Starting phenix.real_space_refine on Thu Jul 2 23:06:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qwl_4660/07_2026/6qwl_4660.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qwl_4660/07_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_4660/07_2026/6qwl_4660.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qwl_4660/07_2026/6qwl_4660.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qwl_4660/07_2026/6qwl_4660.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qwl_4660/07_2026/6qwl_4660.cif" model { file = "/net/cci-nas-00/data/ceres_data/6qwl_4660/07_2026/6qwl_4660.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qwl_4660/07_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-6108/lib/python3.11/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: 2.30, per 1000 atoms: 0.22 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: 0.81 Conformation dependent library (CDL) restraints added in 337.7 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: 1.20 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: 1.83 Time building geometry restraints manager: 1.09 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: 6250 35.58 - 71.16: 148 71.16 - 106.74: 9 106.74 - 142.32: 1 142.32 - 177.90: 1 Dihedral angle restraints: 6409 sinusoidal: 2823 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 6406 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: 1.330 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.270 Find NCS groups from input model: 0.070 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 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 : 16.055 177.903 4097 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/Z covalent geometry : bond 0.00772 / 0.35 (10668) covalent geometry : angle 1.01317 / 0.55 (14523) hydrogen bonds : bond 0.15055 / 10.83 ( 419) hydrogen bonds : angle 7.14981 / 4.85 ( 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 : 0.392 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: 0.1049 time to fit residues: 26.2995 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 : 0.441 ------------------------------------------------------------------------------- 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: 10.0000 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... ** E 206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 271 ASN E 408 ASN E 643 HIS K 261 ASN Q 184 HIS Q 235 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.119436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.097048 restraints weight = 27435.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096314 restraints weight = 25097.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.097347 restraints weight = 21561.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097821 restraints weight = 17410.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.097961 restraints weight = 16393.949| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10668 Z= 0.170 Angle : 0.685 7.910 14523 Z= 0.360 Chirality : 0.045 0.192 1625 Planarity : 0.006 0.066 1767 Dihedral : 11.920 178.149 1644 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -3.48 (0.21), residues: 1226 helix: -1.25 (0.20), residues: 548 sheet: -3.58 (0.45), residues: 92 loop : -3.19 (0.22), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 123 TYR 0.018 0.002 TYR K 556 PHE 0.025 0.002 PHE E 604 TRP 0.018 0.002 TRP E 364 HIS 0.006 0.001 HIS E 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (10668) covalent geometry : angle 0.68462 / 0.36 (14523) hydrogen bonds : bond 0.04396 / 2.96 ( 419) hydrogen bonds : angle 5.33108 / 3.61 ( 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 152 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.354 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: 0.8302 (tpp) cc_final: 0.7969 (tpp) REVERT: E 473 MET cc_start: 0.6670 (ttm) cc_final: 0.5871 (ttp) REVERT: E 584 MET cc_start: 0.7143 (ttp) cc_final: 0.6795 (tmm) REVERT: K 111 MET cc_start: 0.7514 (mtm) cc_final: 0.7209 (mtp) REVERT: K 300 MET cc_start: 0.7134 (mtm) cc_final: 0.6455 (mtm) REVERT: K 392 LEU cc_start: 0.7795 (tp) cc_final: 0.7470 (tt) REVERT: K 410 MET cc_start: 0.6744 (ttm) cc_final: 0.6484 (ttt) REVERT: K 459 MET cc_start: 0.7692 (mmt) cc_final: 0.7198 (mmt) REVERT: Q 166 MET cc_start: 0.4757 (mtt) cc_final: 