Starting phenix.real_space_refine on Fri Mar 14 07:35:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6r3q_4719/03_2025/6r3q_4719.cif Found real_map, /net/cci-nas-00/data/ceres_data/6r3q_4719/03_2025/6r3q_4719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6r3q_4719/03_2025/6r3q_4719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6r3q_4719/03_2025/6r3q_4719.map" model { file = "/net/cci-nas-00/data/ceres_data/6r3q_4719/03_2025/6r3q_4719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6r3q_4719/03_2025/6r3q_4719.cif" } resolution = 3.4 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 81 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3 5.49 5 Mg 1 5.21 5 S 69 5.16 5 C 6130 2.51 5 N 1599 2.21 5 O 1727 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9529 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 841, 6687 Classifications: {'peptide': 841} Link IDs: {'PTRANS': 20, 'TRANS': 820} Chain breaks: 6 Chain: "B" Number of atoms: 2809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2809 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 13, 'TRANS': 327} Chain breaks: 1 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GSP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.70, per 1000 atoms: 0.60 Number of scatterers: 9529 At special positions: 0 Unit cell: (162.8, 105.006, 105.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 P 3 15.00 Mg 1 11.99 O 1727 8.00 N 1599 7.00 C 6130 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: 2.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2238 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 5 sheets defined 60.9% alpha, 16.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.725A pdb=" N MET A 105 " --> pdb=" O GLU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 137 removed outlier: 3.750A pdb=" N THR A 112 " --> pdb=" O CYS A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 164 removed outlier: 3.577A pdb=" N ALA A 149 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N PHE A 164 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 192 Processing helix chain 'A' and resid 219 through 237 removed outlier: 4.227A pdb=" N SER A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 261 removed outlier: 3.552A pdb=" N TYR A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 336 removed outlier: 3.615A pdb=" N PHE A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS A 321 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 351 through 359 removed outlier: 4.185A pdb=" N GLU A 355 " --> pdb=" O ASP A 351 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 434 Processing helix chain 'A' and resid 457 through 481 Processing helix chain 'A' and resid 511 through 523 removed outlier: 3.899A pdb=" N ASN A 515 " --> pdb=" O SER A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 785 through 807 Processing helix chain 'A' and resid 817 through 844 removed outlier: 4.155A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 859 removed outlier: 3.529A pdb=" N TRP A 858 " --> pdb=" O ARG A 854 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 882 Proline residue: A 876 - end of helix Processing helix chain 'A' and resid 892 through 907 Processing helix chain 'A' and resid 916 through 935 removed outlier: 3.842A pdb=" N ARG A 920 " --> pdb=" O SER A 916 " (cutoff:3.500A) Proline residue: A 931 - end of helix Processing helix chain 'A' and resid 978 through 1037 removed outlier: 3.596A pdb=" N ALA A1015 " --> pdb=" O GLY A1011 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG A1019 " --> pdb=" O ALA A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1047 removed outlier: 3.723A pdb=" N VAL A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1069 No H-bonds generated for 'chain 'A' and resid 1067 through 1069' Processing helix chain 'A' and resid 1079 through 1096 Processing helix chain 'A' and resid 1097 through 1099 No H-bonds generated for 'chain 'A' and resid 1097 through 1099' Processing helix chain 'A' and resid 1133 through 1156 removed outlier: 4.092A pdb=" N GLN A1137 " --> pdb=" O GLN A1133 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A1155 " --> pdb=" O ASP A1151 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASN A1156 " --> pdb=" O ASP A1152 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 