT: K 412 MET cc_start: 0.6918 (mtm) cc_final: 0.6430 (mpp) REVERT: K 556 TYR cc_start: 0.8779 (t80) cc_final: 0.8518 (t80) REVERT: K 572 MET cc_start: 0.8197 (mmm) cc_final: 0.7680 (tpp) REVERT: Q 78 GLN cc_start: 0.7828 (mp10) cc_final: 0.7564 (mp10) REVERT: Q 163 ASN cc_start: 0.7889 (t0) cc_final: 0.7353 (t0) REVERT: Q 166 MET cc_start: 0.4515 (mtt) cc_final: 0.3500 (mmt) REVERT: Q 208 MET cc_start: 0.3369 (tpt) cc_final: 0.2599 (tpt) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.0851 time to fit residues: 18.2246 Evaluate side-chains 121 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 45 optimal weight: 0.8980 chunk 115 optimal weight: 0.0370 chunk 103 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 118 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 35 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 206 GLN E 704 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.123075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.101266 restraints weight = 26722.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.101401 restraints weight = 22774.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.102598 restraints weight = 19215.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102920 restraints weight = 14909.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.103046 restraints weight = 14472.894| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10668 Z= 0.114 Angle : 0.628 13.326 14523 Z= 0.317 Chirality : 0.042 0.168 1625 Planarity : 0.004 0.055 1767 Dihedral : 14.252 176.220 1738 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.09 % Allowed : 0.46 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.24), residues: 1226 helix: 0.34 (0.22), residues: 544 sheet: -3.33 (0.55), residues: 71 loop : -2.37 (0.23), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 94 TYR 0.021 0.001 TYR E 497 PHE 0.020 0.001 PHE E 604 TRP 0.029 0.002 TRP K 131 HIS 0.003 0.001 HIS E 643 Details of bonding type rmsd covalent geometry : bond 0.00257 (10668) covalent geometry : angle 0.62785 (14523) hydrogen bonds : bond 0.03421 ( 419) hydrogen bonds : angle 4.44951 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1414.46 seconds wall clock time: 25 minutes 25.63 seconds (1525.63 seconds total)