0.3847 (mmt) REVERT: Q 217 ARG cc_start: 0.7427 (mtt-85) cc_final: 0.6989 (mtp85) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.0986 time to fit residues: 21.4162 Evaluate side-chains 118 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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: 9.9990 chunk 11 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 52 optimal weight: 0.3980 chunk 4 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 704 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 = 0.3852 r_free = 0.3852 target = 0.117498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.095402 restraints weight = 27560.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.095253 restraints weight = 24391.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.096346 restraints weight = 22459.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096584 restraints weight = 16913.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.096579 restraints weight = 17906.240| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 10668 Z= 0.198 Angle : 0.684 8.425 14523 Z= 0.356 Chirality : 0.045 0.176 1625 Planarity : 0.005 0.056 1767 Dihedral : 11.751 177.727 1644 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % 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: 550 sheet: -3.77 (0.48), residues: 84 loop : -2.98 (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 0.024 0.002 PHE E 604 TRP 0.017 0.002 TRP E 364 HIS 0.007 0.002 HIS Q 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (10668) covalent geometry : angle 0.68434 / 0.36 (14523) hydrogen bonds : bond 0.04363 / 2.95 ( 419) hydrogen bonds : angle 5.11326 / 3.46 ( 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 141 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.8259 (tpp) cc_final: 0.7905 (tpp) REVERT: E 279 TYR cc_start: 0.7926 (t80) cc_final: 0.7312 (t80) REVERT: E 473 MET cc_start: 0.6541 (ttm) cc_final: 0.6263 (ttt) REVERT: E 599 MET cc_start: 0.4300 (mmt) cc_final: 0.3768 (tpp) REVERT: E 659 ARG cc_start: 0.7872 (ttm110) cc_final: 0.7546 (mtm180) REVERT: K 111 MET cc_start: 0.7515 (mtm) cc_final: 0.7217 (mtp) REVERT: K 459 MET cc_start: 0.7687 (mmt) cc_final: 0.7067 (mmt) REVERT: Q 156 MET cc_start: 0.6623 (pmm) cc_final: 0.6076 (ptp) REVERT: Q 166 MET cc_start: 0.4554 (mtt) cc_final: 0.3563 (mmt) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0853 time to fit residues: 17.5409 Evaluate side-chains 112 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 7.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 83 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3911 r_free = 0.3911 target = 0.120823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.098034 restraints weight = 27716.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.098043 restraints weight = 22484.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099206 restraints weight = 19043.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099728 restraints weight = 15379.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.100094 restraints weight = 14747.508| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10668 Z= 0.120 Angle : 0.606 7.304 14523 Z= 0.312 Chirality : 0.042 0.162 1625 Planarity : 0.005 0.051 1767 Dihedral : 11.422 177.116 1644 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.55 % 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: -2.41 (0.23), residues: 1226 helix: -0.11 (0.22), residues: 544 sheet: -3.73 (0.49), residues: 83 loop : -2.79 (0.23), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 659 TYR 0.011 0.001 TYR K 556 PHE 0.021 0.001 PHE E 604 TRP 0.019 0.001 TRP E 533 HIS 0.005 0.001 HIS K 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10668) covalent geometry : angle 0.60611 / 0.31 (14523) hydrogen bonds : bond 0.03655 / 2.44 ( 419) hydrogen bonds : angle 4.69994 / 3.19 ( 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 160 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.8282 (tpp) cc_final: 0.7876 (tpp) REVERT: E 473 MET cc_start: 0.6808 (ttm) cc_final: 0.6535 (ttt) REVERT: E 599 MET cc_start: 0.4112 (mmt) cc_final: 0.3616 (tpp) REVERT: K 111 MET cc_start: 0.7496 (mtm) cc_final: 0.7200 (mtp) REVERT: K 247 GLN cc_start: 0.8511 (mp10) cc_final: 0.8270 (mm-40) REVERT: K 300 MET cc_start: 0.6954 (mtp) cc_final: 