3.958A pdb=" N ASN A1193 " --> pdb=" O GLY A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1218 Processing helix chain 'A' and resid 1219 through 1221 No H-bonds generated for 'chain 'A' and resid 1219 through 1221' Processing helix chain 'B' and resid 29 through 40 removed outlier: 3.681A pdb=" N ASP B 33 " --> pdb=" O GLN B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 65 Processing helix chain 'B' and resid 89 through 112 removed outlier: 3.881A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER B 111 " --> pdb=" O VAL B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 134 Processing helix chain 'B' and resid 143 through 155 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 174 through 185 removed outlier: 4.042A pdb=" N ASP B 180 " --> pdb=" O GLN B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 227 through 238 removed outlier: 3.637A pdb=" N ARG B 231 " --> pdb=" O ARG B 228 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 232 " --> pdb=" O ASP B 229 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE B 235 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 236 " --> pdb=" O LYS B 233 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N PHE B 238 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 293 through 303 Processing helix chain 'B' and resid 307 through 311 Processing helix chain 'B' and resid 331 through 351 removed outlier: 3.886A pdb=" N ILE B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 388 removed outlier: 3.558A pdb=" N ILE B 372 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 437 through 441 removed outlier: 7.312A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 386 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY A 493 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 394 " --> pdb=" O HIS A 491 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A 491 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 396 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY A 489 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 398 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A 487 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE A 400 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 485 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 437 through 441 removed outlier: 7.312A pdb=" N TYR A 446 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N THR A 440 " --> pdb=" O CYS A 444 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N CYS A 444 " --> pdb=" O THR A 440 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS A 386 " --> pdb=" O ILE A 499 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLY A 493 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 394 " --> pdb=" O HIS A 491 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N HIS A 491 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU A 396 " --> pdb=" O GLY A 489 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLY A 489 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ALA A 398 " --> pdb=" O ARG A 487 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG A 487 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ILE A 400 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN A 485 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N HIS A 530 " --> pdb=" O MET A 486 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL A 488 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 570 " --> pdb=" O GLU A 546 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1105 through 1111 removed outlier: 7.401A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY A1059 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A1052 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A1177 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN A1054 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A1175 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP A1056 " --> pdb=" O LEU A1173 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU A1173 " --> pdb=" O ASP A1056 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1105 through 1111 removed outlier: 7.401A pdb=" N MET A1116 " --> pdb=" O ILE A1108 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR A1110 " --> pdb=" O THR A1114 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR A1114 " --> pdb=" O THR A1110 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY A1059 " --> pdb=" O SER A1119 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A1052 " --> pdb=" O VAL A1177 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL A1177 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN A1054 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ALA A1175 " --> pdb=" O ASN A1054 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ASP A1056 " --> pdb=" O LEU A1173 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU A1173 " --> pdb=" O ASP A1056 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY A1228 " --> pdb=" O THR A1240 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU A1242 " --> pdb=" O TYR A1226 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N TYR A1226 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 214 removed outlier: 5.626A pdb=" N HIS B 41 " --> pdb=" O HIS B 220 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE B 222 " --> pdb=" O HIS B 41 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU B 43 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ARG B 42 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE B 245 " --> pdb=" O ARG B 42 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU B 44 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N VAL B 287 " --> pdb=" O TYR B 360 " (cutoff:3.500A) 596 hydrogen bonds defined for protein. 1752 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: 3.24 Time building geometry restraints manager: 2.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1897 1.32 - 1.44: 2347 1.44 - 1.57: 5380 1.57 - 1.69: 5 1.69 - 1.81: 106 Bond restraints: 9735 Sorted by residual: bond pdb=" C LYS A 549 " pdb=" N VAL A 550 " ideal model delta sigma weight residual 1.332 1.286 0.046 1.73e-02 3.34e+03 6.96e+00 bond pdb=" CD LYS A1107 " pdb=" CE LYS A1107 " ideal model delta sigma weight residual 1.520 1.448 0.072 3.00e-02 1.11e+03 5.73e+00 bond pdb=" CG LEU A1164 " pdb=" CD2 LEU A1164 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.65e+00 bond pdb=" SD MET A 469 " pdb=" CE MET A 469 " ideal model delta sigma weight residual 1.791 1.732 0.059 2.50e-02 1.60e+03 5.48e+00 bond pdb=" CB TRP A 510 " pdb=" CG TRP A 510 " ideal model delta sigma weight residual 1.498 1.429 0.069 3.10e-02 1.04e+03 4.94e+00 ... (remaining 9730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 12608 2.68 - 5.35: 475 5.35 - 8.03: 60 8.03 - 10.71: 20 10.71 - 13.38: 8 Bond angle restraints: 13171 Sorted by residual: angle pdb=" N LEU A 875 " pdb=" CA LEU A 875 " pdb=" C LEU A 875 " ideal model delta sigma weight residual 109.81 121.90 -12.09 2.21e+00 2.05e-01 2.99e+01 angle pdb=" C ASN B 239 " pdb=" N ASP B 240 " pdb=" CA ASP B 240 " ideal model delta sigma weight residual 121.54 131.43 -9.89 1.91e+00 2.74e-01 2.68e+01 angle pdb=" C THR A1180 " pdb=" N THR A1181 " pdb=" CA THR A1181 " ideal model delta sigma weight residual 121.54 131.19 -9.65 1.91e+00 2.74e-01 2.55e+01 angle pdb=" C LYS A 437 " pdb=" N ILE A 438 " pdb=" CA ILE A 438 " ideal model delta sigma weight residual 122.97 118.46 4.51 9.80e-01 1.04e+00 2.12e+01 angle pdb=" C VAL B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta sigma weight residual 121.54 130.33 -8.79 1.91e+00 2.74e-01 2.12e+01 ... (remaining 13166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 5253 15.24 - 30.48: 382 30.48 - 45.72: 127 45.72 - 60.95: 15 60.95 - 76.19: 10 Dihedral angle restraints: 5787 sinusoidal: 2329 harmonic: 3458 Sorted by residual: dihedral pdb=" CA VAL B 114 " pdb=" C VAL B 114 " pdb=" N PRO B 115 " pdb=" CA PRO B 115 " ideal model delta harmonic sigma weight residual 180.00 144.43 35.57 0 5.00e+00 4.00e-02 5.06e+01 dihedral pdb=" CA TYR A1072 " pdb=" C TYR A1072 " pdb=" N GLU A1073 " pdb=" CA GLU A1073 " ideal model delta harmonic sigma weight residual 180.00 -148.87 -31.13 0 5.00e+00 4.00e-02 3.88e+01 dihedral pdb=" CA CYS A 910 " pdb=" C CYS A 910 " pdb=" N ASN A 911 " pdb=" CA ASN A 911 " ideal model delta harmonic sigma weight residual -180.00 -153.42 -26.58 0 5.00e+00 4.00e-02 2.83e+01 ... (remaining 5784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1308 0.109 - 0.218: 161 0.218 - 0.328: 13 0.328 - 0.437: 0 0.437 - 0.546: 2 Chirality restraints: 1484 Sorted by residual: chirality