Starting phenix.real_space_refine on Mon Jun 9 22:12:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t2c_10368/06_2025/6t2c_10368.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t2c_10368/06_2025/6t2c_10368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t2c_10368/06_2025/6t2c_10368.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t2c_10368/06_2025/6t2c_10368.map" model { file = "/net/cci-nas-00/data/ceres_data/6t2c_10368/06_2025/6t2c_10368.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t2c_10368/06_2025/6t2c_10368.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 6 Type Number sf(0) Gaussians P 29 5.49 5 Mg 1 5.21 5 S 65 5.16 5 C 6670 2.51 5 N 1853 2.21 5 O 2082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10700 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4145 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 21, 'TRANS': 491} Chain: "B" Number of atoms: 4996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4996 Classifications: {'peptide': 626} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 599} Chain breaks: 2 Chain: "C" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 941 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 617 Classifications: {'RNA': 29} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 4, 'rna3p_pur': 12, 'rna3p_pyr': 10} Link IDs: {'rna2p': 7, 'rna3p': 21} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.58, per 1000 atoms: 0.61 Number of scatterers: 10700 At special positions: 0 Unit cell: (104.749, 116.281, 94.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 65 16.00 P 29 15.00 Mg 1 11.99 O 2082 8.00 N 1853 7.00 C 6670 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: 2.49 Conformation dependent library (CDL) restraints added in 1.3 seconds 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 13 sheets defined 47.2% alpha, 13.5% beta 5 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 208 through 216 Processing helix chain 'A' and resid 225 through 235 removed outlier: 3.643A pdb=" N SER A 235 " --> pdb=" O ALA A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.784A pdb=" N ALA A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 347 removed outlier: 3.811A pdb=" N TYR A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 366 Processing helix chain 'A' and resid 401 through 409 Processing helix chain 'A' and resid 428 through 446 Processing helix chain 'A' and resid 448 through 471 removed outlier: 3.752A pdb=" N GLU A 452 " --> pdb=" O CYS A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.614A pdb=" N ASN A 527 " --> pdb=" O ASP A 524 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 524 through 528' Processing helix chain 'A' and resid 566 through 575 Processing helix chain 'A' and resid 577 through 596 removed outlier: 4.078A pdb=" N LEU A 584 " --> pdb=" O LEU A 580 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 589 " --> pdb=" O GLN A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.553A pdb=" N PHE A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 645 Processing helix chain 'A' and resid 647 through 669 removed outlier: 3.593A pdb=" N GLU A 651 " --> pdb=" O SER A 647 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N LYS A 659 " --> pdb=" O ALA A 655 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU A 660 " --> pdb=" O GLU A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 removed outlier: 3.617A pdb=" N LEU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 713 removed outlier: 3.895A pdb=" N MET A 713 " --> pdb=" O VAL A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.762A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 84 through 99 removed outlier: 3.521A pdb=" N VAL B 88 " --> pdb=" O GLN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 115 removed outlier: 3.787A pdb=" N GLN B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 156 through 161 removed outlier: 4.008A pdb=" N SER B 160 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY B 161 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 213 through 222 removed outlier: 3.604A pdb=" N LEU B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 264 removed outlier: 3.614A pdb=" N VAL B 252 " --> pdb=" O ILE B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 290 removed outlier: 4.230A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA B 280 " --> pdb=" O ASN B 276 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 3.602A pdb=" N PHE B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR B 326 " --> pdb=" O VAL B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 345 removed outlier: 4.747A pdb=" N ALA B 340 " --> pdb=" O LEU B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 369 through 376 removed outlier: 3.698A pdb=" N ASN B 372 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE B 376 " --> pdb=" O LEU B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 4.124A pdb=" N TYR B 380 " --> pdb=" O ASN B 377 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 381' Processing helix chain 'B' and resid 382 through 393 removed outlier: 3.513A pdb=" N LYS B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 425 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 471 Processing helix chain 'B' and resid 518 through 536 removed outlier: 3.605A pdb=" N ASP B 522 " --> pdb=" O ASN B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 589 removed outlier: 3.886A pdb=" N LEU B 589 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 600 through 604 removed outlier: 3.651A pdb=" N ASN B 603 " --> pdb=" O ASN B 600 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 604 " --> pdb=" O LEU B 