Starting phenix.real_space_refine on Wed Apr 30 20:46:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9exh_50038/04_2025/9exh_50038.cif Found real_map, /net/cci-nas-00/data/ceres_data/9exh_50038/04_2025/9exh_50038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9exh_50038/04_2025/9exh_50038.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9exh_50038/04_2025/9exh_50038.map" model { file = "/net/cci-nas-00/data/ceres_data/9exh_50038/04_2025/9exh_50038.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9exh_50038/04_2025/9exh_50038.cif" } resolution = 3.9 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= 0.017 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 42 5.16 5 C 6195 2.51 5 N 1660 2.21 5 O 1831 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 9728 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1205, 9728 Classifications: {'peptide': 1205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 40, 'TRANS': 1164} Time building chain proxies: 6.24, per 1000 atoms: 0.64 Number of scatterers: 9728 At special positions: 0 Unit cell: (77.52, 104.72, 137.36, 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 42 16.00 O 1831 8.00 N 1660 7.00 C 6195 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: 2.44 Conformation dependent library (CDL) restraints added in 1.2 seconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2268 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 6 sheets defined 56.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.817A pdb=" N ASN A 5 " --> pdb=" O MET A 1 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 28 removed outlier: 3.611A pdb=" N ASN A 15 " --> pdb=" O PRO A 11 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 removed outlier: 3.597A pdb=" N GLN A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 102 Processing helix chain 'A' and resid 121 through 124 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 137 through 148 Processing helix chain 'A' and resid 150 through 168 removed outlier: 4.249A pdb=" N HIS A 168 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 183 Processing helix chain 'A' and resid 194 through 201 removed outlier: 4.064A pdb=" N GLY A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.752A pdb=" N GLU A 209 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A 210 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.872A pdb=" N GLY A 215 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 218 " --> pdb=" O ILE A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 229 removed outlier: 3.753A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 243 removed outlier: 4.074A pdb=" N ALA A 242 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 243 " --> pdb=" O PRO A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 removed outlier: 3.559A pdb=" N ASN A 258 " --> pdb=" O TYR A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 268 removed outlier: 3.640A pdb=" N GLN A 263 " --> pdb=" O SER A 259 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.994A pdb=" N ILE A 307 " --> pdb=" O PRO A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 335 Processing helix chain 'A' and resid 337 through 339 No H-bonds generated for 'chain 'A' and resid 337 through 339' Processing helix chain 'A' and resid 340 through 349 removed outlier: 3.712A pdb=" N LEU A 344 " --> pdb=" O ASP A 340 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN A 348 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 349 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 375 removed outlier: 3.968A pdb=" N ASP A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 405 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.569A pdb=" N HIS A 409 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 442 removed outlier: 3.781A pdb=" N LEU A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 459 through 474 Processing helix chain 'A' and resid 478 through 499 Proline residue: A 490 - end of helix Processing helix chain 'A' and resid 518 through 529 Processing helix chain 'A' and resid 535 through 545 removed outlier: 3.602A pdb=" N MET A 539 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N PHE A 545 " --> pdb=" O MET A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 564 removed outlier: 3.623A pdb=" N PHE A 564 " --> pdb=" O SER A 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 561 through 564' Processing helix chain 'A' and resid 565 through 567 No H-bonds generated for 'chain 'A' and resid 565 through 567' Processing