pdb=" CB VAL A 986 " pdb=" CA VAL A 986 " pdb=" CG1 VAL A 986 " pdb=" CG2 VAL A 986 " both_signs ideal model delta sigma weight residual False -2.63 -2.08 -0.55 2.00e-01 2.50e+01 7.45e+00 chirality pdb=" CG LEU B 99 " pdb=" CB LEU B 99 " pdb=" CD1 LEU B 99 " pdb=" CD2 LEU B 99 " both_signs ideal model delta sigma weight residual False -2.59 -2.11 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE B 185 " pdb=" CA ILE B 185 " pdb=" CG1 ILE B 185 " pdb=" CG2 ILE B 185 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 1481 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 385 " -0.016 2.00e-02 2.50e+03 2.84e-02 1.41e+01 pdb=" CG PHE A 385 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 385 " -0.038 2.00e-02 2.50e+03 pdb=" CD2 PHE A 385 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 385 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 385 " -0.018 2.00e-02 2.50e+03 pdb=" CZ PHE A 385 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 232 " -0.030 2.00e-02 2.50e+03 2.66e-02 1.24e+01 pdb=" CG PHE A 232 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 232 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE A 232 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 232 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 232 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 232 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 114 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO B 115 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO B 115 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 115 " -0.041 5.00e-02 4.00e+02 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 142 2.64 - 3.21: 8594 3.21 - 3.77: 15256 3.77 - 4.34: 19710 4.34 - 4.90: 32248 Nonbonded interactions: 75950 Sorted by model distance: nonbonded pdb=" O2B GSP B 501 " pdb="MG MG B 502 " model vdw 2.080 2.170 nonbonded pdb=" OG SER B 54 " pdb="MG MG B 502 " model vdw 2.113 2.170 nonbonded pdb=" OG1 THR B 204 " pdb="MG MG B 502 " model vdw 2.119 2.170 nonbonded pdb=" O2G GSP B 501 " pdb="MG MG B 502 " model vdw 2.124 2.170 nonbonded pdb=" O ALA A 412 " pdb=" OG SER A1052 " model vdw 2.205 3.040 ... (remaining 75945 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.010 Normalize map: mean=0, sd=1: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.380 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.011 0.082 9735 Z= 0.705 Angle : 1.245 13.383 13171 Z= 0.651 Chirality : 0.072 0.546 1484 Planarity : 0.008 0.074 1655 Dihedral : 12.612 76.192 3549 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 0.58 % Allowed : 8.36 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.70 (0.20), residues: 1164 helix: -2.14 (0.15), residues: 684 sheet: -2.03 (0.43), residues: 136 loop : -2.85 (0.27), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP A 918 HIS 0.016 0.003 HIS A 491 PHE 0.060 0.005 PHE A 232 TYR 0.050 0.004 TYR A 446 ARG 0.016 0.002 ARG B 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 175 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.7842 (t80) cc_final: 0.7457 (t80) REVERT: A 138 MET cc_start: 0.6930 (ttt) cc_final: 0.6257 (ttt) REVERT: A 152 PHE cc_start: 0.6885 (t80) cc_final: 0.6632 (t80) REVERT: A 182 LEU cc_start: 0.8690 (mp) cc_final: 0.8428 (mp) REVERT: A 333 MET cc_start: 0.8765 (mmt) cc_final: 0.8547 (mmp) REVERT: A 987 PHE cc_start: 0.8294 (m-80) cc_final: 0.8056 (m-80) REVERT: A 1006 ARG cc_start: 0.6909 (ttm-80) cc_final: 0.6473 (mmp-170) REVERT: B 174 CYS cc_start: 0.7864 (p) cc_final: 0.7382 (p) outliers start: 6 outliers final: 2 residues processed: 179 average time/residue: 0.2167 time to fit residues: 54.6043 Evaluate side-chains 101 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 99 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 986 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 47 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 518 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 HIS A1055 HIS A1154 ASN A1169 ASN A1231 ASN B 31 GLN B 98 ASN B 239 ASN B 264 ASN B 357 HIS B 362 HIS B 371 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.105128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.083995 restraints weight = 25734.262| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.03 r_work: 0.3305 