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 600 through 604' Processing helix chain 'B' and resid 607 through 612 removed outlier: 3.570A pdb=" N LYS B 612 " --> pdb=" O GLU B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'C' and resid 43 through 53 removed outlier: 3.645A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 66 removed outlier: 3.835A pdb=" N GLU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET C 66 " --> pdb=" O ILE C 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 66' Processing helix chain 'C' and resid 92 through 103 removed outlier: 4.077A pdb=" N VAL C 96 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.756A pdb=" N PHE C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA2, first strand: chain 'A' and resid 274 through 275 removed outlier: 6.001A pdb=" N LYS A 274 " --> pdb=" O LYS A 397 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 293 removed outlier: 7.390A pdb=" N TYR A 496 " --> pdb=" O PHE A 520 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N LEU A 558 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N GLU A 539 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N VAL A 560 " --> pdb=" O VAL A 537 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N VAL A 537 " --> pdb=" O VAL A 560 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL A 537 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR A 321 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY A 541 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N LYS A 319 " --> pdb=" O GLY A 541 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N MET A 543 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 10.766A pdb=" N TRP A 317 " --> pdb=" O MET A 543 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 293 removed outlier: 5.219A pdb=" N THR A 493 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N CYS A 484 " --> pdb=" O THR A 493 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU A 495 " --> pdb=" O THR A 482 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N THR A 482 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 497 " --> pdb=" O ILE A 480 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN A 476 " --> pdb=" O LYS A 501 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR A 475 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 373 removed outlier: 5.872A pdb=" N GLU A 372 " --> pdb=" O ARG B 365 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N GLN B 367 " --> pdb=" O GLU A 372 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 622 through 626 removed outlier: 6.544A pdb=" N GLY A 622 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU A 618 " --> pdb=" O GLY A 622 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLU A 624 " --> pdb=" O ILE A 616 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 183 removed outlier: 3.630A pdb=" N THR B 183 " --> pdb=" O LYS B 208 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 208 " --> pdb=" O THR B 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 240 through 243 removed outlier: 6.948A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 492 Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 58 Processing sheet with id=AB4, first strand: chain 'C' and resid 128 through 130 457 hydrogen bonds defined for protein. 1266 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 24 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 2.98 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: 2892 1.33 - 1.45: 2066 1.45 - 1.57: 5864 1.57 - 1.69: 55 1.69 - 1.80: 112 Bond restraints: 10989 Sorted by residual: bond pdb=" C SER A 206 " pdb=" N TYR A 207 " ideal model delta sigma weight residual 1.331 1.265 0.066 2.07e-02 2.33e+03 1.01e+01 bond pdb=" N ASP B 445 " pdb=" CA ASP B 445 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.00e-02 1.00e+04 9.21e+00 bond pdb=" N SER B 444 " pdb=" CA SER B 444 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.49e+00 bond pdb=" N SER B 443 " pdb=" CA SER B 443 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.19e-02 7.06e+03 5.49e+00 bond pdb=" CA SER B 443 " pdb=" CB SER B 443 " ideal model delta sigma weight residual 1.532 1.504 0.028 1.58e-02 4.01e+03 3.04e+00 ... (remaining 10984 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 14400 1.71 - 3.42: 504 3.42 - 5.12: 61 5.12 - 6.83: 8 6.83 - 8.54: 5 Bond angle restraints: 14978 Sorted by residual: angle pdb=" N ASP B 445 " pdb=" CA ASP B 445 " pdb=" C ASP B 445 " ideal model delta sigma weight residual 112.54 104.50 8.04 1.51e+00 4.39e-01 2.83e+01 angle pdb=" N VAL C 109 " pdb=" CA VAL C 109 " pdb=" C VAL C 109 " ideal model delta sigma weight residual 113.71 109.15 4.56 9.50e-01 1.11e+00 2.31e+01 angle pdb=" N ASP B 446 " pdb=" CA ASP B 446 " pdb=" C ASP B 446 " ideal model delta sigma weight residual 109.07 116.34 -7.27 1.61e+00 3.86e-01 2.04e+01 angle pdb=" C ILE A 540 " pdb=" N GLY A 541 " pdb=" CA GLY A 541 " ideal model delta sigma weight residual 121.15 115.20 5.95 1.80e+00 3.09e-01 1.09e+01 angle pdb=" N ILE B 248 " pdb=" CA ILE B 248 " pdb=" CB ILE B 248 " ideal model delta sigma weight residual 112.15 107.32 4.83 1.47e+00 4.63e-01 1.08e+01 ... (remaining 14973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 5954 17.68 - 35.36: 509 35.36 - 53.04: 135 53.04 - 70.73: 57 70.73 - 88.41: 12 Dihedral angle restraints: 6667 sinusoidal: 3018 harmonic: 3649 Sorted by residual: dihedral pdb=" CA ILE A 481 " pdb=" C ILE A 481 " pdb=" N THR A 482 " pdb=" CA THR A 482 " ideal model delta harmonic sigma weight residual 180.00 159.47 20.53 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA MET B 408 " pdb=" C MET B 408 " pdb=" N MET B 409 " pdb=" CA MET B 409 " ideal model delta harmonic sigma weight residual -180.00 -159.72 -20.28 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA LEU A 581 " pdb=" C LEU A 581 " pdb=" N GLN A 582 " pdb=" CA GLN A 582 " ideal model delta harmonic sigma weight residual 180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 6664 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1296 0.059 - 0.118: 311 0.118 - 0.177: 42 0.177 - 0.236: 4 0.236 - 0.294: 1 Chirality restraints: 1654 Sorted by residual: chirality pdb=" CA PHE B 447 " pdb=" N PHE B 447 " pdb=" C PHE B 447 " pdb=" CB PHE B 447 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CB ILE A 418 " pdb=" CA ILE A 418 " pdb=" CG1 ILE A 418 " pdb=" CG2 ILE A 418 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CG LEU B 258 " pdb=" CB LEU B 258 " pdb=" CD1 LEU B 258 " pdb=" CD2 LEU B 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 1651 not shown) Planarity restraints: 1818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 111 " 0.052 5.00e-02 4.00e+02 7.71e-02 9.52e+00 pdb=" N PRO C 112 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 619 " -0.044 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO A 620 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 620 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 620 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 584 " 0.012 2.00e-02 2.50e+03 2.33e-02 5.44e+00 pdb=" C LEU A 584 " -0.040 2.00e-02 2.50e+03 pdb=" O LEU A 584 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 585 " 0.014 2.00e-02 2.50e+03 ... (remaining 1815 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 221 2.66 - 3.22: 9032 3.22 - 3.78: 16295 3.78 - 4.34: 22418 4.34 - 4.90: 37425 Nonbonded interactions: 85391 Sorted by model distance: nonbonded pdb=" O ASP B 48 " pdb=" OD1 ASP B 48 " model vdw 2.097 3.040 nonbonded pdb=" OG SER B 374 " pdb=" OD1 ASP B 375 " model vdw 2.270 3.040 nonbonded pdb=" OD2 ASP B 446 " pdb="MG MG B 801 " model vdw 2.278 2.170 nonbonded pdb=" O LYS A 380 " pdb=" OH TYR B 380 " model vdw 2.280 3.040 nonbonded pdb=" O ASP B 120 " pdb=" OG1 THR B 123 " model vdw 2.295 3.040 ... (remaining 85386 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: 1.600 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: 0.040 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.590 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 0.069 10989 Z= 0.323 Angle : 0.756 8.541 14978 Z= 0.427 Chirality : 0.051 0.294 1654 Planarity : 0.007 0.077 1818 Dihedral : 15.430 88.408 4311 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 6.25 % Allowed : 8.06 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.19), residues: 1243 helix: -2.33 (0.16), residues: 537 sheet: -1.15 (0.45), residues: 119 loop : -2.76 (0.21), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 438 HIS 0.005 0.001 HIS B 32 PHE 0.023 0.002 PHE B 490 TYR 0.017 0.002 TYR B 155 ARG 0.005 0.001 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.16559 ( 465) hydrogen bonds : angle 6.38672 ( 1290) covalent geometry : bond 0.00754 (10989) covalent geometry : angle 0.75563 (14978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 223 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9446 (m) cc_final: 0.9076 (t) REVERT: A 288 MET cc_start: 0.8489 (ttp) cc_final: 0.8281 (ttt) REVERT: A 356 LYS cc_start: 0.8287 (mttt) cc_final: 0.8037 (ttpp) REVERT: A 388 TYR cc_start: 0.8859 (OUTLIER) cc_final: 0.8487 (m-10) REVERT: A 414 ASN cc_start: 0.7936 (m110) cc_final: 0.7701 (p0) REVERT: A 474 GLU cc_start: 0.7910 (mp0) cc_final: 0.7527 (mm-30) REVERT: A 585 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7916 (tp40) REVERT: A 598 LYS cc_start: 0.8753 (mmtt) cc_final: 0.7819 (tptm) REVERT: A 679 LYS cc_start: 0.8836 (mttt) cc_final: 0.8613 (mmtt) REVERT: A 707 LYS cc_start: 0.8569 (tttt) cc_final: 0.8367 (tptp) REVERT: B 15 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: B 54 ILE cc_start: 0.9299 (mt) cc_final: 0.8956 (pt) REVERT: B 120 ASP cc_start: 0.7326 (p0) cc_final: 0.7072 (p0) REVERT: B 157 LEU cc_start: 0.8417 (mt) cc_final: 0.7957 (mp) REVERT: B 169 ASP cc_start: 0.8008 (m-30) cc_final: 0.7665 (m-30) REVERT: B 171 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8914 (mm) REVERT: B 175 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6208 (mp0) REVERT: B 248 ILE cc_start: 0.9148 (tt) cc_final: 0.8761 (tp) REVERT: B 249 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.6948 (mpt90) REVERT: B 256 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7895 (mm-30) REVERT: B 353 ARG cc_start: 0.8398 (ptp-170) cc_final: 0.7949 (ptm-80) REVERT: B 468 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7701 (mtt180) REVERT: B 481 LYS cc_start: 0.8700 (mttt) cc_final: 0.8246 (mtmt) REVERT: C 47 MET cc_start: 0.8288 (tpp) cc_final: 0.7696 (tpt) REVERT: C 71 ASP cc_start: 0.7781 (m-30) cc_final: 0.7379 (m-30) REVERT: C 83 ASP cc_start: 0.8266 (t70) cc_final: 0.7301 (t70) REVERT: C 113 ARG cc_start: 0.4380 (OUTLIER) cc_final: 0.3863 (mpt180) outliers start: 69 outliers final: 35 residues processed: 278 average time/residue: 0.2787 time to fit residues: 103.5576 Evaluate side-chains 203 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 476 GLN Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 108 GLN Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 176 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 249 ARG Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 529 VAL Chi-restraints excluded: chain B residue 583 THR Chi-restraints excluded: chain B residue 589 LEU Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 619 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN A 461 ASN A 476 GLN B 47 HIS B 65 GLN B 276 ASN B 346 ASN B 425 ASN B 567 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.129040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.105345 restraints weight = 16052.