Starting phenix.real_space_refine on Fri Apr 5 21:52:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/04_2024/8tgk_41239_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/04_2024/8tgk_41239.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/04_2024/8tgk_41239_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/04_2024/8tgk_41239_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/04_2024/8tgk_41239_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/04_2024/8tgk_41239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/04_2024/8tgk_41239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/04_2024/8tgk_41239_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tgk_41239/04_2024/8tgk_41239_trim_updated.pdb" } resolution = 3.7 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= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 3837 2.51 5 N 900 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 5772 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 384, 2864 Classifications: {'peptide': 384} Link IDs: {'PTRANS': 23, 'TRANS': 360} Chain breaks: 1 Chain: "B" Number of atoms: 2856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 2856 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 21, 'TRANS': 360} Chain breaks: 2 Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'HSM': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'YHR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.62, per 1000 atoms: 0.63 Number of scatterers: 5772 At special positions: 0 Unit cell: (72.5973, 63.744, 114.208, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 978 8.00 N 900 7.00 C 3837 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 - 3.50 Amino acid : False - 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: 2.69 Conformation dependent library (CDL) restraints added in 1.3 seconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 0 sheets defined 84.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 20 through 39 removed outlier: 3.839A pdb=" N LEU A 24 " --> pdb=" O ARG A 20 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 50 removed outlier: 3.789A pdb=" N TYR A 50 " --> pdb=" O PRO A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 removed outlier: 3.550A pdb=" N LEU A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N PHE A 143 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 removed outlier: 3.502A pdb=" N MET A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Proline residue: A 155 - end of helix Proline residue: A 159 - end of helix removed outlier: 4.227A pdb=" N ASN A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 186 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 195 through 218 Processing helix chain 'A' and resid 222 through 254 removed outlier: 4.126A pdb=" N ARG A 227 " --> pdb=" O HIS A 223 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) Proline residue: A 245 - end of helix Processing helix chain 'A' and resid 257 through 277 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.777A pdb=" N LYS A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 330 removed outlier: 3.990A pdb=" N LEU A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLU A 320 " --> pdb=" O VAL A 316 " (cutoff:3.500A) Proline residue: A 321 - end of helix Proline residue: A 324 - end of helix Processing helix chain 'A' and resid 335 through 341 removed outlier: 4.167A pdb=" N GLY A 339 " --> pdb=" O TRP A 336 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 341 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 363 removed outlier: 5.086A pdb=" N ASN A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 362 " --> pdb=" O VAL A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Proline residue: A 384 - end of helix Processing helix chain 'A' and resid 390 through 421 removed outlier: 3.527A pdb=" N ILE A 393 " --> pdb=" O PHE A 390 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N GLY A 394 " --> pdb=" O GLY A 391 " (cutoff:3.500A) Proline residue: A 395 - end of helix removed outlier: 3.512A pdb=" N ASP A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET A 