Starting phenix.real_space_refine on Wed Mar 12 23:49:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5u1c_8481/03_2025/5u1c_8481.cif Found real_map, /net/cci-nas-00/data/ceres_data/5u1c_8481/03_2025/5u1c_8481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5u1c_8481/03_2025/5u1c_8481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5u1c_8481/03_2025/5u1c_8481.map" model { file = "/net/cci-nas-00/data/ceres_data/5u1c_8481/03_2025/5u1c_8481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5u1c_8481/03_2025/5u1c_8481.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 92 5.49 5 Mg 2 5.21 5 S 28 5.16 5 C 5188 2.51 5 N 1534 2.21 5 O 1750 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8596 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1975 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 10, 'TRANS': 240} Chain breaks: 1 Chain: "B" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1362 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 3 Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 162 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "E" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "F" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "C" Number of atoms: 1975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1975 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 10, 'TRANS': 240} Chain breaks: 1 Chain: "D" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1362 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 6, 'TRANS': 165} Chain breaks: 3 Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 162 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "I" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "J" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 512 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 319 SG CYS A 40 21.270 47.273 39.306 1.00 11.69 S ATOM 342 SG CYS A 43 24.958 47.314 38.194 1.00 10.21 S ATOM 4615 SG CYS C 40 65.198 83.727 39.295 1.00 12.83 S ATOM 4638 SG CYS C 43 61.511 83.683 38.178 1.00 11.35 S Time building chain proxies: 4.99, per 1000 atoms: 0.58 Number of scatterers: 8596 At special positions: 0 Unit cell: (87.77, 132.31, 83.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 28 16.00 P 92 15.00 Mg 2 11.99 O 1750 8.00 N 1534 7.00 C 5188 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: 2.16 Conformation dependent library (CDL) restraints added in 771.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" ND1 HIS A 16 " pdb="ZN ZN A 500 " - pdb=" NE2 HIS A 12 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 40 " pdb=" ZN C 500 " pdb="ZN ZN C 500 " - pdb=" ND1 HIS C 16 " pdb="ZN ZN C 500 " - pdb=" NE2 HIS C 12 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 500 " - pdb=" SG CYS C 40 " Number of angles added : 4 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1560 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 46.8% alpha, 18.7% beta 42 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 3.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.585A pdb=" N ASP A 6 " --> pdb=" O LEU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 29 through 40 Processing helix chain 'A' and resid 93 through 106 Processing helix chain 'A' and resid 119 through 122 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.604A pdb=" N LYS A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 147 Processing helix chain 'A' and resid 148 through 166 removed outlier: 3.868A pdb=" N GLN A 152 " --> pdb=" O GLN A 148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 169 No H-bonds generated for 'chain 'A' and resid 167 through 169' Processing helix chain 'A' and resid 171 through 186 removed outlier: 3.959A pdb=" N ALA A 175 " --> pdb=" O HIS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'B' and resid 67 through 71 Processing helix chain 'B' and resid 93 through 108 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 123 through 134 removed outlier: 3.564A pdb=" N LYS B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 166 Processing helix chain 'B' and resid 167 through 169 No H-bonds generated for 'chain 'B' and resid 167 through 169' Processing helix chain 'B' and resid 171 through 186 removed outlier: 3.593A pdb=" N ALA B 175 " --> pdb=" O