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108388 restraints weight = 8192.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.110364 restraints weight = 5286.420| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10989 Z= 0.114 Angle : 0.537 7.835 14978 Z= 0.281 Chirality : 0.039 0.169 1654 Planarity : 0.005 0.045 1818 Dihedral : 13.515 81.240 1879 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 3.80 % Allowed : 11.87 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.22), residues: 1243 helix: -0.02 (0.22), residues: 535 sheet: -1.03 (0.48), residues: 108 loop : -2.13 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 49 HIS 0.004 0.001 HIS A 360 PHE 0.017 0.001 PHE A 352 TYR 0.010 0.001 TYR B 555 ARG 0.005 0.000 ARG B 260 Details of bonding type rmsd hydrogen bonds : bond 0.04247 ( 465) hydrogen bonds : angle 4.39359 ( 1290) covalent geometry : bond 0.00251 (10989) covalent geometry : angle 0.53731 (14978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 1.279 Fit side-chains REVERT: A 218 SER cc_start: 0.9367 (m) cc_final: 0.9010 (t) REVERT: A 388 TYR cc_start: 0.8821 (OUTLIER) cc_final: 0.8538 (m-10) REVERT: A 414 ASN cc_start: 0.8012 (m-40) cc_final: 0.7760 (p0) REVERT: A 568 ILE cc_start: 0.9017 (tp) cc_final: 0.8527 (pt) REVERT: A 585 GLN cc_start: 0.8315 (tt0) cc_final: 0.7913 (tp40) REVERT: A 597 VAL cc_start: 0.8376 (m) cc_final: 0.7985 (t) REVERT: A 598 LYS cc_start: 0.8763 (mmtt) cc_final: 0.7798 (tptm) REVERT: A 707 LYS cc_start: 0.8531 (tttt) cc_final: 0.8311 (tptp) REVERT: B 15 GLN cc_start: 0.9423 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: B 157 LEU cc_start: 0.8438 (mt) cc_final: 0.8122 (mp) REVERT: B 169 ASP cc_start: 0.7945 (m-30) cc_final: 0.7733 (m-30) REVERT: B 175 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6013 (mp0) REVERT: B 256 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7763 (mm-30) REVERT: B 287 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7531 (mtmt) REVERT: B 353 ARG cc_start: 0.8307 (ptp-170) cc_final: 0.7900 (ptm-80) REVERT: B 411 MET cc_start: 0.6137 (mtm) cc_final: 0.5782 (mtm) REVERT: B 468 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7954 (mtt180) REVERT: B 481 LYS cc_start: 0.8562 (mttt) cc_final: 0.8139 (mtmt) REVERT: B 577 LYS cc_start: 0.8353 (tptt) cc_final: 0.7971 (tppt) REVERT: C 47 MET cc_start: 0.8132 (tpp) cc_final: 0.7467 (tpt) REVERT: C 77 LEU cc_start: 0.8602 (mp) cc_final: 0.8215 (mp) REVERT: C 113 ARG cc_start: 0.4333 (OUTLIER) cc_final: 0.3734 (mpt180) outliers start: 42 outliers final: 24 residues processed: 222 average time/residue: 0.2744 time to fit residues: 82.1734 Evaluate side-chains 184 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 468 ARG Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 245 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 119 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 78 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 86 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN B 276 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.127150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.103275 restraints weight = 16621.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.106220 restraints weight = 8502.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.108206 restraints weight = 5549.471| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10989 Z= 0.132 Angle : 0.518 6.998 14978 Z= 0.269 Chirality : 0.039 0.155 1654 Planarity : 0.004 0.043 1818 Dihedral : 12.678 77.720 1841 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 4.35 % Allowed : 13.13 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.23), residues: 1243 helix: 0.67 (0.23), residues: 542 sheet: -0.71 (0.46), residues: 116 loop : -1.92 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 49 HIS 0.003 0.001 HIS A 360 PHE 0.016 0.001 PHE A 352 TYR 0.013 0.001 TYR A 475 ARG 0.006 0.000 ARG C 64 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 465) hydrogen bonds : angle 4.19218 ( 1290) covalent geometry : bond 0.00306 (10989) covalent geometry : angle 0.51770 (14978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 168 time to evaluate : 1.222 Fit side-chains REVERT: A 218 SER cc_start: 0.9339 (m) cc_final: 0.9035 (t) REVERT: A 414 ASN cc_start: 0.8038 (m-40) cc_final: 0.7796 (p0) REVERT: A 568 ILE cc_start: 0.9065 (tp) cc_final: 0.8583 (pt) REVERT: A 575 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7850 (mt-10) REVERT: A 585 GLN cc_start: 0.8404 (tt0) cc_final: 0.8005 (tp40) REVERT: A 597 VAL cc_start: 0.8386 (m) cc_final: 0.7997 (t) REVERT: A 598 LYS cc_start: 0.8773 (mmtt) cc_final: 0.7671 (tptm) REVERT: A 707 LYS cc_start: 0.8550 (tttt) cc_final: 0.8304 (tptp) REVERT: B 15 GLN cc_start: 0.9405 (OUTLIER) cc_final: 0.8070 (mp10) REVERT: B 157 LEU cc_start: 0.8508 (mt) cc_final: 0.8134 (mp) REVERT: B 169 ASP cc_start: 0.7889 (m-30) cc_final: 0.7656 (m-30) REVERT: B 175 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6112 (mp0) REVERT: B 256 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 287 LYS cc_start: 0.8005 (tmtt) cc_final: 0.7496 (mtmt) REVERT: B 353 ARG cc_start: 0.8354 (ptp-170) cc_final: 0.7873 (ptm-80) REVERT: B 442 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8475 (tp40) REVERT: B 481 LYS cc_start: 0.8603 (mttt) cc_final: 0.8064 (ptpt) REVERT: C 47 MET cc_start: 0.8106 (tpp) cc_final: 0.7365 (tpt) REVERT: C 71 ASP cc_start: 0.7615 (m-30) cc_final: 0.7407 (m-30) REVERT: C 113 ARG cc_start: 0.4326 (OUTLIER) cc_final: 0.3737 (mpt180) outliers start: 48 outliers final: 32 residues processed: 205 average time/residue: 0.2509 time to fit residues: 71.4602 Evaluate side-chains 190 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 602 MET Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 105 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN B 108 GLN ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 75 ASN C 80 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.123541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099993 restraints weight = 16639.