Starting phenix.real_space_refine (version: dev) on Sun Dec 18 13:18:40 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/12_2022/6w5u_21548_updated_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/12_2022/6w5u_21548.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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/12_2022/6w5u_21548.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/12_2022/6w5u_21548.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/12_2022/6w5u_21548_updated_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w5u_21548/12_2022/6w5u_21548_updated_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 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 6688 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 348": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 606": "OE1" <-> "OE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A ARG 615": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A GLU 713": "OE1" <-> "OE2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A GLU 718": "OE1" <-> "OE2" Residue "A GLU 742": "OE1" <-> "OE2" Residue "A ARG 789": "NH1" <-> "NH2" Residue "A GLU 791": "OE1" <-> "OE2" Residue "A ARG 934": "NH1" <-> "NH2" Residue "A ARG 978": "NH1" <-> "NH2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A ARG 989": "NH1" <-> "NH2" Residue "A GLU 1067": "OE1" <-> "OE2" Residue "A GLU 1120": "OE1" <-> "OE2" Residue "A GLU 1166": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 9474 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1175, 9158 Classifications: {'peptide': 1175} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1111} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 33 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 182 Unusual residues: {'CLR': 2, 'NAG': 9} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.29, per 1000 atoms: 0.66 Number of scatterers: 9474 At special positions: 0 Unit cell: (103.602, 91.348, 145.934, 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 70 16.00 O 1781 8.00 N 1495 7.00 C 6128 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 31 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 109 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 113 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 238 " distance=2.05 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 160 " distance=1.45 Simple disulfide: pdb=" SG CYS A 177 " - pdb=" SG CYS A 184 " distance=2.03 Simple disulfide: pdb=" SG CYS A 227 " - pdb=" SG CYS A 243 " distance=2.03 Simple disulfide: pdb=" SG CYS A 240 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 468 " - pdb=" SG CYS A 479 " distance=1.99 Simple disulfide: pdb=" SG CYS A 516 " - pdb=" SG CYS A 533 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 914 " distance=2.02 Simple disulfide: pdb=" SG CYS A 956 " - pdb=" SG CYS A1011 " distance=2.02 Simple disulfide: pdb=" SG CYS A 957 " - pdb=" SG CYS A 979 " distance=2.03 Simple disulfide: pdb=" SG CYS A 967 " - pdb=" SG CYS A 976 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM 9237 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Atom "HETATM 9237 O5 NAG D 1 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG C 2 " - " BMA C 3 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A1401 " - " ASN A 452 " " NAG A1402 " - " ASN A 459 " " NAG A1405 " - " ASN A 524 " " NAG A1409 " - " ASN A 598 " " NAG A1410 " - " ASN A 916 " " NAG A1414 " - " ASN A 961 " " NAG A1415 " - " ASN A 968 " " NAG A1416 " - " ASN A1064 " " NAG A1419 " - " ASN A 158 " " NAG B 1 " - " ASN A 478 " " NAG C 1 " - " ASN A 557 " " NAG D 1 " - " ASN A 931 " " NAG E 1 " - " ASN A 222 " Time building additional restraints: 4.35 Conformation dependent library (CDL) restraints added in 1.3 seconds 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 5 sheets defined 52.4% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 56 through 66 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 86 Processing helix chain 'A' and resid 88 through 94 Processing helix chain 'A' and resid 98 through 113 Processing helix chain 'A' and resid 117 through 120 Processing helix chain 'A' and resid 150 through 160 Processing helix chain 'A' and resid 172 through 176 