HIS B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 204 removed outlier: 3.506A pdb=" N ILE B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 16 removed outlier: 3.585A pdb=" N ASP C 6 " --> pdb=" O LEU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 29 through 40 Processing helix chain 'C' and resid 93 through 106 Processing helix chain 'C' and resid 119 through 122 Processing helix chain 'C' and resid 123 through 133 removed outlier: 3.604A pdb=" N LYS C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 147 Processing helix chain 'C' and resid 148 through 166 removed outlier: 3.866A pdb=" N GLN C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN C 164 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 169 No H-bonds generated for 'chain 'C' and resid 167 through 169' Processing helix chain 'C' and resid 171 through 186 removed outlier: 3.959A pdb=" N ALA C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 204 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 93 through 108 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 123 through 134 removed outlier: 3.564A pdb=" N LYS D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 171 through 186 removed outlier: 3.593A pdb=" N ALA D 175 " --> pdb=" O HIS D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 204 removed outlier: 3.507A pdb=" N ILE D 204 " --> pdb=" O ILE D 200 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 4.114A pdb=" N VAL A 72 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TRP A 61 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL A 113 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 227 Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 244 removed outlier: 6.427A pdb=" N VAL A 250 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS A 244 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 88 removed outlier: 6.722A pdb=" N TRP B 61 " --> pdb=" O HIS B 114 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 257 through 261 removed outlier: 6.357A pdb=" N GLN B 252 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU B 241 " --> pdb=" O GLN B 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 89 removed outlier: 4.114A pdb=" N VAL C 72 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N TRP C 61 " --> pdb=" O HIS C 114 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL C 113 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 224 through 227 Processing sheet with id=AA8, first strand: chain 'C' and resid 240 through 244 removed outlier: 6.427A pdb=" N VAL C 250 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LYS C 244 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ALA C 248 " --> pdb=" O LYS C 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 83 through 88 removed outlier: 6.722A pdb=" N TRP D 61 " --> pdb=" O HIS D 114 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 257 through 261 removed outlier: 6.357A pdb=" N GLN D 252 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU D 241 " --> pdb=" O GLN D 252 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 930 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 104 hydrogen bonds 208 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 2.57 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2023 1.33 - 1.45: 2224 1.45 - 1.57: 4499 1.57 - 1.69: 180 1.69 - 1.81: 40 Bond restraints: 8966 Sorted by residual: bond pdb=" C GLY A 118 " pdb=" N SER A 119 " ideal model delta sigma weight residual 1.334 1.381 -0.047 1.20e-02 6.94e+03 1.56e+01 bond pdb=" C THR A 122 " pdb=" N SER A 123 " ideal model delta sigma weight residual 1.330 1.293 0.038 1.30e-02 5.92e+03 8.33e+00 bond pdb=" C1' DT E 28 " pdb=" N1 DT E 28 " ideal model delta sigma weight residual 1.490 1.548 -0.058 3.00e-02 1.11e+03 3.69e+00 bond pdb=" C1' DT I 28 " pdb=" N1 DT I 28 " ideal model delta sigma weight residual 1.490 1.547 -0.057 3.00e-02 1.11e+03 3.63e+00 bond pdb=" C4' DC H 6 " pdb=" C3' DC H 6 " ideal model delta sigma weight residual 1.523 1.560 -0.037 2.00e-02 2.50e+03 3.47e+00 ... (remaining 8961 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.28: 12133 2.28 - 4.57: 353 4.57 - 6.85: 25 6.85 - 9.13: 1 9.13 - 11.41: 4 Bond angle restraints: 12516 Sorted by residual: angle pdb=" O GLY C 118 " pdb=" C GLY C 118 " pdb=" N SER C 119 " ideal model delta sigma weight residual 122.70 111.29 11.41 1.30e+00 5.92e-01 7.71e+01 angle pdb=" O GLY A 118 " pdb=" C GLY A 118 " pdb=" N SER A 119 " ideal model delta sigma weight residual 122.70 111.62 11.08 1.30e+00 5.92e-01 7.26e+01 angle pdb=" CA GLY C 118 " pdb=" C GLY C 118 " pdb=" N SER C 119 " ideal model delta sigma weight residual 116.69 127.81 -11.12 2.04e+00 2.40e-01 2.97e+01 angle pdb=" CA GLY A 118 " pdb=" C GLY A 118 " pdb=" N SER A 119 " ideal model delta sigma weight residual 116.69 127.67 -10.98 2.04e+00 2.40e-01 2.90e+01 angle pdb=" C GLY C 118 " pdb=" N SER C 119 " pdb=" CA SER C 119 " ideal model delta sigma weight residual 120.79 127.08 -6.29 1.39e+00 5.18e-01 2.05e+01 ... (remaining 12511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.72: 4642 33.72 - 67.44: 418 67.44 - 101.15: 10 101.15 - 134.87: 0 134.87 - 168.59: 2 Dihedral angle restraints: 5072 sinusoidal: 2656 harmonic: 2416 Sorted by residual: dihedral pdb=" CA GLN A 148 " pdb=" C GLN A 148 " pdb=" N GLY A 149 " pdb=" CA GLY A 149 " ideal model delta harmonic sigma weight residual 180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA GLN C 148 " pdb=" C GLN C 148 " pdb=" N GLY C 149 " pdb=" CA GLY C 149 " ideal model delta harmonic sigma weight residual -180.00 -157.75 -22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA SER C 195 " pdb=" C SER C 195 " pdb=" N ALA C 196 " pdb=" CA ALA C 196 " ideal model delta harmonic sigma weight residual -180.00 -158.85 -21.15 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 5069 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 861 0.045 - 0.091: 394 0.091 - 0.136: 110 0.136 - 0.182: 21 0.182 - 0.227: 2 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA LYS C 46 " pdb=" N LYS C 46 " pdb=" C LYS C 46 " pdb=" CB LYS C 46 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LYS A 46 " pdb=" N LYS A 46 " pdb=" C LYS A 46 " pdb=" CB LYS A 46 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 89 " pdb=" N ILE A 89 " pdb=" C ILE A 89 " pdb=" CB ILE A 89 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 1385 not shown) Planarity restraints: 1258 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC F 20 " -0.014 2.00e-02 2.50e+03 1.47e-02 4.87e+00 pdb=" N1 DC F 20 " 0.013 2.00e-02 2.50e+03 pdb=" C2 DC F 20 " -0.031 2.00e-02 2.50e+03 pdb=" O2 DC F 20 " 0.022 2.00e-02 2.50e+03 pdb=" N3 DC F 20 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC F 20 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC F 20 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC F 20 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DC F 20 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 20 " 0.014 2.00e-02 2.50e+03 1.45e-02 4.73e+00 pdb=" N1 DC J 20 " -0.013 2.00e-02 2.50e+03 pdb=" C2 DC J 20 " 0.030 2.00e-02 2.50e+03 pdb=" O2 DC J 20 " -0.021 2.00e-02 2.50e+03 pdb=" N3 DC J 20 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC J 20 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 20 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DC J 20 " -0.008 2.00e-02 2.50e+03 pdb=" C6 DC J 20 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 19 " -0.026 2.00e-02 2.50e+03 1.43e-02 4.62e+00 pdb=" N1 DC I 19 " 0.033 2.00e-02 2.50e+03 pdb=" C2 DC I 19 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC I 19 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DC I 19 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC I 19 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC I 19 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DC I 19 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC I 19 " 0.002 2.00e-02 2.50e+03 ... (remaining 1255 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 64 2.55 - 3.14: 6733 3.14 - 3.73: 13641 3.73 - 4.31: 19417 4.31 - 4.90: 30282 Nonbonded interactions: 70137 Sorted by model distance: nonbonded pdb=" O ARG A 228 " pdb=" OD1 ASP A 229 " model vdw 1.964 3.040 nonbonded pdb=" O ARG C 228 " pdb=" OD1 ASP C 229 " model vdw 1.965 3.040 nonbonded pdb=" OD2 ASP A 64 " pdb="MG MG A 501 " model vdw 1.976 2.170 nonbonded pdb=" OD2 ASP C 64 " pdb="MG MG C 501 " model vdw 1.977 2.170 nonbonded pdb=" OG1 THR A 93 " pdb=" OP1 