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102867 restraints weight = 8677.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.104771 restraints weight = 5700.740| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 10989 Z= 0.271 Angle : 0.616 8.211 14978 Z= 0.319 Chirality : 0.043 0.162 1654 Planarity : 0.004 0.040 1818 Dihedral : 12.744 83.833 1832 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 4.35 % Allowed : 14.31 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.24), residues: 1243 helix: 0.79 (0.23), residues: 539 sheet: -0.80 (0.46), residues: 123 loop : -1.85 (0.24), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 438 HIS 0.004 0.001 HIS B 465 PHE 0.015 0.002 PHE A 352 TYR 0.018 0.002 TYR A 475 ARG 0.004 0.000 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.05220 ( 465) hydrogen bonds : angle 4.42162 ( 1290) covalent geometry : bond 0.00644 (10989) covalent geometry : angle 0.61588 (14978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9402 (m) cc_final: 0.9060 (t) REVERT: A 388 TYR cc_start: 0.8944 (OUTLIER) cc_final: 0.8532 (m-10) REVERT: A 414 ASN cc_start: 0.8057 (m-40) cc_final: 0.7757 (p0) REVERT: A 575 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7908 (mt-10) REVERT: A 585 GLN cc_start: 0.8473 (tt0) cc_final: 0.8103 (tp40) REVERT: A 598 LYS cc_start: 0.8836 (mmtt) cc_final: 0.7778 (tptm) REVERT: A 707 LYS cc_start: 0.8571 (tttt) cc_final: 0.8351 (tptp) REVERT: B 15 GLN cc_start: 0.9448 (OUTLIER) cc_final: 0.8075 (mp10) REVERT: B 118 ARG cc_start: 0.7978 (mmm-85) cc_final: 0.7657 (tpp80) REVERT: B 157 LEU cc_start: 0.8584 (mt) cc_final: 0.8154 (mp) REVERT: B 169 ASP cc_start: 0.7971 (m-30) cc_final: 0.7694 (m-30) REVERT: B 175 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5981 (mp0) REVERT: B 287 LYS cc_start: 0.8070 (tmtt) cc_final: 0.7570 (mtmt) REVERT: B 442 GLN cc_start: 0.9079 (OUTLIER) cc_final: 0.8685 (tp40) REVERT: B 481 LYS cc_start: 0.8690 (mttt) cc_final: 0.8223 (mtmt) REVERT: C 47 MET cc_start: 0.8136 (tpp) cc_final: 0.7454 (tpt) REVERT: C 113 ARG cc_start: 0.4246 (OUTLIER) cc_final: 0.3568 (mpt180) outliers start: 48 outliers final: 35 residues processed: 197 average time/residue: 0.2433 time to fit residues: 66.6142 Evaluate side-chains 189 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 388 TYR Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 529 ILE Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 102 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 242 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.126740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.102754 restraints weight = 16473.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.105711 restraints weight = 8504.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.107716 restraints weight = 5574.323| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10989 Z= 0.107 Angle : 0.490 8.428 14978 Z= 0.256 Chirality : 0.038 0.152 1654 Planarity : 0.004 0.041 1818 Dihedral : 12.395 77.356 1830 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.71 % Allowed : 15.94 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.24), residues: 1243 helix: 1.26 (0.23), residues: 540 sheet: -0.32 (0.47), residues: 117 loop : -1.73 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 437 HIS 0.003 0.001 HIS B 47 PHE 0.021 0.001 PHE A 352 TYR 0.012 0.001 TYR A 475 ARG 0.004 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.03740 ( 465) hydrogen bonds : angle 4.05936 ( 1290) covalent geometry : bond 0.00242 (10989) covalent geometry : angle 0.49040 (14978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 1.284 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9349 (m) cc_final: 0.9010 (t) REVERT: A 414 ASN cc_start: 0.8012 (m-40) cc_final: 0.7733 (p0) REVERT: A 568 ILE cc_start: 0.9058 (tp) cc_final: 0.8547 (pt) REVERT: A 575 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 585 GLN cc_start: 0.8369 (tt0) cc_final: 0.8032 (tp40) REVERT: A 597 VAL cc_start: 0.8558 (m) cc_final: 0.8218 (t) REVERT: A 598 LYS cc_start: 0.8774 (mmtt) cc_final: 0.7676 (tptm) REVERT: A 707 LYS cc_start: 0.8540 (tttt) cc_final: 0.8326 (tptp) REVERT: B 118 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7531 (tpp80) REVERT: B 157 LEU cc_start: 0.8543 (mt) cc_final: 0.8088 (mp) REVERT: B 169 ASP cc_start: 0.7937 (m-30) cc_final: 0.7625 (m-30) REVERT: B 175 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5974 (mp0) REVERT: B 256 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7873 (mm-30) REVERT: B 287 LYS cc_start: 0.7947 (tmtt) cc_final: 0.7438 (mtmt) REVERT: B 302 ILE cc_start: 0.9202 (mt) cc_final: 0.8992 (tt) REVERT: B 353 ARG cc_start: 0.8275 (ptp-170) cc_final: 0.7836 (ptm160) REVERT: B 442 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.8406 (tp40) REVERT: B 481 LYS cc_start: 0.8606 (mttt) cc_final: 0.8020 (ptpt) REVERT: C 47 MET cc_start: 0.8101 (tpp) cc_final: 0.7454 (tpt) REVERT: C 113 ARG cc_start: 0.4181 (OUTLIER) cc_final: 0.3639 (mpt180) outliers start: 41 outliers final: 30 residues processed: 204 average time/residue: 0.2662 time to fit residues: 77.1967 Evaluate side-chains 191 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 19 SER Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 0.0870 chunk 2 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 106 optimal weight: 0.0030 overall best weight: 1.7572 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.103861 restraints weight = 16465.