411 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 412 - end of helix removed outlier: 4.063A pdb=" N ARG A 421 " --> pdb=" O VAL A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 454 removed outlier: 3.924A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) Proline residue: A 445 - end of helix removed outlier: 5.337A pdb=" N GLY A 449 " --> pdb=" O PRO A 445 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ALA A 450 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 479 Proline residue: A 473 - end of helix removed outlier: 4.913A pdb=" N TYR A 476 " --> pdb=" O ALA A 472 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TYR A 477 " --> pdb=" O PRO A 473 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N LEU A 478 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG A 479 " --> pdb=" O CYS A 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 53 removed outlier: 4.071A pdb=" N LEU B 24 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL B 42 " --> pdb=" O PHE B 38 " (cutoff:3.500A) Proline residue: B 43 - end of helix Proline residue: B 46 - end of helix removed outlier: 3.689A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 164 removed outlier: 4.443A pdb=" N THR B 137 " --> pdb=" O GLU B 133 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 143 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA B 147 " --> pdb=" O PHE B 143 " (cutoff:3.500A) Proline residue: B 155 - end of helix removed outlier: 4.199A pdb=" N GLY B 158 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Proline residue: B 159 - end of helix removed outlier: 3.798A pdb=" N ASN B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 186 removed outlier: 3.536A pdb=" N ALA B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 218 removed outlier: 3.513A pdb=" N VAL B 195 " --> pdb=" O THR B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 249 removed outlier: 4.282A pdb=" N ALA B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) Proline residue: B 245 - end of helix removed outlier: 3.808A pdb=" N SER B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 275 removed outlier: 3.547A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 5.194A pdb=" N LYS B 298 " --> pdb=" O PHE B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 330 removed outlier: 4.212A pdb=" N GLY B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU B 319 " --> pdb=" O GLY B 315 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) Proline residue: B 321 - end of helix Proline residue: B 324 - end of helix Processing helix chain 'B' and resid 340 through 363 Proline residue: B 344 - end of helix removed outlier: 4.798A pdb=" N SER B 348 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE B 356 " --> pdb=" O THR B 353 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA B 360 " --> pdb=" O GLY B 357 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN B 361 " --> pdb=" O VAL B 358 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N MET B 363 " --> pdb=" O ALA B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 Proline residue: B 384 - end of helix Processing helix chain 'B' and resid 389 through 420 removed outlier: 3.590A pdb=" N ILE B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B 394 " --> pdb=" O GLY B 391 " (cutoff:3.500A) Proline residue: B 395 - end of helix removed outlier: 3.505A pdb=" N ASP B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER B 408 " --> pdb=" O MET B 405 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N MET B 411 " --> pdb=" O SER B 408 " (cutoff:3.500A) Proline residue: B 412 - end of helix removed outlier: 3.602A pdb=" N LEU B 420 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 454 Proline residue: B 445 - end of helix removed outlier: 3.829A pdb=" N GLY B 449 " --> pdb=" O PRO B 445 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ALA B 450 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 478 removed outlier: 3.597A pdb=" N MET B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) Proline residue: B 473 - end of helix removed outlier: 5.114A pdb=" N TYR B 476 " --> pdb=" O ALA B 472 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N TYR B 477 " --> pdb=" O PRO B 473 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LEU B 478 " --> pdb=" O LEU B 474 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 861 1.31 - 1.44: 1567 1.44 - 1.56: 3386 1.56 - 1.69: 2 1.69 - 1.81: 100 Bond restraints: 5916 Sorted by residual: bond pdb=" C10 YHR B 601 " pdb=" C11 YHR B 601 " ideal model delta sigma weight residual 1.572 1.433 0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" CG HSM A 601 " pdb=" ND1 HSM A 601 " ideal model delta sigma weight residual 1.383 1.314 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C13 YHR B 601 " pdb=" C14 YHR B 601 " ideal model delta sigma weight residual 1.567 1.499 0.068 2.00e-02 2.50e+03 1.16e+01 bond pdb=" CD2 HSM A 601 " pdb=" NE2 HSM A 601 " ideal model delta sigma weight residual 1.376 1.313 0.063 2.00e-02 2.50e+03 1.00e+01 bond pdb=" N ILE B 136 " pdb=" CA ILE B 136 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.88e+00 ... (remaining 5911 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.70: 180 105.70 - 113.61: 3297 113.61 - 121.51: 3496 121.51 - 129.41: 1054 129.41 - 137.32: 31 Bond angle restraints: 8058 Sorted by residual: angle pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C9 YHR B 601 " ideal model delta sigma weight residual 99.45 132.70 -33.25 3.00e+00 1.11e-01 1.23e+02 angle pdb=" N PHE B 131 " pdb=" CA PHE B 131 " pdb=" C PHE B 131 " ideal model delta sigma weight residual 112.92 99.68 13.24 1.23e+00 6.61e-01 1.16e+02 angle pdb=" N GLY B 243 " pdb=" CA GLY B 243 " pdb=" C GLY B 243 " ideal model delta sigma weight residual 112.50 118.55 -6.05 1.16e+00 7.43e-01 2.72e+01 angle pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta sigma weight residual 103.25 97.80 5.45 1.05e+00 9.07e-01 2.69e+01 angle pdb=" C25 YHR B 601 " pdb=" C26 YHR B 601 " pdb=" O28 YHR B 601 " ideal model delta sigma weight residual 137.71 122.23 15.48 3.00e+00 1.11e-01 2.66e+01 ... (remaining 8053 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.43: 3054 22.43 - 44.85: 326 44.85 - 67.28: 43 67.28 - 89.71: 2 89.71 - 112.13: 2 Dihedral angle restraints: 3427 sinusoidal: 1272 harmonic: 2155 Sorted by residual: dihedral pdb=" CA PRO A 43 " pdb=" C PRO A 43 " pdb=" N ILE A 44 " pdb=" CA ILE A 44 " ideal model delta harmonic sigma weight residual -180.00 -158.98 -21.02 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C13 YHR B 601 " pdb=" C7 YHR B 601 " pdb=" N8 YHR B 601 " pdb=" C6 YHR B 601 " ideal model delta sinusoidal sigma weight residual 53.17 -58.96 112.13 1 3.00e+01 1.11e-03 1.47e+01 dihedral pdb=" C PRO B 482 " pdb=" N PRO B 482 " pdb=" CA PRO B 482 " pdb=" CB PRO B 482 " ideal model delta harmonic sigma weight residual -120.70 -111.15 -9.55 0 2.50e+00 1.60e-01 1.46e+01 ... (remaining 3424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 809 0.058 - 0.116: 137 0.116 - 0.175: 17 0.175 - 0.233: 2 0.233 - 0.291: 3 Chirality restraints: 968 Sorted by residual: chirality pdb=" CA PHE B 131 " pdb=" N PHE B 131 " pdb=" C PHE B 131 " pdb=" CB PHE B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" C6 YHR B 601 " pdb=" C15 YHR B 601 " pdb=" C5 YHR B 601 " pdb=" C7 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.70 2.43 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C15 YHR B 601 " pdb=" C14 YHR B 601 " pdb=" C16 YHR B 601 " pdb=" C6 YHR B 601 " both_signs ideal model delta sigma weight residual False 2.66 2.42 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 965 not shown) Planarity restraints: 982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 472 " 0.090 5.00e-02 4.00e+02 1.34e-01 2.88e+01 pdb=" N PRO A 473 " -0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 473 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO A 473 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 20 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.30e+01 pdb=" C ARG B 20 " 0.062 2.00e-02 2.50e+03 pdb=" O ARG B 20 " -0.023 2.00e-02 2.50e+03 pdb=" N GLN B 21 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 42 