DC F 30 " model vdw 2.051 3.040 ... (remaining 70132 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: 0.04 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 24.790 Find NCS groups from input model: 0.160 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: 0.000 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 8966 Z= 0.478 Angle : 0.912 11.414 12516 Z= 0.545 Chirality : 0.054 0.227 1388 Planarity : 0.005 0.035 1258 Dihedral : 20.206 168.589 3512 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.28 % Allowed : 0.28 % Favored : 99.43 % 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: -4.03 (0.24), residues: 822 helix: -2.67 (0.22), residues: 320 sheet: -2.02 (0.34), residues: 194 loop : -2.86 (0.30), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP D 235 HIS 0.014 0.002 HIS B 183 PHE 0.024 0.003 PHE C 121 TYR 0.020 0.003 TYR B 99 ARG 0.007 0.001 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 271 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ILE cc_start: 0.8554 (mt) cc_final: 0.8226 (tp) REVERT: A 85 GLU cc_start: 0.7344 (tp30) cc_final: 0.7080 (tp30) REVERT: C 22 MET cc_start: 0.7141 (mtm) cc_final: 0.6867 (mtp) REVERT: C 60 ILE cc_start: 0.8428 (mt) cc_final: 0.8197 (tp) REVERT: C 85 GLU cc_start: 0.7345 (tp30) cc_final: 0.6977 (tp30) outliers start: 2 outliers final: 0 residues processed: 273 average time/residue: 0.2702 time to fit residues: 94.1579 Evaluate side-chains 134 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 183 HIS B 114 HIS ** B 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 177 GLN ** C 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 144 ASN C 183 HIS C 252 GLN ** D 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.114804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.096534 restraints weight = 21374.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.098620 restraints weight = 12979.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.099969 restraints weight = 9536.618| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 8966 Z= 0.345 Angle : 0.696 6.269 12516 Z= 0.393 Chirality : 0.046 0.155 1388 Planarity : 0.006 0.056 1258 Dihedral : 26.466 179.872 1916 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.55 % Allowed : 12.93 % Favored : 83.52 % 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: -2.01 (0.26), residues: 822 helix: -0.89 (0.24), residues: 340 sheet: -0.81 (0.34), residues: 210 loop : -2.10 (0.34), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 61 HIS 0.009 0.001 HIS B 183 PHE 0.019 0.002 PHE C 181 TYR 0.018 0.002 TYR A 99 ARG 0.006 0.001 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.871 Fit side-chains REVERT: A 69 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7324 (tt0) REVERT: A 103 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8263 (mtpt) REVERT: A 178 MET cc_start: 0.8794 (mtt) cc_final: 0.6833 (mtt) REVERT: A 230 SER cc_start: 0.7439 (m) cc_final: 0.6977 (t) REVERT: B 65 CYS cc_start: 0.7429 (p) cc_final: 0.7157 (t) REVERT: B 132 TRP cc_start: 0.8795 (t60) cc_final: 0.7915 (t60) REVERT: C 15 TYR cc_start: 0.8729 (m-10) cc_final: 0.8515 (m-10) REVERT: C 20 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8265 (ttm-80) REVERT: C 107 ARG cc_start: 0.7102 (mpp80) cc_final: 0.6850 (mpp80) REVERT: C 178 MET cc_start: 0.8798 (mtt) cc_final: 0.6778 (mtt) REVERT: C 230 SER cc_start: 0.7403 (m) cc_final: 0.6946 (t) REVERT: D 65 CYS cc_start: 0.7442 (p) cc_final: 0.7117 (t) REVERT: D 132 TRP cc_start: 0.8828 (t60) cc_final: 0.7980 (t60) outliers start: 25 outliers final: 14 residues processed: 177 average time/residue: 0.2310 time to fit residues: 54.7167 Evaluate side-chains 132 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 4 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 HIS A 184 ASN B 114 HIS C 171 HIS C 184 ASN D 114 HIS ** D 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.098276 restraints weight = 21737.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.100641 restraints weight = 12515.