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.106824 restraints weight = 8435.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.108781 restraints weight = 5525.893| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10989 Z= 0.146 Angle : 0.508 8.384 14978 Z= 0.264 Chirality : 0.040 0.157 1654 Planarity : 0.004 0.039 1818 Dihedral : 12.291 78.971 1827 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.53 % Allowed : 16.03 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1243 helix: 1.41 (0.23), residues: 540 sheet: -0.10 (0.48), residues: 116 loop : -1.66 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 363 HIS 0.003 0.001 HIS B 47 PHE 0.020 0.001 PHE A 352 TYR 0.013 0.001 TYR A 475 ARG 0.002 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 465) hydrogen bonds : angle 4.04520 ( 1290) covalent geometry : bond 0.00345 (10989) covalent geometry : angle 0.50848 (14978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9344 (m) cc_final: 0.9039 (t) REVERT: A 414 ASN cc_start: 0.8003 (m-40) cc_final: 0.7736 (p0) REVERT: A 568 ILE cc_start: 0.9077 (tp) cc_final: 0.8563 (pt) REVERT: A 575 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7899 (mt-10) REVERT: A 585 GLN cc_start: 0.8342 (tt0) cc_final: 0.8064 (tp40) REVERT: A 598 LYS cc_start: 0.8794 (mmtt) cc_final: 0.7700 (tptm) REVERT: A 707 LYS cc_start: 0.8536 (tttt) cc_final: 0.8334 (tptp) REVERT: B 118 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7520 (tpp80) REVERT: B 157 LEU cc_start: 0.8562 (mt) cc_final: 0.8082 (mp) REVERT: B 169 ASP cc_start: 0.7956 (m-30) cc_final: 0.7605 (m-30) REVERT: B 175 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.5993 (mp0) REVERT: B 256 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7732 (mm-30) REVERT: B 287 LYS cc_start: 0.7964 (tmtt) cc_final: 0.7448 (mtmt) REVERT: B 302 ILE cc_start: 0.9195 (mt) cc_final: 0.8972 (tt) REVERT: B 353 ARG cc_start: 0.8340 (ptp-170) cc_final: 0.7851 (ptm160) REVERT: B 442 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8482 (tp40) REVERT: B 481 LYS cc_start: 0.8607 (mttt) cc_final: 0.8029 (ptpt) REVERT: B 566 THR cc_start: 0.8375 (p) cc_final: 0.8174 (t) REVERT: B 670 ARG cc_start: 0.6940 (mtp180) cc_final: 0.6654 (ptt180) REVERT: C 47 MET cc_start: 0.8107 (tpp) cc_final: 0.7504 (tpt) outliers start: 39 outliers final: 32 residues processed: 191 average time/residue: 0.2483 time to fit residues: 65.8751 Evaluate side-chains 189 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 2 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 8 optimal weight: 0.0040 chunk 18 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104365 restraints weight = 16723.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.107381 restraints weight = 8517.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109364 restraints weight = 5515.203| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10989 Z= 0.138 Angle : 0.499 8.573 14978 Z= 0.260 Chirality : 0.040 0.154 1654 Planarity : 0.003 0.038 1818 Dihedral : 12.194 79.579 1822 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.62 % Allowed : 16.76 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1243 helix: 1.52 (0.23), residues: 540 sheet: -0.13 (0.49), residues: 118 loop : -1.58 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 PHE 0.022 0.001 PHE A 352 TYR 0.015 0.001 TYR A 475 ARG 0.002 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 465) hydrogen bonds : angle 4.01235 ( 1290) covalent geometry : bond 0.00323 (10989) covalent geometry : angle 0.49928 (14978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 159 time to evaluate : 1.123 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9332 (m) cc_final: 0.9040 (t) REVERT: A 414 ASN cc_start: 0.8031 (m-40) cc_final: 0.7754 (p0) REVERT: A 568 ILE cc_start: 0.9071 (tp) cc_final: 0.8566 (pt) REVERT: A 575 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7920 (mt-10) REVERT: A 585 GLN cc_start: 0.8325 (tt0) cc_final: 0.8043 (tp40) REVERT: A 598 LYS cc_start: 0.8773 (mmtt) cc_final: 0.7656 (tptm) REVERT: B 118 ARG cc_start: 0.7926 (mmm-85) cc_final: 0.7483 (tpp80) REVERT: B 157 LEU cc_start: 0.8561 (mt) cc_final: 0.8074 (mp) REVERT: B 169 ASP cc_start: 0.7899 (m-30) cc_final: 0.7554 (m-30) REVERT: B 175 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5940 (mp0) REVERT: B 287 LYS cc_start: 0.7949 (tmtt) cc_final: 0.7457 (mtmt) REVERT: B 353 ARG cc_start: 0.8283 (ptp-170) cc_final: 0.7752 (ptm160) REVERT: B 442 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8479 (tp40) REVERT: B 481 LYS cc_start: 0.8597 (mttt) cc_final: 0.8028 (ptpt) REVERT: B 670 ARG cc_start: 0.6952 (mtp180) cc_final: 0.6558 (ptt180) REVERT: C 47 MET cc_start: 0.8112 (tpp) cc_final: 0.7510 (tpt) REVERT: C 113 ARG cc_start: 0.4126 (OUTLIER) cc_final: 0.3568 (mpt180) outliers start: 40 outliers final: 29 residues processed: 189 average time/residue: 0.2496 time to fit residues: 65.3566 Evaluate side-chains 184 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 152 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 660 LEU Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 597 ASN Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 658 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 45 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 26 optimal weight: 3.9990 overall best weight: 1.