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9735 Z= 0.220 Angle : 0.699 12.664 13171 Z= 0.352 Chirality : 0.044 0.193 1484 Planarity : 0.005 0.066 1655 Dihedral : 5.668 34.843 1300 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.65 % Allowed : 11.24 % Favored : 85.11 % 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: -1.49 (0.23), residues: 1164 helix: -0.04 (0.19), residues: 686 sheet: -1.98 (0.41), residues: 137 loop : -2.31 (0.30), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1159 HIS 0.004 0.001 HIS B 387 PHE 0.018 0.002 PHE A 232 TYR 0.026 0.002 TYR A 446 ARG 0.004 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 133 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 TYR cc_start: 0.8028 (t80) cc_final: 0.7353 (t80) REVERT: A 138 MET cc_start: 0.7397 (ttt) cc_final: 0.7110 (ttm) REVERT: A 181 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8180 (mm) REVERT: A 232 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8601 (m-10) REVERT: A 239 HIS cc_start: 0.8394 (t-90) cc_final: 0.8073 (t-90) REVERT: A 248 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7953 (tp) REVERT: A 795 THR cc_start: 0.8877 (t) cc_final: 0.8670 (m) REVERT: A 896 MET cc_start: 0.8234 (mtm) cc_final: 0.7999 (mtp) REVERT: A 1002 GLU cc_start: 0.8078 (pp20) cc_final: 0.7828 (tm-30) REVERT: A 1006 ARG cc_start: 0.7179 (ttm-80) cc_final: 0.6708 (mmp-170) REVERT: A 1164 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8860 (pt) REVERT: B 110 MET cc_start: 0.8159 (mmt) cc_final: 0.7813 (mmt) REVERT: B 174 CYS cc_start: 0.8116 (p) cc_final: 0.7719 (p) outliers start: 38 outliers final: 16 residues processed: 163 average time/residue: 0.1755 time to fit residues: 43.9081 Evaluate side-chains 133 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 55 optimal weight: 0.1980 chunk 64 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 0.2980 chunk 5 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.106357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085558 restraints weight = 26082.096| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 3.08 r_work: 0.3341 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9735 Z= 0.157 Angle : 0.645 13.951 13171 Z= 0.314 Chirality : 0.042 0.168 1484 Planarity : 0.004 0.059 1655 Dihedral : 5.025 32.045 1300 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.17 % Allowed : 13.93 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.40 (0.24), residues: 1164 helix: 0.94 (0.20), residues: 684 sheet: -1.71 (0.42), residues: 133 loop : -2.04 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1159 HIS 0.003 0.001 HIS B 357 PHE 0.019 0.001 PHE A 897 TYR 0.020 0.001 TYR A 446 ARG 0.004 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 181 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8143 (mm) REVERT: A 232 PHE cc_start: 0.9038 (OUTLIER) cc_final: 0.8534 (m-10) REVERT: A 248 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7922 (tp) REVERT: A 340 ARG cc_start: 0.8072 (mmp80) cc_final: 0.7865 (mmp80) REVERT: A 1002 GLU cc_start: 0.7953 (pp20) cc_final: 0.7729 (tp30) REVERT: A 1006 ARG cc_start: 0.7100 (ttm-80) cc_final: 0.6652 (mmp-170) REVERT: B 99 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9306 (tp) outliers start: 33 outliers final: 18 residues processed: 151 average time/residue: 0.1853 time to fit residues: 41.7862 Evaluate side-chains 126 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 16 optimal weight: 0.2980 chunk 64 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 0.0670 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 overall best weight: 0.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.105538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084673 restraints weight = 25776.683| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 3.03 r_work: 0.3320 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9735 Z= 0.174 Angle : 0.644 14.345 13171 Z= 0.311 Chirality : 0.042 0.165 1484 Planarity : 0.004 0.057 1655 Dihedral : 4.736 30.850 1298 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.75 % Allowed : 14.89 % Favored : 81.36 % 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: 0.13 (0.25), residues: 1164 helix: 1.34 (0.20), residues: 687 sheet: -1.40 (0.43), residues: 131 loop : -1.84 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.004 