0.6744 (mtp) REVERT: K 392 LEU cc_start: 0.7384 (tp) cc_final: 0.7045 (tt) REVERT: K 459 MET cc_start: 0.7537 (mmt) cc_final: 0.7082 (mmt) REVERT: Q 163 ASN cc_start: 0.7656 (t0) cc_final: 0.7137 (t0) REVERT: Q 166 MET cc_start: 0.4676 (mtt) cc_final: 0.3720 (mmt) REVERT: Q 211 ARG cc_start: 0.7006 (tpt90) cc_final: 0.6669 (tpt90) outliers start: 1 outliers final: 0 residues processed: 160 average time/residue: 0.0920 time to fit residues: 21.1024 Evaluate side-chains 120 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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: 0.6980 chunk 108 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 467 ASN ** E 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 643 HIS K 663 HIS Q 150 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.118910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.096953 restraints weight = 27631.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096814 restraints weight = 24777.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097916 restraints weight = 22444.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.098160 restraints weight = 16934.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.098376 restraints weight = 15821.851| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10668 Z= 0.175 Angle : 0.670 8.621 14523 Z= 0.345 Chirality : 0.045 0.181 1625 Planarity : 0.005 0.050 1767 Dihedral : 11.396 177.080 1644 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.19 % Allowed : 4.36 % 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: -2.37 (0.23), residues: 1226 helix: -0.11 (0.22), residues: 546 sheet: -3.74 (0.49), residues: 83 loop : -2.74 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Q 216 TYR 0.013 0.001 TYR K 556 PHE 0.023 0.002 PHE E 604 TRP 0.015 0.002 TRP E 533 HIS 0.006 0.001 HIS K 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.17 (10668) covalent geometry : angle 0.67000 / 0.35 (14523) hydrogen bonds : bond 0.03970 / 2.67 ( 419) hydrogen bonds : angle 4.78115 / 3.24 ( 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 152 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 150 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.8160 (tpp) cc_final: 0.7798 (tpp) REVERT: E 483 ASN cc_start: 0.8347 (t0) cc_final: 0.8067 (t0) REVERT: K 111 MET cc_start: 0.7521 (mtm) cc_final: 0.7242 (mtp) REVERT: K 247 GLN cc_start: 0.8530 (mp10) cc_final: 0.8276 (mm-40) REVERT: K 300 MET cc_start: 0.7141 (mtp) cc_final: 0.6920 (mtp) REVERT: K 459 MET cc_start: 0.7494 (mmt) cc_final: 0.7042 (mmt) REVERT: Q 156 MET cc_start: 0.6823 (pmm) cc_final: 0.6368 (ptp) REVERT: Q 163 ASN cc_start: 0.7701 (t0) cc_final: 0.7334 (t0) REVERT: Q 166 MET cc_start: 0.4544 (mtt) cc_final: 0.3652 (mmt) REVERT: Q 211 ARG cc_start: 0.6685 (tpt90) cc_final: 0.6353 (tpm170) outliers start: 2 outliers final: 0 residues processed: 152 average time/residue: 0.0915 time to fit residues: 20.4429 Evaluate side-chains 117 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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: 5.9990 chunk 100 optimal weight: 0.0870 chunk 114 optimal weight: 0.9980 chunk 116 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 89 optimal weight: 0.3980 chunk 40 optimal weight: 9.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.122466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100312 restraints weight = 27390.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100428 restraints weight = 24108.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.101745 restraints weight = 19812.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.102033 restraints weight = 14578.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.102171 restraints weight = 14660.585| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10668 Z= 0.112 Angle : 0.608 8.241 14523 Z= 0.310 Chirality : 0.042 0.192 1625 Planarity : 0.004 0.051 1767 Dihedral : 11.179 176.734 1644 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.09 % Allowed : 1.48 % Favored : 98.42 % 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: -1.97 (0.24), residues: 1226 helix: 0.34 (0.23), residues: 536 sheet: -3.66 (0.47), residues: 83 loop : -2.57 (0.23), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 216 TYR 0.012 0.001 TYR E 229 PHE 0.020 0.001 PHE E 604 