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO B 43 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 43 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 43 " -0.039 5.00e-02 4.00e+02 ... (remaining 979 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 572 2.74 - 3.28: 6067 3.28 - 3.82: 9639 3.82 - 4.36: 10536 4.36 - 4.90: 18982 Nonbonded interactions: 45796 Sorted by model distance: nonbonded pdb=" O ALA B 442 " pdb=" OG SER B 446 " model vdw 2.204 2.440 nonbonded pdb=" O GLY B 140 " pdb=" N PHE B 143 " model vdw 2.262 2.520 nonbonded pdb=" O SER A 424 " pdb=" OG SER A 424 " model vdw 2.274 2.440 nonbonded pdb=" OG SER A 333 " pdb=" OE1 GLN A 337 " model vdw 2.293 2.440 nonbonded pdb=" O GLN B 21 " pdb=" N LEU B 24 " model vdw 2.303 2.520 ... (remaining 45791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 278 or resid 288 through 483)) selection = (chain 'B' and (resid 19 through 51 or resid 135 through 483)) } 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: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.650 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.890 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.139 5916 Z= 0.358 Angle : 0.970 33.250 8058 Z= 0.509 Chirality : 0.047 0.291 968 Planarity : 0.009 0.134 982 Dihedral : 17.061 112.134 2057 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.66 % Allowed : 1.72 % Favored : 97.62 % Rotamer: Outliers : 0.81 % Allowed : 34.47 % Favored : 64.72 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.29), residues: 756 helix: 1.03 (0.21), residues: 588 sheet: None (None), residues: 0 loop : -1.29 (0.44), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 326 HIS 0.003 0.001 HIS B 416 PHE 0.039 0.002 PHE B 48 TYR 0.009 0.001 TYR A 251 ARG 0.005 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 134 time to evaluate : 0.676 Fit side-chains REVERT: A 160 LEU cc_start: 0.8559 (tp) cc_final: 0.8290 (tt) REVERT: A 414 MET cc_start: 0.7811 (mmm) cc_final: 0.7286 (mmm) REVERT: B 132 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6711 (mm) REVERT: B 135 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6711 (mp0) REVERT: B 250 MET cc_start: 0.7854 (ttp) cc_final: 0.6951 (ppp) REVERT: B 291 THR cc_start: 0.8024 (m) cc_final: 0.7745 (p) REVERT: B 355 LEU cc_start: 0.7929 (tp) cc_final: 0.7649 (tt) outliers start: 5 outliers final: 2 residues processed: 137 average time/residue: 0.1469 time to fit residues: 27.4717 Evaluate side-chains 129 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 125 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 482 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 19 optimal weight: 0.2980 chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 59 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5916 Z= 0.243 Angle : 0.660 7.291 8058 Z= 0.332 Chirality : 0.044 0.191 968 Planarity : 0.006 0.042 982 Dihedral : 6.484 52.929 834 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 5.04 % Allowed : 29.43 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.93 (0.31), residues: 756 helix: 1.17 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.50 (0.48), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.003 0.000 HIS A 167 PHE 0.023 0.002 PHE A 356 TYR 0.009 0.001 TYR A 349 ARG 0.002 0.000 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 130 time to evaluate : 0.504 Fit side-chains REVERT: A 157 VAL cc_start: 0.8481 (t) cc_final: 0.8234 (p) REVERT: A 160 LEU cc_start: 0.8567 (tp) cc_final: 0.8296 (tt) REVERT: A 212 LEU cc_start: 0.6733 (mt) cc_final: 0.6311 (mp) REVERT: A 250 MET cc_start: 0.7399 (mmm) cc_final: 0.7155 (mmm) REVERT: A 411 MET cc_start: 0.8303 (mmt) cc_final: 0.7956 (mmm) REVERT: A 414 MET cc_start: 0.7634 (mmm) cc_final: 0.7118 (mmm) REVERT: B 135 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.6657 (mp0) REVERT: B 153 VAL cc_start: 0.8383 (t) cc_final: 0.8111 (p) REVERT: B 250 MET cc_start: 0.7888 (ttp) cc_final: 0.7561 (ttp) REVERT: B 439 MET cc_start: 0.7803 (mmm) cc_final: 0.7524 (mmm) outliers start: 31 outliers final: 13 residues processed: 146 average time/residue: 0.1390 time to fit residues: 28.1881 Evaluate side-chains 144 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.0980 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 61 optimal weight: 0.0170 chunk 68 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5916 Z= 0.244 Angle : 0.633 9.068 8058 Z= 0.311 Chirality : 0.043 0.151 968 Planarity : 0.005 0.035 982 Dihedral : 5.916 55.063 826 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 6.02 % Allowed : 28.94 % Favored : 65.