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 196 through 198 No H-bonds generated for 'chain 'A' and resid 196 through 198' Processing helix chain 'A' and resid 269 through 293 removed outlier: 4.246A pdb=" N ALA A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 348 removed outlier: 3.944A pdb=" N LEU A 335 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG A 336 " --> pdb=" O GLU A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 370 removed outlier: 4.734A pdb=" N GLY A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU A 368 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N VAL A 369 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N PHE A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 381 Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.605A pdb=" N GLN A 397 " --> pdb=" O GLU A 393 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS A 398 " --> pdb=" O TYR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 437 through 452 Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 509 through 518 Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 575 through 593 removed outlier: 3.600A pdb=" N GLU A 586 " --> pdb=" O ALA A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 621 through 638 Processing helix chain 'A' and resid 654 through 678 Processing helix chain 'A' and resid 686 through 710 Proline residue: A 691 - end of helix Processing helix chain 'A' and resid 721 through 749 Proline residue: A 733 - end of helix Processing helix chain 'A' and resid 755 through 788 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 825 through 829 Processing helix chain 'A' and resid 832 through 851 Proline residue: A 836 - end of helix Processing helix chain 'A' and resid 853 through 855 No H-bonds generated for 'chain 'A' and resid 853 through 855' Processing helix chain 'A' and resid 871 through 882 Processing helix chain 'A' and resid 902 through 906 Processing helix chain 'A' and resid 919 through 929 Processing helix chain 'A' and resid 943 through 950 Processing helix chain 'A' and resid 984 through 987 No H-bonds generated for 'chain 'A' and resid 984 through 987' Processing helix chain 'A' and resid 993 through 1003 Proline residue: A1000 - end of helix Processing helix chain 'A' and resid 1016 through 1019 No H-bonds generated for 'chain 'A' and resid 1016 through 1019' Processing helix chain 'A' and resid 1048 through 1069 Processing helix chain 'A' and resid 1083 through 1085 No H-bonds generated for 'chain 'A' and resid 1083 through 1085' Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1094 through 1116 Processing helix chain 'A' and resid 1121 through 1145 Processing helix chain 'A' and resid 1151 through 1176 removed outlier: 3.907A pdb=" N GLY A1162 " --> pdb=" O VAL A1158 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL A1165 " --> pdb=" O CYS A1161 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU A1166 " --> pdb=" O GLY A1162 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE A1167 " --> pdb=" O ILE A1163 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N HIS A1170 " --> pdb=" O GLU A1166 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A1171 " --> pdb=" O PHE A1167 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A1172 " --> pdb=" O CYS A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1183 through 1213 removed outlier: 4.397A pdb=" N SER A1197 " --> pdb=" O HIS A1193 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A1202 " --> pdb=" O VAL A1198 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A1203 " --> pdb=" O PHE A1199 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A1204 " --> pdb=" O SER A1200 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A1205 " --> pdb=" O GLY A1201 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1212 " --> pdb=" O GLY A1208 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU A1213 " --> pdb=" O GLY A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1251 removed outlier: 4.655A pdb=" N PHE A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) Proline residue: A1245 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= B, first strand: chain 'A' and resid 205 through 210 removed outlier: 6.573A pdb=" N LEU A 144 