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.128055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.104547 restraints weight = 16601.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.107495 restraints weight = 8563.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109442 restraints weight = 5622.533| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10989 Z= 0.141 Angle : 0.505 8.245 14978 Z= 0.262 Chirality : 0.040 0.164 1654 Planarity : 0.004 0.038 1818 Dihedral : 12.157 80.905 1821 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.26 % Allowed : 17.57 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1243 helix: 1.57 (0.23), residues: 541 sheet: -0.01 (0.49), residues: 118 loop : -1.58 (0.25), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 438 HIS 0.003 0.001 HIS B 47 PHE 0.022 0.001 PHE A 352 TYR 0.013 0.001 TYR A 475 ARG 0.002 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 465) hydrogen bonds : angle 4.01577 ( 1290) covalent geometry : bond 0.00334 (10989) covalent geometry : angle 0.50493 (14978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 157 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9321 (m) cc_final: 0.9041 (t) REVERT: A 414 ASN cc_start: 0.8023 (m-40) cc_final: 0.7751 (p0) REVERT: A 568 ILE cc_start: 0.9063 (tp) cc_final: 0.8571 (pt) REVERT: A 575 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7891 (mt-10) REVERT: A 585 GLN cc_start: 0.8320 (tt0) cc_final: 0.8003 (tp40) REVERT: A 598 LYS cc_start: 0.8748 (mmtt) cc_final: 0.7631 (tptm) REVERT: B 118 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7533 (tpp80) REVERT: B 157 LEU cc_start: 0.8555 (mt) cc_final: 0.8055 (mp) REVERT: B 169 ASP cc_start: 0.7941 (m-30) cc_final: 0.7561 (m-30) REVERT: B 175 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.5915 (mp0) REVERT: B 287 LYS cc_start: 0.7958 (tmtt) cc_final: 0.7485 (mtmt) REVERT: B 296 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5887 (mt-10) REVERT: B 353 ARG cc_start: 0.8216 (ptp-170) cc_final: 0.7592 (ptm-80) REVERT: B 442 GLN cc_start: 0.8964 (OUTLIER) cc_final: 0.8513 (tp40) REVERT: B 481 LYS cc_start: 0.8602 (mttt) cc_final: 0.8063 (ptpt) REVERT: B 670 ARG cc_start: 0.6952 (mtp180) cc_final: 0.6567 (ptt180) REVERT: C 47 MET cc_start: 0.8132 (tpp) cc_final: 0.7533 (tpt) REVERT: C 113 ARG cc_start: 0.4147 (OUTLIER) cc_final: 0.3595 (mpt180) outliers start: 36 outliers final: 27 residues processed: 183 average time/residue: 0.2505 time to fit residues: 63.3388 Evaluate side-chains 182 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 290 MET Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain B residue 617 ASP Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 60 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 11 optimal weight: 0.0060 chunk 116 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.130239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.106690 restraints weight = 16652.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.109768 restraints weight = 8420.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.111764 restraints weight = 5445.163| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10989 Z= 0.102 Angle : 0.478 8.031 14978 Z= 0.249 Chirality : 0.038 0.149 1654 Planarity : 0.003 0.038 1818 Dihedral : 12.007 78.604 1816 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.08 % Allowed : 17.84 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1243 helix: 1.68 (0.23), residues: 542 sheet: 0.07 (0.51), residues: 115 loop : -1.52 (0.25), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 437 HIS 0.003 0.001 HIS B 47 PHE 0.020 0.001 PHE A 352 TYR 0.010 0.001 TYR B 555 ARG 0.002 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.03400 ( 465) hydrogen bonds : angle 3.86974 ( 1290) covalent geometry : bond 0.00236 (10989) covalent geometry : angle 0.47848 (14978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9297 (m) cc_final: 0.9042 (t) REVERT: A 414 ASN cc_start: 0.8057 (m-40) cc_final: 0.7782 (p0) REVERT: A 568 ILE cc_start: 0.8993 (tp) cc_final: 0.8542 (pt) REVERT: A 575 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 585 GLN cc_start: 0.8290 (tt0) cc_final: 0.8039 (tp40) REVERT: A 598 LYS cc_start: 0.8689 (mmtt) cc_final: 0.7561 (tptm) REVERT: B 118 ARG cc_start: 0.7941 (mmm-85) cc_final: 0.7505 (tpp80) REVERT: B 157 LEU cc_start: 0.8458 (mt) cc_final: 0.7990 (mp) REVERT: B 169 ASP cc_start: 0.7920 (m-30) cc_final: 0.7548 (m-30) REVERT: B 175 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5949 (mp0) REVERT: B 287 LYS cc_start: 0.7956 (tmtt) cc_final: 0.7480 (mtmt) REVERT: B 296 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5725 (mt-10) REVERT: B 353 ARG cc_start: 0.8104 (ptp-170) cc_final: 0.7500 (ptm-80) REVERT: B 442 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8432 (tp40) REVERT: B 481 LYS cc_start: 0.8553 (mttt) cc_final: 0.7982 (ptpt) REVERT: B 670 ARG cc_start: 0.6969 (mtp180) cc_final: 0.6579 (ptt180) REVERT: C 47 MET cc_start: 0.8104 (tpp) cc_final: 0.7532 (tpt) REVERT: C 113 ARG cc_start: 0.4141 (OUTLIER) cc_final: 0.3583 (mpt180) outliers start: 34 outliers final: 23 residues processed: 188 average time/residue: 0.2433 time to fit residues: 63.8470 Evaluate side-chains 180 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 296 GLU Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain C residue 73 ASP Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 60 optimal weight: 0.0010 chunk 23 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN ** C 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.129417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.106021 restraints weight = 16564.