TRP 0.022 0.001 TRP K 131 HIS 0.005 0.001 HIS E 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10668) covalent geometry : angle 0.60820 / 0.31 (14523) hydrogen bonds : bond 0.03469 / 2.31 ( 419) hydrogen bonds : angle 4.48298 / 3.06 ( 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 157 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 156 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 246 MET cc_start: 0.8121 (tpp) cc_final: 0.7730 (tpp) REVERT: E 483 ASN cc_start: 0.8349 (t0) cc_final: 0.8102 (t0) REVERT: E 599 MET cc_start: 0.3867 (mmt) cc_final: 0.3480 (tpp) REVERT: Q 156 MET cc_start: 0.6851 (pmm) cc_final: 0.6302 (ptp) REVERT: Q 163 ASN cc_start: 0.7932 (t0) cc_final: 0.7383 (t0) REVERT: Q 166 MET cc_start: 0.4489 (mtt) cc_final: 0.3596 (mmt) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.0895 time to fit residues: 20.4100 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 : 0.428 ------------------------------------------------------------------------------- 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: 0.5980 chunk 119 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 61 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 7.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 604 HIS ** 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 = 0.3887 r_free = 0.3887 target = 0.119434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.097988 restraints weight = 27680.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.098716 restraints weight = 25278.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.099443 restraints weight = 21950.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099698 restraints weight = 17754.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099827 restraints weight = 16942.056| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10668 Z= 0.172 Angle : 0.666 8.814 14523 Z= 0.341 Chirality : 0.044 0.189 1625 Planarity : 0.005 0.053 1767 Dihedral : 11.278 176.805 1644 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % 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: 0.16 (0.22), residues: 543 sheet: -3.71 (0.46), residues: 83 loop : -2.57 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 211 TYR 0.020 0.002 TYR E 361 PHE 0.022 0.002 PHE E 604 TRP 0.022 0.002 TRP K 131 HIS 0.008 0.001 HIS K 604 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 (10668) covalent geometry : angle 0.66574 / 0.34 (14523) hydrogen bonds : bond 0.03850 / 2.59 ( 419) hydrogen bonds : angle 4.69098 / 3.23 ( 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 147 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.321 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: 0.8165 (tpp) cc_final: 0.7795 (tpp) REVERT: E 285 MET cc_start: 0.7934 (mtt) cc_final: 0.7640 (ttm) REVERT: E 483 ASN cc_start: 0.8289 (t0) cc_final: 0.8055 (t0) REVERT: E 599 MET cc_start: 0.3920 (mmt) cc_final: 0.3476 (tpp) REVERT: K 336 PHE cc_start: 0.6900 (t80) cc_final: 0.6690 (m-80) REVERT: Q 156 MET cc_start: 0.6865 (pmm) cc_final: 0.6479 (ptp) REVERT: Q 166 MET cc_start: 0.4513 (mtt) cc_final: 0.3626 (mmt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0901 time to fit residues: 19.4223 Evaluate side-chains 120 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.369 ------------------------------------------------------------------------------- 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: 10.0000 chunk 106 optimal weight: 10.0000 chunk 65 optimal weight: 0.0010 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 704 ASN Q 163 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.120979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.099281 restraints weight = 27341.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.100029 restraints weight = 20731.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.100834 restraints weight = 18997.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.101092 restraints weight = 14016.