helix chain 'A' and resid 568 through 579 removed outlier: 3.951A pdb=" N ASN A 578 " --> pdb=" O TRP A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 637 Processing helix chain 'A' and resid 645 through 651 Processing helix chain 'A' and resid 662 through 671 removed outlier: 4.071A pdb=" N ILE A 666 " --> pdb=" O THR A 662 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS A 671 " --> pdb=" O ASN A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.564A pdb=" N PHE A 692 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU A 693 " --> pdb=" O ILE A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 688 through 693' Processing helix chain 'A' and resid 695 through 699 removed outlier: 3.673A pdb=" N VAL A 699 " --> pdb=" O TRP A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 747 Processing helix chain 'A' and resid 752 through 756 Processing helix chain 'A' and resid 784 through 786 No H-bonds generated for 'chain 'A' and resid 784 through 786' Processing helix chain 'A' and resid 798 through 807 removed outlier: 3.640A pdb=" N ASN A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 819 Processing helix chain 'A' and resid 825 through 830 Processing helix chain 'A' and resid 838 through 856 removed outlier: 3.934A pdb=" N ASP A 842 " --> pdb=" O ASN A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 removed outlier: 4.021A pdb=" N HIS A 872 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 910 Processing helix chain 'A' and resid 927 through 933 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 976 through 980 removed outlier: 4.035A pdb=" N ASN A 979 " --> pdb=" O HIS A 976 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS A 980 " --> pdb=" O GLU A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 980' Processing helix chain 'A' and resid 981 through 989 Processing helix chain 'A' and resid 1013 through 1027 Processing helix chain 'A' and resid 1030 through 1046 removed outlier: 4.178A pdb=" N TYR A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1066 Processing helix chain 'A' and resid 1066 through 1076 Processing helix chain 'A' and resid 1104 through 1135 removed outlier: 4.278A pdb=" N VAL A1115 " --> pdb=" O THR A1111 " (cutoff:3.500A) Proline residue: A1116 - end of helix removed outlier: 3.973A pdb=" N ASP A1133 " --> pdb=" O ASN A1129 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU A1134 " --> pdb=" O ASP A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1170 removed outlier: 3.547A pdb=" N ALA A1140 " --> pdb=" O SER A1136 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU A1143 " --> pdb=" O GLU A1139 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU A1146 " --> pdb=" O ARG A1142 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ARG A1147 " --> pdb=" O LEU A1143 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1170 " --> pdb=" O HIS A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1175 through 1178 Processing helix chain 'A' and resid 1179 through 1184 Processing helix chain 'A' and resid 1185 through 1188 removed outlier: 4.026A pdb=" N GLY A1188 " --> pdb=" O GLY A1185 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1185 through 1188' Processing helix chain 'A' and resid 1193 through 1199 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.553A pdb=" N PHE A 55 " --> pdb=" O TYR A 52 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 389 removed outlier: 8.507A pdb=" N VAL A 388 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A 352 " --> pdb=" O VAL A 388 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N VAL A 309 " --> pdb=" O PHE A 351 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N LEU A 353 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ASP A 311 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 506 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASP A 503 " --> pdb=" O PHE A 553 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ALA A 555 " --> pdb=" O ASP A 503 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 505 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N VAL A 557 " --> pdb=" O VAL A 505 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ALA A 507 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N MET A 559 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N THR A 602 " --> pdb=" O LEU A 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 619 through 620 removed outlier: 3.830A pdb=" N PHE A 641 " --> pdb=" O PHE A 619 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 680 removed outlier: 3.561A pdb=" N ALA A 788 " --> pdb=" O VAL A 680 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 733 through 735 Processing sheet with id=AA6, first strand: chain 'A' and resid 1001 through 1004 removed outlier: 4.138A pdb=" N GLU A1093 " --> pdb=" O LEU A1004 " (cutoff:3.500A) 442 hydrogen bonds defined for protein. 