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N VAL A 208 " --> pdb=" O LEU A 144 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N TYR A 146 " --> pdb=" O VAL A 208 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER A 210 " --> pdb=" O TYR A 146 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N VAL A 148 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLN A 145 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL A 123 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TYR A 147 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N LEU A 121 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 409 through 411 Processing sheet with id= D, first strand: chain 'A' and resid 418 through 420 Processing sheet with id= E, first strand: chain 'A' and resid 1039 through 1041 409 hydrogen bonds defined for protein. 1209 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: 2.85 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2877 1.34 - 1.46: 2333 1.46 - 1.58: 4407 1.58 - 1.71: 1 1.71 - 1.83: 99 Bond restraints: 9717 Sorted by residual: bond pdb=" C ALA A 165 " pdb=" N PRO A 166 " ideal model delta sigma weight residual 1.330 1.465 -0.135 1.25e-02 6.40e+03 1.17e+02 bond pdb=" C TYR A 56 " pdb=" N ASP A 57 " ideal model delta sigma weight residual 1.334 1.258 0.077 1.27e-02 6.20e+03 3.65e+01 bond pdb=" C PHE A 565 " pdb=" N PRO A 566 " ideal model delta sigma weight residual 1.332 1.259 0.072 1.30e-02 5.92e+03 3.11e+01 bond pdb=" C TYR A 102 " pdb=" N ASN A 103 " ideal model delta sigma weight residual 1.335 1.408 -0.074 1.36e-02 5.41e+03 2.93e+01 bond pdb=" C ASP A 170 " pdb=" N LYS A 171 " ideal model delta sigma weight residual 1.332 1.396 -0.064 1.40e-02 5.10e+03 2.09e+01 ... (remaining 9712 not shown) Histogram of bond angle deviations from ideal: 84.63 - 98.22: 1 98.22 - 111.81: 4792 111.81 - 125.39: 8295 125.39 - 138.98: 157 138.98 - 152.57: 2 Bond angle restraints: 13247 Sorted by residual: angle pdb=" N LYS A 171 " pdb=" CA LYS A 171 " pdb=" CB LYS A 171 " ideal model delta sigma weight residual 110.49 152.57 -42.08 1.69e+00 3.50e-01 6.20e+02 angle pdb=" C ALA A 165 " pdb=" N PRO A 166 " pdb=" CA PRO A 166 " ideal model delta sigma weight residual 120.21 107.42 12.79 9.60e-01 1.09e+00 1.78e+02 angle pdb=" N LYS A 171 " pdb=" CA LYS A 171 " pdb=" C LYS A 171 " ideal model delta sigma weight residual 110.80 84.63 26.17 2.13e+00 2.20e-01 1.51e+02 angle pdb=" N VAL A 26 " pdb=" CA VAL A 26 " pdb=" C VAL A 26 " ideal model delta sigma weight residual 113.53 104.89 8.64 9.80e-01 1.04e+00 7.77e+01 angle pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 109.64 114.30 -4.66 5.38e-01 3.45e+00 7.51e+01 ... (remaining 13242 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 5181 21.85 - 43.69: 394 43.69 - 65.54: 96 65.54 - 87.39: 17 87.39 - 109.23: 15 Dihedral angle restraints: 5703 sinusoidal: 2282 harmonic: 3421 Sorted by residual: dihedral pdb=" C ASP A 170 " pdb=" N ASP A 170 " pdb=" CA ASP A 170 " pdb=" CB ASP A 170 " ideal model delta harmonic sigma weight residual -122.60 -167.11 44.51 0 2.50e+00 1.60e-01 3.17e+02 dihedral pdb=" N ASP A 170 " pdb=" C ASP A 170 " pdb=" CA ASP A 170 " pdb=" CB ASP A 170 " ideal model delta harmonic sigma weight residual 122.80 165.01 -42.21 0 2.50e+00 1.60e-01 2.85e+02 dihedral pdb=" N LYS A 171 " pdb=" C LYS A 171 " pdb=" CA LYS A 171 " pdb=" CB LYS A 171 " ideal model delta harmonic sigma weight residual 122.80 156.62 -33.82 0 2.50e+00 1.60e-01 1.83e+02 ... (remaining 5700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.950: 1552 0.950 - 1.899: 2 1.899 - 2.849: 1 2.849 - 3.798: 0 3.798 - 4.748: 1 Chirality restraints: 1556 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 2.35 -4.75 2.00e-02 2.50e+03 5.63e+04 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.78 -0.62 2.00e-02 2.50e+03 9.72e+02 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-02 2.50e+03 6.14e+02 ... (remaining 1553 not shown) Planarity restraints: 1673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.308 2.00e-02 2.50e+03 2.60e-01 8.43e+02 pdb=" C7 NAG D 1 " -0.080 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.189 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.447 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 