Starting phenix.real_space_refine on Sun May 11 14:27:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f3q_31434/05_2025/7f3q_31434.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f3q_31434/05_2025/7f3q_31434.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f3q_31434/05_2025/7f3q_31434.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f3q_31434/05_2025/7f3q_31434.map" model { file = "/net/cci-nas-00/data/ceres_data/7f3q_31434/05_2025/7f3q_31434.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f3q_31434/05_2025/7f3q_31434.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 5055 2.51 5 N 1339 2.21 5 O 1578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8003 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "H" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1594 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "L" Number of atoms: 1596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1596 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 195} Chain: "C" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1691 Classifications: {'peptide': 227} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 215} Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1560 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 13, 'TRANS': 191} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MES': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.76, per 1000 atoms: 0.59 Number of scatterers: 8003 At special positions: 0 Unit cell: (97.11, 87.98, 146.08, 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 31 16.00 O 1578 8.00 N 1339 7.00 C 5055 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 146 " - pdb=" SG CYS H 202 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 87 " distance=2.04 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 36 " - pdb=" SG CYS C 110 " distance=2.05 Simple disulfide: pdb=" SG CYS C 168 " - pdb=" SG CYS C 224 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.02 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 193 " distance=2.04 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 1.98 Conformation dependent library (CDL) restraints added in 929.6 milliseconds 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 25 sheets defined 9.5% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.516A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.970A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.798A pdb=" N SER H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.792A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.848A pdb=" N SER H 194 " --> pdb=" O PRO H 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 30 Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 183 through 188 Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.733A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 183 through 187 removed outlier: 3.880A pdb=" N GLU B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 187 " --> pdb=" O ASP B 184 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 183 through 187' Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.614A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.800A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.051A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 126 through 130 removed outlier: 4.051A pdb=" N GLY H 145 " --> pdb=" O LEU H 130 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TYR H 182 " --> pdb=" O ASP H 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 157 through 160 removed outlier: 3.698A pdb=" N VAL H 213 " --> pdb=" O VAL H 204 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.750A pdb=" N THR L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER L 66 " --> pdb=" O THR L 69 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 44 through 47 removed outlier: 7.046A pdb=" N TRP L 34 " --> pdb=" O VAL L 46 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 117 through 118 Processing sheet with id=AB4, first strand: chain 'L' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'L' and resid 155 through 156 removed outlier: 3.720A pdb=" N THR L 147 " --> pdb=" O THR L 198 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 167 through 169 removed outlier: 6.494A pdb=" N SER L 167 " --> pdb=" O TYR L 174 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N TYR L 174 " --> pdb=" O SER L 167 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN L 169 " --> pdb=" O ASN L 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 17 through 21 Processing sheet with id=AB8, first strand: chain 'C' and resid 25 through 26 removed outlier: 6.319A pdb=" N ARG C 52 " --> pdb=" O TRP C 61 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N TRP C 61 " --> pdb=" O ARG C 52 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 25 through 26 removed outlier: 4.094A pdb=" N TYR C 130 " --> pdb=" O LYS C 112 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AC2, first strand: chain 'C' and resid 148 through 151 Processing sheet with id=AC3, first strand: chain 'C' and resid 179 through 182 Processing sheet with id=AC4, first strand: chain 'B' and resid 5 through 6 removed outlier: 3.523A pdb=" N ASP B 70 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.596A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 113 through 117 removed outlier: 3.569A pdb=" N ASN B 136 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER B 176 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N TYR B 172 " --> pdb=" O ASN B 137 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.574A pdb=" N CYS B 193 " --> pdb=" O LYS B 206 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 744 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: 2.35 Time building geometry restraints manager: 2.24 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: 2497 1.34 - 1.47: 2164 1.47 - 1.59: 3508 1.59 - 1.72: 1 1.72 - 1.85: 35 Bond restraints: 8205 Sorted by residual: bond pdb=" C8 MES H 301 " pdb=" S MES H 301 " ideal model delta sigma weight residual 1.814 1.662 0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" CB ASN B 31 " pdb=" CG ASN B 31 " ideal model delta sigma weight residual 1.516 1.415 0.101 2.50e-02 1.60e+03 1.63e+01 bond pdb=" N TYR L 174 " pdb=" CA TYR L 174 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.22e-02 6.72e+03 7.68e+00 bond pdb=" N LYS C 237 " pdb=" CA LYS C 237 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.26e+00 bond pdb=" N LYS B 45 " pdb=" CA LYS B 45 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.19e-02 7.06e+03 5.76e+00 ... (remaining 8200 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 10725 1.86 - 3.72: 391 3.72 - 5.58: 54 5.58 - 7.45: 11 7.45 - 9.31: 3 Bond angle restraints: 11184 Sorted by residual: angle pdb=" N CYS A 379 " pdb=" CA CYS A 379 " pdb=" C CYS A 379 " ideal model delta sigma weight residual 108.60 114.22 -5.62 1.46e+00 4.69e-01 1.48e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 122.28 -7.88 2.30e+00 1.89e-01 1.17e+01 angle pdb=" C ALA B 50 " pdb=" N ALA B 51 " pdb=" CA ALA B 51 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.43e+00 angle pdb=" CA GLN C 53 " pdb=" CB GLN C 53 " pdb=" CG GLN C 53 " ideal model delta sigma weight residual 114.10 108.41 5.69 2.00e+00 2.50e-01 8.08e+00 angle pdb=" C3 MES H 301 " pdb=" N4 MES H 301 " pdb=" C5 MES H 301 " ideal model delta sigma weight residual 109.71 117.80 -8.09 3.00e+00 1.11e-01 7.27e+00 ... (remaining 11179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4472 17.95 - 35.90: 314 35.90 - 53.85: 63 53.85 - 71.80: 27 71.80 - 89.74: 7 Dihedral angle restraints: 4883 sinusoidal: 1859 harmonic: 3024 Sorted by residual: dihedral pdb=" CA TYR L 142 " pdb=" C TYR L 142 " pdb=" N PRO L 143 " pdb=" CA PRO L 143 " ideal model delta harmonic sigma weight residual 180.00 142.62 37.38 0 5.00e+00 4.00e-02 5.59e+01 dihedral pdb=" CB CYS H 146 " pdb=" SG CYS H 146 " pdb=" SG CYS H 202 " pdb=" CB CYS H 202 " ideal model delta sinusoidal sigma weight residual 93.00 147.11 -54.11 1 1.00e+01 1.00e-02 3.97e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 150.49 29.51 0 5.00e+00 4.00e-02 3.48e+01 ... (remaining 4880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.228: 1244 0.228 - 0.455: 0 0.455 - 0.683: 0 0.683 - 0.910: 0 0.910 - 1.137: 1 Chirality restraints: 1245 Sorted by residual: chirality pdb=" N4 MES H 301 " pdb=" C3 MES H 301 " pdb=" C5 MES H 301 " pdb=" C7 MES H 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.26 -1.14 2.00e-01 2.50e+01 3.23e+01 chirality pdb=" CG LEU B 33 " pdb=" CB LEU B 33 " pdb=" CD1 LEU B 33 " pdb=" CD2 LEU B 33 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1242 not shown) Planarity restraints: 1439 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 128 " 0.030 2.00e-02 2.50e+03 1.97e-02 6.81e+00 pdb=" CG PHE C 128 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 PHE C 128 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 128 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 128 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 128 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 128 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR L 142 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.77e+00 pdb=" N PRO L 143 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO L 143 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 143 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 187 " 0.014 2.00e-02 2.50e+03 1.51e-02 5.68e+00 pdb=" CG TRP L 187 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP L 187 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP L 187 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 187 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 187 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 187 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 187 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 187 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 187 " 0.001 2.00e-02 2.50e+03 ... (remaining 1436 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 21 2.46 - 3.07: 5098 3.07 - 3.68: 11450 3.68 - 4.29: 17115 4.29 - 4.90: 29261 Nonbonded interactions: 62945 Sorted by model distance: nonbonded pdb=" O ASP L 153 " pdb=" OG SER L 154 " model vdw 1.848 3.040 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.212 3.040 nonbonded pdb=" OD1 ASP B 169 " pdb=" OG1 THR B 171 " model vdw 2.229 3.040 nonbonded pdb=" OG1 THR A 393 " pdb=" O GLU A 516 " model vdw 2.256 3.040 nonbonded pdb=" NH1 ARG B 107 " pdb=" O THR B 108 " model vdw 2.264 3.120 ... (remaining 62940 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: 0.000 Normalize map: mean=0, sd=1: 0.