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.31), residues: 756 helix: 1.27 (0.22), residues: 603 sheet: None (None), residues: 0 loop : -1.63 (0.47), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.002 0.000 HIS A 167 PHE 0.025 0.001 PHE A 356 TYR 0.012 0.001 TYR A 349 ARG 0.002 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 0.615 Fit side-chains revert: symmetry clash REVERT: A 38 PHE cc_start: 0.8446 (t80) cc_final: 0.8183 (t80) REVERT: A 41 VAL cc_start: 0.8263 (OUTLIER) cc_final: 0.8050 (p) REVERT: A 157 VAL cc_start: 0.8461 (t) cc_final: 0.8254 (p) REVERT: A 246 PHE cc_start: 0.7796 (t80) cc_final: 0.7575 (t80) REVERT: A 370 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7876 (tp) REVERT: A 411 MET cc_start: 0.8308 (mmt) cc_final: 0.8097 (mmp) REVERT: A 414 MET cc_start: 0.7574 (mmm) cc_final: 0.7111 (mmm) REVERT: B 48 PHE cc_start: 0.8556 (t80) cc_final: 0.8336 (t80) REVERT: B 135 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6605 (mp0) REVERT: B 153 VAL cc_start: 0.8365 (t) cc_final: 0.8091 (p) REVERT: B 250 MET cc_start: 0.7963 (ttp) cc_final: 0.7478 (ttp) REVERT: B 411 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7618 (mpp) REVERT: B 439 MET cc_start: 0.7757 (mmm) cc_final: 0.7429 (mmm) outliers start: 37 outliers final: 23 residues processed: 152 average time/residue: 0.1405 time to fit residues: 29.7489 Evaluate side-chains 153 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 36 optimal weight: 0.2980 chunk 65 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5916 Z= 0.282 Angle : 0.638 6.533 8058 Z= 0.317 Chirality : 0.044 0.170 968 Planarity : 0.005 0.036 982 Dihedral : 5.934 62.429 826 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 6.18 % Allowed : 28.29 % Favored : 65.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.00 (0.32), residues: 756 helix: 1.24 (0.22), residues: 607 sheet: None (None), residues: 0 loop : -1.59 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 PHE 0.027 0.001 PHE A 356 TYR 0.015 0.002 TYR A 349 ARG 0.002 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 129 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8397 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 157 VAL cc_start: 0.8457 (t) cc_final: 0.8226 (p) REVERT: A 229 MET cc_start: 0.7409 (mmm) cc_final: 0.7112 (mmm) REVERT: A 254 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.7655 (p) REVERT: A 370 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7937 (tp) REVERT: A 411 MET cc_start: 0.8454 (mmt) cc_final: 0.8221 (mmp) REVERT: B 153 VAL cc_start: 0.8362 (t) cc_final: 0.8103 (p) REVERT: B 250 MET cc_start: 0.7947 (ttp) cc_final: 0.7534 (ttt) REVERT: B 411 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7661 (mpp) REVERT: B 439 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7552 (mmm) outliers start: 38 outliers final: 21 residues processed: 148 average time/residue: 0.1247 time to fit residues: 26.0641 Evaluate side-chains 154 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 128 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 419 ASP Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5916 Z= 0.259 Angle : 0.641 10.018 8058 Z= 0.313 Chirality : 0.043 0.148 968 Planarity : 0.005 0.038 982 Dihedral : 5.679 61.751 823 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.85 % Allowed : 28.46 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.03 (0.32), residues: 756 helix: 1.28 (0.22), residues: 603 sheet: None (None), residues: 0 loop : -1.63 (0.48), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 PHE 0.028 0.001 PHE A 356 TYR 0.013 0.001 TYR A 349 ARG 0.002 