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.108980 restraints weight = 8402.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.111002 restraints weight = 5482.634| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10989 Z= 0.113 Angle : 0.494 10.065 14978 Z= 0.254 Chirality : 0.039 0.155 1654 Planarity : 0.003 0.037 1818 Dihedral : 11.958 79.058 1815 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.36 % Allowed : 18.12 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1243 helix: 1.72 (0.23), residues: 542 sheet: 0.13 (0.51), residues: 119 loop : -1.47 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 363 HIS 0.006 0.001 HIS C 233 PHE 0.021 0.001 PHE A 352 TYR 0.011 0.001 TYR A 475 ARG 0.002 0.000 ARG B 468 Details of bonding type rmsd hydrogen bonds : bond 0.03540 ( 465) hydrogen bonds : angle 3.88136 ( 1290) covalent geometry : bond 0.00264 (10989) covalent geometry : angle 0.49391 (14978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2486 Ramachandran restraints generated. 1243 Oldfield, 0 Emsley, 1243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 155 time to evaluate : 1.269 Fit side-chains revert: symmetry clash REVERT: A 218 SER cc_start: 0.9286 (m) cc_final: 0.9051 (t) REVERT: A 414 ASN cc_start: 0.8050 (m-40) cc_final: 0.7784 (p0) REVERT: A 568 ILE cc_start: 0.8995 (tp) cc_final: 0.8524 (pt) REVERT: A 575 GLU cc_start: 0.8142 (mt-10) cc_final: 0.7820 (mt-10) REVERT: A 585 GLN cc_start: 0.8254 (tt0) cc_final: 0.8004 (tp40) REVERT: A 598 LYS cc_start: 0.8674 (mmtt) cc_final: 0.7554 (tptm) REVERT: B 118 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7519 (tpp80) REVERT: B 157 LEU cc_start: 0.8463 (mt) cc_final: 0.7976 (mp) REVERT: B 169 ASP cc_start: 0.7932 (m-30) cc_final: 0.7531 (m-30) REVERT: B 175 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5956 (mp0) REVERT: B 287 LYS cc_start: 0.7962 (tmtt) cc_final: 0.7482 (mtmt) REVERT: B 353 ARG cc_start: 0.8006 (ptp-170) cc_final: 0.7614 (ptm160) REVERT: B 392 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.9014 (tt) REVERT: B 442 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8465 (tp40) REVERT: B 481 LYS cc_start: 0.8564 (mttt) cc_final: 0.8010 (ptpt) REVERT: B 670 ARG cc_start: 0.6989 (mtp180) cc_final: 0.6589 (ptt180) REVERT: C 47 MET cc_start: 0.8106 (tpp) cc_final: 0.7529 (tpt) REVERT: C 113 ARG cc_start: 0.4110 (OUTLIER) cc_final: 0.3565 (mpt180) outliers start: 26 outliers final: 22 residues processed: 172 average time/residue: 0.2695 time to fit residues: 64.1102 Evaluate side-chains 175 residues out of total 1106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLN Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 315 TRP Chi-restraints excluded: chain A residue 418 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 507 ARG Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 263 CYS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 368 ILE Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 392 ILE Chi-restraints excluded: chain B residue 442 GLN Chi-restraints excluded: chain B residue 610 CYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain C residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.3851 > 50: distance: 54 - 58: 13.509 distance: 58 - 59: 43.315 distance: 58 - 189: 11.782 distance: 59 - 60: 55.611 distance: 59 - 62: 17.473 distance: 60 - 61: 30.295 distance: 60 - 64: 49.473 distance: 61 - 186: 6.273 distance: 62 - 63: 41.601 distance: 64 - 65: 22.088 distance: 65 - 66: 61.551 distance: 65 - 68: 53.438 distance: 66 - 67: 52.137 distance: 66 - 72: 48.797 distance: 68 - 69: 6.091 distance: 69 - 70: 39.399 distance: 69 - 71: 31.468 distance: 72 - 73: 46.423 distance: 73 - 74: 17.517 distance: 73 - 76: 21.630 distance: 74 - 75: 43.789 distance: 74 - 79: 46.420 distance: 76 - 77: 45.125 distance: 76 - 78: 34.421 distance: 79 - 80: 34.226 distance: 80 - 81: 40.833 distance: 80 - 83: 21.935 distance: 81 - 82: 42.093 distance: 81 - 87: 41.323 distance: 83 - 84: 34.525 distance: 84 - 85: 32.686 distance: 84 - 86: 41.682 distance: 87 - 88: 40.913 distance: 87 - 93: 22.705 distance: 88 - 89: 51.404 distance: 88 - 91: 37.221 distance: 89 - 90: 38.946 distance: 89 - 94: 33.463 distance: 91 - 92: 51.507 distance: 92 - 93: 25.599 distance: 94 - 95: 12.758 distance: 95 - 96: 51.656 distance: 95 - 98: 28.075 distance: 96 - 97: 44.558 distance: 96 - 105: 60.786 distance: 98 - 99: 27.363 distance: 99 - 100: 25.529 distance: 100 - 101: 21.019 distance: 101 - 102: 21.569 distance: 102 - 103: 22.281 distance: 102 - 104: 13.035 distance: 105 - 106: 41.985 distance: 106 - 107: 31.653 distance: 106 - 109: 29.333 distance: 107 - 108: 48.225 distance: 107 - 113: 21.417 distance: 109 - 110: 39.330 distance: 110 - 111: 69.385 distance: 110 - 112: 45.470 distance: 113 - 114: 22.599 distance: 114 - 115: 42.141 distance: 114 - 117: 15.763 distance: 115 - 116: 44.340 distance: 115 - 122: 44.156 distance: 117 - 118: 16.121 distance: 118 - 119: 15.188 distance: 119 - 120: 28.791 distance: 119 - 121: 10.590 distance: 122 - 123: 33.323 distance: 123 - 124: 25.538 distance: 123 - 126: 33.870 distance: 124 - 125: 15.976 distance: 124 - 130: 4.982 distance: 126 - 127: 15.998 distance: 126 - 128: 39.791 distance: 127 - 129: 15.872 distance: 130 - 131: 17.262 distance: 131 - 132: 41.199 distance: 131 - 134: 34.319 distance: 132 - 133: 55.558 distance: 132 - 140: 34.283 distance: 134 - 135: 25.680 distance: 135 - 136: 45.722 distance: 135 - 137: 15.263 distance: 136 - 138: 32.250 distance: 138 - 139: 4.891