0.001 HIS B 357 PHE 0.013 0.001 PHE A 385 TYR 0.019 0.001 TYR A 446 ARG 0.005 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 1.041 Fit side-chains REVERT: A 138 MET cc_start: 0.7476 (ttt) cc_final: 0.7108 (ttm) REVERT: A 181 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8082 (mm) REVERT: A 232 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8556 (m-10) REVERT: A 248 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7975 (tp) REVERT: A 841 MET cc_start: 0.6165 (ttp) cc_final: 0.5939 (ptm) REVERT: A 1002 GLU cc_start: 0.8083 (pp20) cc_final: 0.7864 (tp30) REVERT: A 1006 ARG cc_start: 0.7112 (ttm-80) cc_final: 0.6653 (mmp-170) REVERT: B 99 LEU cc_start: 0.9558 (OUTLIER) cc_final: 0.9314 (tp) outliers start: 39 outliers final: 22 residues processed: 145 average time/residue: 0.1643 time to fit residues: 36.4717 Evaluate side-chains 135 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 17 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 chunk 83 optimal weight: 4.9990 overall best weight: 1.3302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.104568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.083525 restraints weight = 26206.013| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 3.04 r_work: 0.3292 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9735 Z= 0.211 Angle : 0.659 14.761 13171 Z= 0.319 Chirality : 0.043 0.219 1484 Planarity : 0.004 0.055 1655 Dihedral : 4.702 30.634 1298 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.03 % Allowed : 14.70 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.25), residues: 1164 helix: 1.58 (0.20), residues: 679 sheet: -1.54 (0.42), residues: 135 loop : -1.72 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1159 HIS 0.005 0.001 HIS B 357 PHE 0.015 0.001 PHE A 232 TYR 0.020 0.001 TYR A 446 ARG 0.005 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 1.221 Fit side-chains REVERT: A 138 MET cc_start: 0.7490 (ttt) cc_final: 0.7138 (ttm) REVERT: A 181 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8084 (mm) REVERT: A 232 PHE cc_start: 0.9095 (OUTLIER) cc_final: 0.8611 (m-10) REVERT: A 248 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7971 (tp) REVERT: A 385 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7916 (p90) REVERT: A 464 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8348 (mm-30) REVERT: A 537 LYS cc_start: 0.8502 (ptpp) cc_final: 0.8229 (ptpp) REVERT: A 841 MET cc_start: 0.5908 (ttp) cc_final: 0.5695 (ptm) REVERT: A 896 MET cc_start: 0.8233 (mtm) cc_final: 0.7982 (mmm) REVERT: A 1002 GLU cc_start: 0.8055 (pp20) cc_final: 0.7567 (tm-30) REVERT: A 1006 ARG cc_start: 0.7138 (ttm-80) cc_final: 0.6638 (mmp-170) REVERT: B 99 LEU cc_start: 0.9567 (OUTLIER) cc_final: 0.9324 (tp) outliers start: 42 outliers final: 27 residues processed: 143 average time/residue: 0.1652 time to fit residues: 36.5755 Evaluate side-chains 141 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 385 PHE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 799 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 72 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.105755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084818 restraints weight = 26223.730| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.05 r_work: 0.3323 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9735 Z= 0.166 Angle : 0.641 15.381 13171 Z= 0.305 Chirality : 0.042 0.186 1484 Planarity : 0.004 0.046 1655 Dihedral : 4.554 30.370 1298 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.75 % Allowed : 15.37 % Favored : 80.88 % 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: 0.63 (0.25), residues: 1164 helix: 1.72 (0.20), residues: 690 sheet: -1.36 (0.42), residues: 131 loop : -1.55 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1159 HIS 0.006 0.001 HIS A 530 PHE 0.012 0.001 PHE A 232 TYR 0.019 0.001 TYR A 446 ARG 0.004 0.000 ARG A 920 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2328 Ramachandran restraints generated. 