1263 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: 4.22 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3218 1.34 - 1.46: 2190 1.46 - 1.58: 4463 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 9943 Sorted by residual: bond pdb=" C ALA A 10 " pdb=" N PRO A 11 " ideal model delta sigma weight residual 1.335 1.351 -0.015 1.30e-02 5.92e+03 1.40e+00 bond pdb=" CB PRO A 656 " pdb=" CG PRO A 656 " ideal model delta sigma weight residual 1.492 1.535 -0.043 5.00e-02 4.00e+02 7.39e-01 bond pdb=" CA VAL A 600 " pdb=" CB VAL A 600 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.16e-01 bond pdb=" N PRO A 342 " pdb=" CA PRO A 342 " ideal model delta sigma weight residual 1.469 1.478 -0.009 1.28e-02 6.10e+03 4.73e-01 bond pdb=" N GLN A 150 " pdb=" CA GLN A 150 " ideal model delta sigma weight residual 1.461 1.472 -0.010 1.52e-02 4.33e+03 4.70e-01 ... (remaining 9938 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.03: 13095 1.03 - 2.05: 272 2.05 - 3.08: 52 3.08 - 4.10: 15 4.10 - 5.13: 11 Bond angle restraints: 13445 Sorted by residual: angle pdb=" N GLY A 728 " pdb=" CA GLY A 728 " pdb=" C GLY A 728 " ideal model delta sigma weight residual 111.63 115.28 -3.65 1.15e+00 7.56e-01 1.01e+01 angle pdb=" CA TYR A 86 " pdb=" CB TYR A 86 " pdb=" CG TYR A 86 " ideal model delta sigma weight residual 113.90 119.03 -5.13 1.80e+00 3.09e-01 8.12e+00 angle pdb=" N PHE A 727 " pdb=" CA PHE A 727 " pdb=" C PHE A 727 " ideal model delta sigma weight residual 108.52 112.79 -4.27 1.52e+00 4.33e-01 7.89e+00 angle pdb=" C PRO A 114 " pdb=" N GLU A 115 " pdb=" CA GLU A 115 " ideal model delta sigma weight residual 121.54 125.67 -4.13 1.91e+00 2.74e-01 4.67e+00 angle pdb=" N LYS A 8 " pdb=" CA LYS A 8 " pdb=" C LYS A 8 " ideal model delta sigma weight residual 113.72 110.66 3.06 1.52e+00 4.33e-01 4.07e+00 ... (remaining 13440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.87: 5440 10.87 - 21.73: 372 21.73 - 32.60: 111 32.60 - 43.47: 38 43.47 - 54.33: 7 Dihedral angle restraints: 5968 sinusoidal: 2444 harmonic: 3524 Sorted by residual: dihedral pdb=" CA SER A 430 " pdb=" C SER A 430 " pdb=" N ALA A 431 " pdb=" CA ALA A 431 " ideal model delta harmonic sigma weight residual 180.00 164.08 15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ARG A1017 " pdb=" CB ARG A1017 " pdb=" CG ARG A1017 " pdb=" CD ARG A1017 " ideal model delta sinusoidal sigma weight residual -180.00 -126.50 -53.50 3 1.50e+01 4.44e-03 9.21e+00 dihedral pdb=" CA LYS A1153 " pdb=" CB LYS A1153 " pdb=" CG LYS A1153 " pdb=" CD LYS A1153 " ideal model delta sinusoidal sigma weight residual -60.00 -113.47 53.47 3 1.50e+01 4.44e-03 9.21e+00 ... (remaining 5965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 983 0.030 - 0.060: 325 0.060 - 0.091: 86 0.091 - 0.121: 44 0.121 - 0.151: 6 Chirality restraints: 1444 Sorted by residual: chirality pdb=" CA TRP A 696 " pdb=" N TRP A 696 " pdb=" C TRP A 696 " pdb=" CB TRP A 696 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA VAL A 557 " pdb=" N VAL A 557 " pdb=" C VAL A 557 " pdb=" CB VAL A 557 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA ILE A1001 " pdb=" N ILE A1001 " pdb=" C ILE A1001 " pdb=" CB ILE A1001 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1441 not shown) Planarity restraints: 1749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 86 " 0.011 2.00e-02 2.50e+03 9.65e-03 1.86e+00 pdb=" CG TYR A 86 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR A 86 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 86 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 86 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 86 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 86 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1148 " 0.007 2.00e-02 2.50e+03 1.34e-02 1.80e+00 pdb=" C ASP A1148 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP A1148 " 0.009 2.00e-02 2.50e+03 pdb=" N SER A1149 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 832 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 833 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 833 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 833 " -0.017 5.00e-02 4.00e+02 ... (remaining 1746 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 705 2.74 - 3.28: 10282 3.28 - 3.82: 15929 3.82 - 4.36: 18325 4.36 - 4.90: 30798 Nonbonded interactions: 76039 Sorted by model distance: nonbonded pdb=" OG1 THR A 420 " pdb=" OG1 THR A 423 " model vdw 2.199 3.040 nonbonded pdb=" OG SER A1054 " pdb=" OE1 GLU A1057 " model vdw 2.204 3.040 nonbonded pdb=" O LYS A1152 " pdb=" OG SER A1155 " model vdw 2.235 3.040 nonbonded pdb=" O HIS A 318 " pdb=" OG1 THR A 321 " model vdw 2.240 3.040 nonbonded pdb=" O GLU A1156 " pdb=" OG SER A1159 " model vdw 2.253 3.040 ... (remaining 76034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 44.