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.101315 restraints weight = 13806.429| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10668 Z= 0.133 Angle : 0.626 9.162 14523 Z= 0.320 Chirality : 0.043 0.180 1625 Planarity : 0.004 0.053 1767 Dihedral : 11.174 176.486 1644 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: -1.90 (0.23), residues: 1226 helix: 0.18 (0.22), residues: 549 sheet: -3.33 (0.53), residues: 74 loop : -2.43 (0.24), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 216 TYR 0.022 0.002 TYR K 482 PHE 0.021 0.001 PHE E 604 TRP 0.026 0.002 TRP K 131 HIS 0.003 0.001 HIS E 643 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (10668) covalent geometry : angle 0.62607 / 0.32 (14523) hydrogen bonds : bond 0.03566 / 2.39 ( 419) hydrogen bonds : angle 4.55827 / 3.16 ( 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 148 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.394 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: 0.8124 (tpp) cc_final: 0.7770 (tpp) REVERT: E 483 ASN cc_start: 0.8274 (t0) cc_final: 0.8023 (t0) REVERT: E 599 MET cc_start: 0.3812 (mmt) cc_final: 0.3394 (tpp) REVERT: K 300 MET cc_start: 0.6682 (mtp) cc_final: 0.6475 (mtp) REVERT: K 412 MET cc_start: 0.6696 (mtm) cc_final: 0.6138 (mpp) REVERT: K 572 MET cc_start: 0.8146 (mmm) cc_final: 0.7731 (tpp) REVERT: Q 163 ASN cc_start: 0.7968 (t0) cc_final: 0.7576 (t0) REVERT: Q 166 MET cc_start: 0.4556 (mtt) cc_final: 0.3608 (mmt) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.0815 time to fit residues: 17.8960 Evaluate side-chains 122 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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: 5.9990 chunk 88 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 206 GLN Q 244 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.121064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099559 restraints weight = 27427.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.099851 restraints weight = 21941.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.100910 restraints weight = 19717.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101203 restraints weight = 14860.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.101279 restraints weight = 15340.479| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10668 Z= 0.130 Angle : 0.635 12.873 14523 Z= 0.321 Chirality : 0.043 0.177 1625 Planarity : 0.004 0.054 1767 Dihedral : 11.085 176.435 1644 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % 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: -1.86 (0.24), residues: 1226 helix: 0.24 (0.22), residues: 549 sheet: -3.56 (0.47), residues: 83 loop : -2.38 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 216 TYR 0.017 0.001 TYR E 497 PHE 0.021 0.001 PHE E 604 TRP 0.023 0.002 TRP E 533 HIS 0.003 0.001 HIS Q 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (10668) covalent geometry : angle 0.63464 / 0.32 (14523) hydrogen bonds : bond 0.03502 / 2.35 ( 419) hydrogen bonds : angle 4.53529 / 3.15 ( 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 147 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 146 time to evaluate : 0.394 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: 0.8118 (tpp) cc_final: 0.7765 (tpp) REVERT: E 483 ASN cc_start: 0.8266 (t0) cc_final: 0.8012 (t0) REVERT: E 599 MET cc_start: 0.3937 (mmt) cc_final: 0.3511 (tpp) REVERT: K 336 PHE cc_start: 0.6867 (t80) cc_final: 0.6628 (m-80) REVERT: K 412 MET cc_start: 0.6678 (mtm) cc_final: 0.6220 (mpp) REVERT: K 572 MET cc_start: 0.8091 (mmm) cc_final: 0.7521 (tpp) REVERT: Q 78 GLN cc_start: 0.7698 (mp10) cc_final: 0.7438 (mp10) REVERT: Q 156 MET cc_start: 0.6750 (pmm) cc_final: 0.6293 (ptp) REVERT: Q 163 ASN cc_start: 0.7986 (t0) cc_final: 0.7640 (t0) REVERT: Q 166 MET cc_start: 0.4534 (mtt) cc_final: 0.3603 (mmt) outliers start: 1 outliers final: 0 residues processed: 147 average time/residue: 0.0844 time to fit residues: 18.5060 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 : 0.329 ------------------------------------------------------------------------------- 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: 0.4980 chunk 55 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 chunk 120 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 206 GLN E 467 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.121403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.099853 restraints weight = 27656.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.100313 restraints weight = 21774.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.101008 restraints weight = 19955.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.101569 restraints weight = 15647.