1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 138 MET cc_start: 0.7529 (ttt) cc_final: 0.7235 (ttm) REVERT: A 181 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8114 (mm) REVERT: A 232 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8530 (m-10) REVERT: A 242 LEU cc_start: 0.8665 (tt) cc_final: 0.8410 (pp) REVERT: A 248 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7967 (tp) REVERT: A 464 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8368 (mm-30) REVERT: A 537 LYS cc_start: 0.8492 (ptpp) cc_final: 0.8278 (ptpp) REVERT: A 1002 GLU cc_start: 0.7928 (pp20) cc_final: 0.7713 (tp30) REVERT: A 1006 ARG cc_start: 0.7072 (ttm-80) cc_final: 0.6643 (mmp-170) REVERT: B 99 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9338 (tp) outliers start: 39 outliers final: 25 residues processed: 142 average time/residue: 0.1841 time to fit residues: 40.3779 Evaluate side-chains 136 residues out of total 1041 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 CYS Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 232 PHE Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 782 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 792 LEU Chi-restraints excluded: chain A residue 880 VAL Chi-restraints excluded: chain A residue 904 THR Chi-restraints excluded: chain A residue 907 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 993 LEU Chi-restraints excluded: chain A residue 1016 ASP Chi-restraints excluded: chain A residue 1020 THR Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1111 ILE Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1158 LEU Chi-restraints excluded: chain A residue 1166 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 178 PHE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 325 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/cctbx_project/iotbx/cli_parser.py", line 980, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/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-5624/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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-5624/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-5624/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-5624/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-5624/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: 71.7314 > 50: distance: 68 - 88: 33.317 distance: 72 - 94: 34.367 distance: 77 - 105: 30.722 distance: 84 - 88: 32.890 distance: 85 - 113: 32.398 distance: 88 - 89: 4.005 distance: 89 - 90: 39.462 distance: 89 - 92: 41.310 distance: 90 - 91: 6.659 distance: 91 - 121: 67.223 distance: 92 - 93: 34.266 distance: 95 - 98: 27.177 distance: 96 - 97: 40.620 distance: 96 - 105: 7.327 distance: 97 - 129: 41.324 distance: 98 - 99: 23.576 distance: 99 - 100: 5.654 distance: 100 - 101: 4.181 distance: 101 - 102: 20.172 distance: 102 - 103: 22.201 distance: 102 - 104: 25.801 distance: 105 - 106: 22.781 distance: 106 - 107: 8.924 distance: 106 - 109: 38.053 distance: 107 - 108: 17.738 distance: 107 - 113: 25.976 distance: 108 - 138: 26.920 distance: 109 - 110: 6.010 distance: 110 - 111: 18.588 distance: 110 - 112: 4.321 distance: 113 - 114: 41.324 distance: 114 - 115: 21.125 distance: 114 - 117: 23.516 distance: 116 - 149: 42.845 distance: 117 - 118: 24.148 distance: 117 - 119: 44.264 distance: 118 - 120: 52.715 distance: 121 - 122: 25.076 distance: 122 - 123: 40.255 distance: 122 - 125: 18.315 distance: 123 - 124: 13.336 distance: 123 - 129: 10.372 distance: 124 - 157: 32.927 distance: 125 - 126: 34.627 distance: 125 - 127: 34.519 distance: 129 - 130: 4.673 distance: 130 - 131: 9.713 distance: 130 - 133: 30.405 distance: 131 - 132: 40.684 distance: 131 - 138: 43.924 distance: 132 - 167: 37.669 distance: 133 - 134: 41.166 distance: 134 - 135: 16.818 distance: 135 - 136: 14.460 distance: 135 - 137: 46.922 distance: 138 - 139: 17.994 distance: 139 - 140: 41.039 distance: 139 - 142: 39.966 distance: 140 - 141: 23.637 distance: 140 - 149: 15.870 distance: 142 - 143: 6.287 distance: 143 - 144: 3.392 distance: 144 - 145: 40.473 distance: 145 - 146: 48.517 distance: 146 - 147: 33.786 distance: 146 - 148: 14.023 distance: 149 - 150: 17.288 distance: 150 - 151: 53.336 distance: 150 - 153: 50.542 distance: 151 - 152: 5.509 distance: 151 - 157: 13.746 distance: 153 - 154: 16.092 distance: 154 - 155: 48.638 distance: 157 - 158: 16.336 distance: 158 - 159: 10.859 distance: 158 - 161: 21.682 distance: 159 - 160: 54.108 distance: 159 - 167: 3.005 distance: 161 - 162: 25.010 distance: 167 - 168: 40.906 distance: 168 - 169: 39.421 distance: 169 - 175: 35.296 distance: 172 - 174: 40.160