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.510 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.060 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:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 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 : 0.002 0.043 9943 Z= 0.090 Angle : 0.414 5.128 13445 Z= 0.231 Chirality : 0.036 0.151 1444 Planarity : 0.003 0.031 1749 Dihedral : 8.923 54.334 3700 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.29 % Allowed : 5.11 % Favored : 94.61 % 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: 0.79 (0.25), residues: 1203 helix: 1.78 (0.23), residues: 570 sheet: -0.27 (0.70), residues: 58 loop : -0.67 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 862 HIS 0.003 0.001 HIS A 167 PHE 0.009 0.001 PHE A 537 TYR 0.024 0.001 TYR A 86 ARG 0.001 0.000 ARG A1147 Details of bonding type rmsd hydrogen bonds : bond 0.17395 ( 442) hydrogen bonds : angle 6.50050 ( 1263) covalent geometry : bond 0.00174 ( 9943) covalent geometry : angle 0.41413 (13445) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 409 HIS cc_start: 0.7616 (t-90) cc_final: 0.7078 (t-90) REVERT: A 410 MET cc_start: 0.7418 (mtm) cc_final: 0.6805 (mtm) REVERT: A 437 MET cc_start: 0.9072 (mmm) cc_final: 0.8714 (mmm) REVERT: A 512 MET cc_start: 0.8350 (ttm) cc_final: 0.8146 (tmm) REVERT: A 517 MET cc_start: 0.7741 (mtp) cc_final: 0.7235 (mtp) REVERT: A 584 MET cc_start: 0.8796 (ttm) cc_final: 0.8400 (tmm) REVERT: A 638 MET cc_start: 0.8460 (mmp) cc_final: 0.8197 (mmm) REVERT: A 773 MET cc_start: 0.8944 (ttm) cc_final: 0.8720 (ttm) REVERT: A 948 ASP cc_start: 0.8970 (m-30) cc_final: 0.8680 (m-30) REVERT: A 1109 MET cc_start: 0.9545 (ttm) cc_final: 0.9243 (tmm) outliers start: 3 outliers final: 1 residues processed: 64 average time/residue: 0.2919 time to fit residues: 26.5287 Evaluate side-chains 38 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.3980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 70 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 253 GLN ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 ASN A1071 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.035996 restraints weight = 66117.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.037242 restraints weight = 39167.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.038121 restraints weight = 29129.445| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9943 Z= 0.132 Angle : 0.522 11.953 13445 Z= 0.276 Chirality : 0.039 0.160 1444 Planarity : 0.003 0.034 1749 Dihedral : 3.723 16.119 1322 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.67 % Allowed : 6.65 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.25), residues: 1203 helix: 2.37 (0.22), residues: 576 sheet: -0.54 (0.68), residues: 60 loop : -0.76 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 216 HIS 0.005 0.001 HIS A 586 PHE 0.009 0.001 PHE A1154 TYR 0.021 0.001 TYR A 86 ARG 0.008 0.001 ARG A1145 Details of bonding type rmsd hydrogen bonds : bond 0.04471 ( 442) hydrogen bonds : angle 4.76497 ( 1263) covalent geometry : bond 0.00287 ( 9943) covalent geometry : angle 0.52217 (13445) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 1.256 Fit side-chains revert: symmetry clash REVERT: A 98 MET cc_start: 0.9394 (tpp) cc_final: 0.9011 (tpp) REVERT: A 437 MET cc_start: 0.9011 (mmm) cc_final: 0.8590 (mmm) REVERT: A 512 MET cc_start: 0.8412 (ttm) cc_final: 0.7729 (tmm) REVERT: A 517 MET cc_start: 0.7792 (mtp) cc_final: 0.7177 (mpp) REVERT: A 584 MET cc_start: 0.8861 (ttm) cc_final: 0.8418 (tmm) REVERT: A 638 MET cc_start: 0.8485 (mmp) cc_final: 0.8154 (mmm) REVERT: A 948 ASP cc_start: 0.8907 (m-30) cc_final: 0.8659 (m-30) REVERT: A 1072 MET cc_start: 0.9254 (mtm) cc_final: 0.8971 (mtm) REVERT: A 1109 MET cc_start: 0.9550 (ttm) cc_final: 0.9248 (tmm) outliers start: 7 outliers final: 2 residues processed: 46 average time/residue: 0.2621 time to fit residues: 17.9683 Evaluate side-chains 37 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 GLN Chi-restraints excluded: chain A residue 539 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 78 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.050919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.035676 restraints weight = 67077.