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.102238 restraints weight = 8881.474| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8966 Z= 0.194 Angle : 0.596 9.179 12516 Z= 0.334 Chirality : 0.043 0.165 1388 Planarity : 0.004 0.052 1258 Dihedral : 26.405 178.880 1916 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.41 % Allowed : 15.62 % Favored : 81.96 % 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: -0.86 (0.28), residues: 822 helix: 0.26 (0.26), residues: 350 sheet: -0.17 (0.35), residues: 210 loop : -1.91 (0.35), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 132 HIS 0.007 0.001 HIS D 183 PHE 0.011 0.001 PHE A 100 TYR 0.018 0.002 TYR A 99 ARG 0.006 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.785 Fit side-chains revert: symmetry clash REVERT: A 69 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7336 (tt0) REVERT: A 144 ASN cc_start: 0.9033 (t0) cc_final: 0.8827 (t0) REVERT: A 178 MET cc_start: 0.8941 (mtt) cc_final: 0.7007 (mtt) REVERT: A 181 PHE cc_start: 0.8798 (t80) cc_final: 0.8578 (t80) REVERT: A 184 ASN cc_start: 0.8488 (m-40) cc_final: 0.8190 (m110) REVERT: A 230 SER cc_start: 0.7506 (m) cc_final: 0.7000 (t) REVERT: A 269 ARG cc_start: 0.4755 (tmt170) cc_final: 0.4482 (tpt90) REVERT: B 65 CYS cc_start: 0.7366 (p) cc_final: 0.6998 (t) REVERT: B 132 TRP cc_start: 0.8830 (t60) cc_final: 0.8174 (t60) REVERT: C 20 ARG cc_start: 0.8312 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: C 144 ASN cc_start: 0.9053 (t0) cc_final: 0.8833 (t0) REVERT: C 178 MET cc_start: 0.8932 (mtt) cc_final: 0.7128 (mtt) REVERT: C 184 ASN cc_start: 0.8471 (m-40) cc_final: 0.8236 (m110) REVERT: C 230 SER cc_start: 0.7474 (m) cc_final: 0.6965 (t) REVERT: D 65 CYS cc_start: 0.7393 (p) cc_final: 0.7063 (t) REVERT: D 132 TRP cc_start: 0.8803 (t60) cc_final: 0.7921 (t60) REVERT: D 229 ASP cc_start: 0.7809 (m-30) cc_final: 0.7608 (m-30) outliers start: 17 outliers final: 11 residues processed: 153 average time/residue: 0.1969 time to fit residues: 41.7301 Evaluate side-chains 127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 259 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain D residue 162 ILE Chi-restraints excluded: chain D residue 259 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- 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: 71.7869 > 50: distance: 2 - 20: 27.824 distance: 6 - 29: 32.788 distance: 10 - 38: 35.888 distance: 14 - 20: 31.603 distance: 15 - 48: 36.539 distance: 20 - 21: 23.576 distance: 21 - 22: 25.240 distance: 21 - 24: 30.218 distance: 22 - 23: 4.537 distance: 22 - 29: 32.371 distance: 23 - 57: 46.708 distance: 24 - 25: 41.248 distance: 25 - 26: 19.955 distance: 26 - 27: 28.850 distance: 29 - 30: 19.019 distance: 30 - 31: 58.210 distance: 30 - 33: 19.571 distance: 31 - 32: 41.016 distance: 31 - 38: 39.853 distance: 32 - 66: 39.547 distance: 34 - 35: 10.107 distance: 35 - 36: 44.073 distance: 35 - 37: 30.000 distance: 38 - 39: 67.610 distance: 39 - 42: 58.917 distance: 40 - 41: 56.164 distance: 40 - 48: 40.793 distance: 41 - 78: 40.215 distance: 42 - 43: 19.620 distance: 43 - 44: 56.044 distance: 43 - 45: 56.163 distance: 44 - 46: 41.298 distance: 45 - 47: 25.881 distance: 46 - 47: 46.310 distance: 47 - 252: 28.302 distance: 50 - 57: 4.920 distance: 53 - 54: 39.796 distance: 54 - 55: 40.881 distance: 54 - 56: 39.926 distance: 57 - 58: 42.627 distance: 58 - 59: 44.719 distance: 58 - 61: 39.742 distance: 59 - 66: 40.336 distance: 61 - 62: 49.865 distance: 62 - 63: 55.128 distance: 63 - 64: 40.489 distance: 66 - 67: 31.951 distance: 67 - 68: 10.295 distance: 67 - 70: 8.394 distance: 71 - 72: 20.128 distance: 72 - 74: 21.932 distance: 73 - 75: 8.333 distance: 74 - 76: 49.098 distance: 75 - 76: 50.083 distance: 76 - 77: 8.632 distance: 78 - 79: 37.606 distance: 80 - 88: 39.691 distance: 82 - 83: 40.810 distance: 83 - 84: 4.602 distance: 83 - 85: 19.204 distance: 84 - 252: 31.392 distance: 85 - 87: 20.272 distance: 88 - 89: 38.882 distance: 89 - 90: 36.600 distance: 89 - 92: 39.400 distance: 90 - 91: 41.131 distance: 90 - 94: 7.950 distance: 94 - 95: 52.669 distance: 95 - 98: 38.663 distance: 96 - 97: 62.812 distance: 96 - 102: 39.432 distance: 97 - 131: 27.135 distance: 103 - 104: 43.667 distance: 103 - 106: 55.548 distance: 104 - 105: 3.831 distance: 104 - 116: 28.501 distance: 105 - 138: 26.478 distance: 106 - 107: 19.429 distance: 107 - 108: 17.894 distance: 107 - 109: 18.711 distance: 108 - 110: 33.067