2 " 0.301 2.00e-02 2.50e+03 2.53e-01 8.00e+02 pdb=" C7 NAG B 2 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG B 2 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG B 2 " -0.433 2.00e-02 2.50e+03 pdb=" O7 NAG B 2 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 524 " -0.128 2.00e-02 2.50e+03 2.34e-01 6.83e+02 pdb=" CG ASN A 524 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A 524 " 0.259 2.00e-02 2.50e+03 pdb=" ND2 ASN A 524 " -0.342 2.00e-02 2.50e+03 pdb=" C1 NAG A1405 " 0.265 2.00e-02 2.50e+03 ... (remaining 1670 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 42 2.37 - 3.00: 6679 3.00 - 3.64: 14145 3.64 - 4.27: 21564 4.27 - 4.90: 35220 Nonbonded interactions: 77650 Sorted by model distance: nonbonded pdb=" OD1 ASN A 931 " pdb=" O5 NAG D 1 " model vdw 1.741 3.040 nonbonded pdb=" CG ASN A 931 " pdb=" O5 NAG D 1 " model vdw 1.856 2.616 nonbonded pdb=" O3 NAG A1402 " pdb=" O7 NAG A1402 " model vdw 1.982 2.440 nonbonded pdb=" OD2 ASP A 131 " pdb=" N THR A 134 " model vdw 2.035 2.520 nonbonded pdb=" N GLY A1181 " pdb=" OE2 GLU A1185 " model vdw 2.053 2.520 ... (remaining 77645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 70 5.16 5 C 6128 2.51 5 N 1495 2.21 5 O 1781 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.000 Extract box with map and model: 3.740 Check model and map are aligned: 0.140 Convert atoms to be neutral: 0.090 Process input model: 29.120 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 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 0.135 9717 Z= 0.720 Angle : 1.504 42.080 13247 Z= 0.881 Chirality : 0.156 4.748 1556 Planarity : 0.012 0.260 1660 Dihedral : 17.074 109.232 3458 Min Nonbonded Distance : 1.741 Molprobity Statistics. All-atom Clashscore : 63.68 Ramachandran Plot: Outliers : 1.03 % Allowed : 8.48 % Favored : 90.49 % Rotamer Outliers : 6.82 % Cbeta Deviations : 0.36 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.76 (0.23), residues: 1167 helix: -0.93 (0.20), residues: 601 sheet: -2.10 (0.60), residues: 86 loop : -2.94 (0.25), residues: 480 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 229 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 23 residues processed: 276 average time/residue: 0.2050 time to fit residues: 79.3034 Evaluate side-chains 178 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 155 time to evaluate : 1.059 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1658 time to fit residues: 7.1660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 49 optimal weight: 0.0770 chunk 30 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 106 optimal weight: 0.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 122 ASN A 145 GLN A 215 HIS A 349 ASN A 447 GLN A 489 GLN ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 530 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN A 775 GLN A 793 ASN A 884 HIS A1016 HIS ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 9717 Z= 0.274 Angle : 0.871 12.836 13247 Z= 0.446 Chirality : 0.052 0.480 1556 Planarity : 0.005 0.062 1660 Dihedral : 12.976 114.813 1398 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.51 % Favored : 93.23 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.35 (0.24), residues: 1167 helix: -0.01 (0.20), residues: 604 sheet: -1.43 (0.57), residues: 79 loop : -1.92 (0.27), residues: 484 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 201 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 17 residues processed: 221 average time/residue: 0.1978 time to fit residues: 62.8809 Evaluate side-chains 162 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.200 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 17 outliers final: 1 residues processed: 17 average time/residue: 0.0974 time to fit residues: 4.5335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 106 optimal weight: 0.0870 chunk 114 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 497 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 884 HIS A1008 ASN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 9717 Z= 0.254 Angle : 0.754 8.936 13247 Z= 0.387 Chirality : 0.053 0.926 1556 Planarity : 0.005 0.054 1660 Dihedral : 12.929 110.430 1398 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.51 % Favored : 93.23 % Rotamer Outliers : 1.