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.101893 restraints weight = 14652.639| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10668 Z= 0.132 Angle : 0.631 12.556 14523 Z= 0.318 Chirality : 0.043 0.175 1625 Planarity : 0.004 0.054 1767 Dihedral : 11.045 176.320 1644 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.09 % Allowed : 0.37 % Favored : 99.54 % 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: -1.82 (0.24), residues: 1226 helix: 0.23 (0.22), residues: 552 sheet: -3.38 (0.49), residues: 81 loop : -2.35 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 216 TYR 0.020 0.001 TYR E 229 PHE 0.021 0.001 PHE E 604 TRP 0.021 0.001 TRP K 131 HIS 0.003 0.001 HIS Q 184 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10668) covalent geometry : angle 0.63094 / 0.32 (14523) hydrogen bonds : bond 0.03433 / 2.31 ( 419) hydrogen bonds : angle 4.55593 / 3.16 ( 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 149 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 148 time to evaluate : 0.363 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: 0.8118 (tpp) cc_final: 0.7741 (tpp) REVERT: E 483 ASN cc_start: 0.8332 (t0) cc_final: 0.8029 (t0) REVERT: E 599 MET cc_start: 0.3870 (mmt) cc_final: 0.3492 (tpp) REVERT: K 336 PHE cc_start: 0.6841 (t80) cc_final: 0.6617 (m-80) REVERT: K 412 MET cc_start: 0.6718 (mtm) cc_final: 0.6500 (mpp) REVERT: K 572 MET cc_start: 0.8151 (mmm) cc_final: 0.7576 (tpp) REVERT: Q 78 GLN cc_start: 0.7749 (mp10) cc_final: 0.7473 (mp10) REVERT: Q 156 MET cc_start: 0.6813 (pmm) cc_final: 0.6392 (ptp) REVERT: Q 163 ASN cc_start: 0.7994 (t0) cc_final: 0.7661 (t0) REVERT: Q 166 MET cc_start: 0.4557 (mtt) cc_final: 0.3599 (mmt) REVERT: Q 208 MET cc_start: 0.3550 (tpt) cc_final: 0.2673 (tpt) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.0846 time to fit residues: 18.9217 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.6091 > 50: distance: 67 - 225: 30.682 distance: 139 - 189: 15.667 distance: 164 - 169: 20.782 distance: 169 - 170: 22.389 distance: 170 - 171: 33.444 distance: 170 - 173: 38.810 distance: 171 - 172: 40.077 distance: 171 - 177: 42.911 distance: 173 - 174: 26.205 distance: 174 - 175: 15.038 distance: 174 - 176: 19.129 distance: 177 - 178: 36.859 distance: 178 - 179: 29.189 distance: 178 - 181: 36.816 distance: 179 - 180: 22.419 distance: 179 - 189: 21.366 distance: 181 - 182: 39.153 distance: 182 - 183: 9.487 distance: 182 - 184: 11.157 distance: 183 - 185: 12.138 distance: 184 - 186: 9.267 distance: 185 - 187: 7.588 distance: 186 - 187: 10.245 distance: 187 - 188: 6.585 distance: 189 - 190: 21.542 distance: 190 - 191: 24.706 distance: 190 - 193: 15.900 distance: 191 - 192: 35.975 distance: 191 - 195: 35.233 distance: 193 - 194: 12.816 distance: 195 - 196: 23.771 distance: 196 - 197: 40.681 distance: 196 - 199: 12.956 distance: 197 - 198: 35.897 distance: 197 - 206: 41.000 distance: 199 - 200: 17.877 distance: 200 - 201: 16.325 distance: 201 - 202: 15.026 distance: 202 - 203: 10.802 distance: 203 - 204: 14.210 distance: 203 - 205: 13.629 distance: 206 - 207: 45.728 distance: 207 - 208: 29.123 distance: 207 - 210: 33.955 distance: 208 - 209: 40.748 distance: 208 - 213: 52.353 distance: 210 - 211: 30.823 distance: 210 - 212: 19.593 distance: 213 - 214: 36.821 distance: 214 - 215: 48.826 distance: 214 - 217: 43.784 distance: 215 - 216: 41.015 distance: 215 - 221: 42.743 distance: 217 - 218: 11.227 distance: 218 - 219: 31.470 distance: 218 - 220: 39.599 distance: 221 - 222: 52.996 distance: 222 - 223: 56.231 distance: 223 - 224: 50.251 distance: 223 - 225: 60.609 distance: 225 - 226: 24.952 distance: 226 - 227: 22.731 distance: 226 - 229: 25.162 distance: 227 - 228: 16.739 distance: 227 - 232: 21.736 distance: 229 - 230: 38.533 distance: 229 - 231: 26.459 distance: 232 - 233: 32.466 distance: 233 - 234: 30.364 distance: 233 - 236: 35.009 distance: 234 - 235: 24.125 distance: 234 - 240: 14.517 distance: 236 - 237: 27.719 distance: 237 - 238: 31.596 distance: 237 - 239: 32.570 distance: 240 - 241: 19.262 distance: 241 - 242: 14.312 distance: 241 - 244: 22.523 distance: 242 - 243: 26.251 distance: 242 - 249: 19.014 distance: 243 - 270: 12.595 distance: 244 - 245: 20.227 distance: 245 - 246: 20.501 distance: 246 - 247: 20.901 distance: 247 - 248: 16.442