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 125 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8203 (p) REVERT: A 157 VAL cc_start: 0.8435 (t) cc_final: 0.8189 (p) REVERT: A 229 MET cc_start: 0.7465 (mmm) cc_final: 0.7169 (mmm) REVERT: A 313 ASN cc_start: 0.7579 (OUTLIER) cc_final: 0.6964 (m-40) REVERT: A 370 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7898 (tp) REVERT: A 411 MET cc_start: 0.8448 (mmt) cc_final: 0.8203 (mmp) REVERT: A 414 MET cc_start: 0.7621 (mmm) cc_final: 0.7249 (mmm) REVERT: B 153 VAL cc_start: 0.8386 (t) cc_final: 0.8106 (p) REVERT: B 250 MET cc_start: 0.7872 (ttp) cc_final: 0.7475 (ttt) REVERT: B 316 VAL cc_start: 0.8004 (OUTLIER) cc_final: 0.7759 (m) REVERT: B 411 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7698 (mpp) REVERT: B 439 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7517 (mmm) outliers start: 36 outliers final: 22 residues processed: 145 average time/residue: 0.1481 time to fit residues: 29.6971 Evaluate side-chains 152 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 439 MET Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 0.0980 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5916 Z= 0.259 Angle : 0.630 8.288 8058 Z= 0.311 Chirality : 0.043 0.156 968 Planarity : 0.005 0.053 982 Dihedral : 5.705 63.873 823 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.18 % Allowed : 28.13 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.32), residues: 756 helix: 1.32 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.66 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 PHE 0.026 0.001 PHE A 38 TYR 0.014 0.001 TYR A 349 ARG 0.001 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 120 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8431 (OUTLIER) cc_final: 0.8207 (p) REVERT: A 153 VAL cc_start: 0.8079 (t) cc_final: 0.7749 (p) REVERT: A 157 VAL cc_start: 0.8438 (t) cc_final: 0.8227 (p) REVERT: A 160 LEU cc_start: 0.8498 (tp) cc_final: 0.8268 (tt) REVERT: A 229 MET cc_start: 0.7475 (mmm) cc_final: 0.7132 (mmm) REVERT: A 246 PHE cc_start: 0.7730 (t80) cc_final: 0.7526 (t80) REVERT: A 254 VAL cc_start: 0.7989 (OUTLIER) cc_final: 0.7761 (p) REVERT: A 268 LEU cc_start: 0.8040 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 313 ASN cc_start: 0.7588 (OUTLIER) cc_final: 0.6955 (m-40) REVERT: A 370 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7892 (tp) REVERT: B 153 VAL cc_start: 0.8388 (t) cc_final: 0.8102 (p) REVERT: B 250 MET cc_start: 0.7861 (ttp) cc_final: 0.7459 (ttt) REVERT: B 316 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7769 (m) REVERT: B 411 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7656 (mpp) REVERT: B 439 MET cc_start: 0.7821 (mmm) cc_final: 0.7555 (mmm) outliers start: 38 outliers final: 22 residues processed: 144 average time/residue: 0.1369 time to fit residues: 27.6278 Evaluate side-chains 148 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 119 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 274 GLN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 370 LEU Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 8 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 73 optimal weight: 0.4980 chunk 45 optimal weight: 0.0170 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 29 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5916 Z= 0.228 Angle : 0.620 10.251 8058 Z= 0.302 Chirality : 0.042 0.136 968 Planarity : 0.005 0.051 982 Dihedral : 5.637 62.283 823 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.18 % Allowed : 27.97 % Favored : 65.