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.73 (0.25), residues: 1167 helix: 0.63 (0.21), residues: 587 sheet: -1.13 (0.54), residues: 89 loop : -1.73 (0.28), residues: 491 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 173 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 187 average time/residue: 0.1984 time to fit residues: 53.8229 Evaluate side-chains 162 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 1.110 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 12 outliers final: 1 residues processed: 12 average time/residue: 0.1169 time to fit residues: 3.8451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 0.0040 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 ASN A 497 HIS A1008 ASN ** A1239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 9717 Z= 0.246 Angle : 0.739 9.524 13247 Z= 0.377 Chirality : 0.058 1.010 1556 Planarity : 0.005 0.039 1660 Dihedral : 12.943 109.888 1398 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.11 % Favored : 92.80 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -0.60 (0.25), residues: 1167 helix: 0.73 (0.21), residues: 588 sheet: -1.03 (0.53), residues: 89 loop : -1.67 (0.28), residues: 490 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2334 Ramachandran restraints generated. 1167 Oldfield, 0 Emsley, 1167 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 166 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 13 residues processed: 183 average time/residue: 0.1860 time to fit residues: 50.7987 Evaluate side-chains 160 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.091 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 13 outliers final: 1 residues processed: 13 average time/residue: 0.0965 time to fit residues: 3.8056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/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-4807/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-4807/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-4807/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-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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-4807/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-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 66.0632 > 50: distance: 29 - 31: 8.190 distance: 31 - 32: 14.324 distance: 32 - 33: 25.433 distance: 32 - 35: 38.395 distance: 33 - 34: 23.934 distance: 33 - 39: 18.860 distance: 35 - 36: 19.986 distance: 36 - 37: 29.291 distance: 36 - 38: 18.287 distance: 39 - 40: 27.122 distance: 40 - 41: 34.289 distance: 40 - 43: 28.625 distance: 41 - 42: 45.033 distance: 41 - 47: 10.365 distance: 43 - 44: 11.018 distance: 44 - 45: 40.013 distance: 47 - 48: 8.547 distance: 48 - 49: 14.655 distance: 49 - 50: 34.402 distance: 49 - 56: 15.344 distance: 52 - 53: 29.923 distance: 53 - 54: 9.092 distance: 53 - 55: 38.950 distance: 56 - 57: 47.948 distance: 57 - 58: 8.359 distance: 57 - 60: 34.857 distance: 58 - 59: 22.250 distance: 58 - 62: 29.670 distance: 60 - 61: 9.267 distance: 62 - 63: 20.100 distance: 63 - 64: 19.112 distance: 63 - 66: 21.027 distance: 64 - 65: 35.343 distance: 64 - 70: 14.651 distance: 66 - 67: 46.672 distance: 67 - 68: 17.277 distance: 67 - 69: 45.820 distance: 70 - 71: 12.070 distance: 71 - 72: 14.651 distance: 71 - 74: 7.895 distance: 72 - 73: 6.001 distance: 72 - 76: 35.410 distance: 74 - 75: 11.193 distance: 76 - 77: 39.556 distance: 77 - 78: 26.853 distance: 77 - 80: 31.656 distance: 78 - 79: 42.099 distance: 78 - 84: 26.830 distance: 80 - 81: 23.534 distance: 81 - 82: 12.005 distance: 82 - 83: 39.156 distance: 84 - 85: 40.814 distance: 85 - 86: 49.020 distance: 85 - 88: 44.115 distance: 86 - 87: 13.842 distance: 86 - 91: 27.908 distance: 88 - 89: 28.669 distance: 89 - 90: 25.199 distance: 91 - 92: 14.519 distance: 92 - 93: 41.572 distance: 92 - 95: 20.465 distance: 93 - 94: 20.078 distance: 93 - 99: 10.773 distance: 95 - 96: 9.562 distance: 96 - 97: 12.229 distance: 96 - 98: 16.327 distance: 99 - 100: 13.682 distance: 100 - 101: 15.571 distance: 100 - 103: 18.085 distance: 101 - 102: 19.888 distance: 101 - 107: 11.483 distance: 103 - 104: 23.612 distance: 104 - 105: 39.619 distance: 104 - 106: 32.678