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.037011 restraints weight = 39955.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.037898 restraints weight = 29532.587| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9943 Z= 0.114 Angle : 0.473 6.585 13445 Z= 0.251 Chirality : 0.038 0.140 1444 Planarity : 0.003 0.033 1749 Dihedral : 3.665 15.834 1320 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.96 % Allowed : 6.26 % Favored : 92.77 % 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: 1.33 (0.25), residues: 1203 helix: 2.54 (0.22), residues: 581 sheet: -0.55 (0.68), residues: 60 loop : -0.78 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 862 HIS 0.004 0.001 HIS A1166 PHE 0.010 0.001 PHE A 174 TYR 0.021 0.001 TYR A 86 ARG 0.006 0.000 ARG A1127 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 442) hydrogen bonds : angle 4.31616 ( 1263) covalent geometry : bond 0.00251 ( 9943) covalent geometry : angle 0.47343 (13445) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.9435 (tpp) cc_final: 0.9069 (tpp) REVERT: A 437 MET cc_start: 0.9128 (mmm) cc_final: 0.8730 (mmm) REVERT: A 512 MET cc_start: 0.8481 (ttm) cc_final: 0.7789 (tmm) REVERT: A 517 MET cc_start: 0.7550 (mtp) cc_final: 0.7021 (mpp) REVERT: A 584 MET cc_start: 0.8853 (ttm) cc_final: 0.8416 (tmm) REVERT: A 638 MET cc_start: 0.8519 (mmp) cc_final: 0.8193 (mmm) REVERT: A 1072 MET cc_start: 0.9242 (mtm) cc_final: 0.8919 (mtm) REVERT: A 1109 MET cc_start: 0.9514 (ttm) cc_final: 0.9253 (tmm) outliers start: 10 outliers final: 5 residues processed: 44 average time/residue: 0.1938 time to fit residues: 13.8449 Evaluate side-chains 40 residues out of total 1038 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 35 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 TYR Chi-restraints excluded: chain A residue 367 MET Chi-restraints excluded: chain A residue 409 HIS Chi-restraints excluded: chain A residue 539 MET Chi-restraints excluded: chain A residue 717 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 52.7192 > 50: distance: 76 - 81: 27.582 distance: 81 - 82: 22.329 distance: 82 - 83: 14.724 distance: 82 - 85: 41.302 distance: 83 - 84: 11.944 distance: 83 - 89: 17.410 distance: 85 - 86: 28.460 distance: 86 - 87: 28.803 distance: 89 - 90: 14.604 distance: 90 - 91: 10.373 distance: 90 - 93: 6.027 distance: 91 - 92: 15.850 distance: 91 - 100: 12.750 distance: 93 - 94: 19.960 distance: 94 - 95: 17.892 distance: 95 - 96: 5.026 distance: 100 - 101: 7.705 distance: 101 - 102: 19.860 distance: 101 - 104: 15.859 distance: 102 - 103: 20.955 distance: 102 - 108: 17.062 distance: 104 - 105: 10.144 distance: 104 - 106: 12.555 distance: 105 - 107: 8.886 distance: 108 - 109: 12.545 distance: 109 - 110: 13.366 distance: 109 - 112: 26.006 distance: 110 - 111: 7.045 distance: 110 - 114: 14.985 distance: 112 - 113: 33.189 distance: 114 - 115: 15.697 distance: 115 - 116: 17.860 distance: 115 - 118: 10.207 distance: 116 - 117: 14.649 distance: 116 - 122: 25.232 distance: 118 - 119: 8.579 distance: 118 - 120: 11.647 distance: 119 - 121: 14.340 distance: 122 - 123: 22.377 distance: 123 - 124: 10.774 distance: 123 - 126: 11.203 distance: 124 - 125: 3.191 distance: 124 - 130: 7.546 distance: 125 - 146: 41.888 distance: 126 - 127: 4.210 distance: 127 - 128: 8.629 distance: 127 - 129: 5.937 distance: 130 - 131: 11.468 distance: 131 - 132: 16.538 distance: 131 - 134: 13.249 distance: 132 - 133: 12.581 distance: 132 - 138: 25.938 distance: 134 - 135: 10.128 distance: 135 - 137: 8.849 distance: 138 - 139: 17.231 distance: 139 - 140: 17.639 distance: 139 - 142: 16.836 distance: 140 - 141: 20.553 distance: 140 - 146: 27.402 distance: 142 - 143: 5.886 distance: 143 - 144: 8.551 distance: 143 - 145: 11.649 distance: 146 - 147: 22.148 distance: 147 - 148: 14.819 distance: 147 - 150: 18.433 distance: 148 - 149: 20.748 distance: 148 - 154: 8.572 distance: 150 - 151: 9.174 distance: 151 - 152: 3.835 distance: 151 - 153: 3.012 distance: 154 - 155: 7.802 distance: 155 - 156: 10.488 distance: 156 - 157: 8.537 distance: 156 - 158: 13.487 distance: 157 - 176: 12.431