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.32), residues: 756 helix: 1.39 (0.22), residues: 602 sheet: None (None), residues: 0 loop : -1.63 (0.49), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 326 HIS 0.002 0.001 HIS A 167 PHE 0.024 0.001 PHE A 38 TYR 0.013 0.001 TYR A 349 ARG 0.001 0.000 ARG A 421 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 0.641 Fit side-chains revert: symmetry clash REVERT: A 41 VAL cc_start: 0.8430 (OUTLIER) cc_final: 0.8215 (p) REVERT: A 153 VAL cc_start: 0.8063 (t) cc_final: 0.7737 (p) REVERT: A 157 VAL cc_start: 0.8431 (t) cc_final: 0.8207 (p) REVERT: A 229 MET cc_start: 0.7460 (mmm) cc_final: 0.7142 (mmm) REVERT: A 246 PHE cc_start: 0.7686 (t80) cc_final: 0.7481 (t80) REVERT: A 254 VAL cc_start: 0.7983 (OUTLIER) cc_final: 0.7734 (p) REVERT: A 268 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7836 (mm) REVERT: A 313 ASN cc_start: 0.7553 (OUTLIER) cc_final: 0.6904 (m-40) REVERT: A 414 MET cc_start: 0.7558 (mmm) cc_final: 0.7162 (mtm) REVERT: B 153 VAL cc_start: 0.8378 (t) cc_final: 0.8093 (p) REVERT: B 250 MET cc_start: 0.7813 (ttp) cc_final: 0.7420 (ttt) REVERT: B 316 VAL cc_start: 0.8014 (OUTLIER) cc_final: 0.7778 (m) REVERT: B 405 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.6978 (ttm) REVERT: B 411 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7620 (mpp) REVERT: B 439 MET cc_start: 0.7795 (mmm) cc_final: 0.7524 (mmm) outliers start: 38 outliers final: 21 residues processed: 143 average time/residue: 0.1325 time to fit residues: 26.4531 Evaluate side-chains 149 residues out of total 615 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 MET Chi-restraints excluded: chain A residue 455 ILE Chi-restraints excluded: chain A residue 464 THR Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 198 THR Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 293 LEU Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 409 SER Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 474 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/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-5288/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-5288/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-5288/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-5288/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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-5288/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-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 72.2633 > 50: distance: 3 - 5: 33.881 distance: 5 - 6: 57.649 distance: 6 - 7: 67.940 distance: 7 - 8: 69.400 distance: 7 - 12: 57.075 distance: 9 - 10: 69.321 distance: 9 - 11: 64.356 distance: 12 - 13: 55.295 distance: 12 - 18: 40.637 distance: 13 - 16: 40.961 distance: 14 - 15: 41.118 distance: 14 - 19: 56.829 distance: 16 - 17: 53.813 distance: 17 - 18: 52.574 distance: 19 - 20: 40.467 distance: 20 - 21: 39.962 distance: 20 - 23: 57.185 distance: 21 - 22: 57.242 distance: 21 - 27: 57.877 distance: 22 - 54: 3.247 distance: 23 - 24: 39.312 distance: 24 - 25: 38.696 distance: 24 - 26: 39.640 distance: 27 - 28: 30.952 distance: 28 - 29: 41.055 distance: 28 - 31: 40.131 distance: 29 - 30: 55.596 distance: 29 - 38: 39.056 distance: 31 - 32: 55.149 distance: 32 - 33: 40.901 distance: 32 - 34: 38.671 distance: 33 - 35: 54.020 distance: 34 - 36: 67.245 distance: 35 - 37: 55.799 distance: 36 - 37: 34.947 distance: 38 - 39: 41.083 distance: 39 - 40: 39.102 distance: 39 - 42: 56.848 distance: 40 - 41: 57.557 distance: 40 - 46: 56.421 distance: 42 - 43: 56.196 distance: 43 - 44: 68.431 distance: 44 - 45: 56.966 distance: 46 - 47: 39.389 distance: 47 - 48: 40.427 distance: 47 - 50: 40.810 distance: 48 - 49: 40.641 distance: 48 - 54: 41.222 distance: 50 - 51: 56.195 distance: 51 - 52: 56.916 distance: 51 - 53: 39.385 distance: 54 - 55: 38.995 distance: 55 - 56: 56.638 distance: 55 - 58: 39.050 distance: 56 - 57: 56.240 distance: 56 - 62: 57.335 distance: 58 - 59: 56.122 distance: 59 - 60: 60.694 distance: 59 - 61: 70.721 distance: 62 - 63: 47.357 distance: 63 - 64: 47.180 distance: 63 - 66: 41.565 distance: 64 - 65: 69.906 distance: 64 - 71: 39.751 distance: 66 - 67: 55.736 distance: 67 - 68: 70.897 distance: 68 - 69: 55.503 distance: 69 - 70: 38.874 distance: 71 - 72: 40.325 distance: 72 - 73: 39.653 distance: 72 - 75: 67.897 distance: 73 - 74: 56.757 distance: 75 - 76: 41.169 distance: 76 - 77: 42.313 distance: 76 - 78: 38.818 distance: 79 - 80: 59.335 distance: 79 - 85: 56.687 distance: 80 - 81: 46.680 distance: 80 - 83: 24.460 distance: 81 - 82: 48.884 distance: 81 - 86: 28.211 distance: 82 - 109: 32.730 distance: 83 - 84: 57.063 distance: 84 - 85: 69.189