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.006 0.152 8218 Z= 0.283 Angle : 0.811 9.306 11211 Z= 0.443 Chirality : 0.058 1.137 1245 Planarity : 0.005 0.065 1438 Dihedral : 13.817 89.744 2921 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.59 % Favored : 94.32 % Rotamer: Outliers : 2.14 % Allowed : 3.61 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.94 (0.26), residues: 1038 helix: -3.16 (0.55), residues: 57 sheet: 0.48 (0.26), residues: 425 loop : -1.26 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 187 HIS 0.006 0.001 HIS C 118 PHE 0.038 0.002 PHE C 128 TYR 0.019 0.003 TYR C 108 ARG 0.006 0.001 ARG C 33 Details of bonding type rmsd link_NAG-ASN : bond 0.00193 ( 1) link_NAG-ASN : angle 1.05542 ( 3) hydrogen bonds : bond 0.19233 ( 289) hydrogen bonds : angle 8.81459 ( 744) SS BOND : bond 0.00875 ( 12) SS BOND : angle 1.37889 ( 24) covalent geometry : bond 0.00580 ( 8205) covalent geometry : angle 0.80942 (11184) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 213 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: H 31 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7512 (mt-10) REVERT: H 207 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8454 (ttmt) REVERT: L 78 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7472 (mt-10) REVERT: L 187 TRP cc_start: 0.7702 (t60) cc_final: 0.7244 (t-100) REVERT: B 17 ASP cc_start: 0.7164 (m-30) cc_final: 0.6837 (m-30) REVERT: B 153 LEU cc_start: 0.8540 (mp) cc_final: 0.8010 (mp) REVERT: B 166 ASP cc_start: 0.8446 (t0) cc_final: 0.8176 (t70) outliers start: 19 outliers final: 5 residues processed: 225 average time/residue: 0.2433 time to fit residues: 70.1671 Evaluate side-chains 161 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 156 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 29 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.7980 chunk 78 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 50.0000 chunk 41 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 49 optimal weight: 0.3980 chunk 60 optimal weight: 30.0000 chunk 93 optimal weight: 3.9990 overall best weight: 4.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN L 25 ASN L 169 GLN L 171 ASN L 186 GLN ** C 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.127128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088958 restraints weight = 12214.774| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.85 r_work: 0.2851 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8218 Z= 0.181 Angle : 0.671 11.062 11211 Z= 0.345 Chirality : 0.045 0.164 1245 Planarity : 0.005 0.076 1438 Dihedral : 5.206 33.341 1173 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.48 % Allowed : 11.17 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.10 % 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: -0.62 (0.25), residues: 1038 helix: -3.08 (0.49), residues: 58 sheet: 0.73 (0.26), residues: 415 loop : -1.01 (0.24), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP H 103 HIS 0.004 0.001 HIS C 228 PHE 0.020 0.001 PHE C 150 TYR 0.024 0.002 TYR H 151 ARG 0.004 0.001 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00006 ( 1) link_NAG-ASN : angle 1.53933 ( 3) hydrogen bonds : bond 0.04012 ( 289) hydrogen bonds : angle 5.80888 ( 744) SS BOND : bond 0.00506 ( 12) SS BOND : angle 1.47413 ( 24) covalent geometry : bond 0.00426 ( 8205) covalent geometry : angle 0.66744 (11184) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 184 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: H 31 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8673 (mt-10) REVERT: H 80 TYR cc_start: 0.9115 (m-80) cc_final: 0.8847 (m-10) REVERT: L 78 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7771 (mt-10) REVERT: L 110 GLN cc_start: 0.8633 (mm110) cc_final: 0.8339 (mt0) REVERT: C 20 GLU cc_start: 0.8393 (mp0) cc_final: 0.8169 (mp0) REVERT: C 60 GLU cc_start: 0.8595 (pt0) cc_final: 0.8379 (pt0) REVERT: C 173 TYR cc_start: 0.8601 (p90) cc_final: 0.8050 (p90) REVERT: C 238 LYS cc_start: 0.8092 (tttp) cc_final: 0.7877 (tttp) REVERT: B 17 ASP cc_start: 0.8103 (m-30) cc_final: 0.7408 (m-30) REVERT: B 121 ASP cc_start: 0.7571 (p0) cc_final: 0.6981 (p0) REVERT: B 153 LEU cc_start: 0.8630 (mp) cc_final: 0.8420 (tt) outliers start: 22 outliers final: 12 residues processed: 195 average time/residue: 0.2648 time to fit residues: 65.0197 Evaluate side-chains 152 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain H residue 215 LYS Chi-restraints excluded: chain L residue 47 ILE Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 77 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 0.0370 chunk 95 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 68 optimal weight: 10.0000 chunk 73 optimal weight: 20.0000 overall best weight: 1.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN C 228 HIS ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.127631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.093605 restraints weight = 12320.674| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 3.39 r_work: 0.2797 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8218 Z= 0.111 Angle : 0.576 8.635 11211 Z= 0.296 Chirality : 0.043 0.153 1245 Planarity : 0.004 0.066 1438 Dihedral : 4.714 30.742 1167 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 12.75 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.45 % Cis-general : 0.00 % Twisted Proline : 1.61 % 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: -0.31 (0.26), residues: 1038 helix: -2.67 (0.56), residues: 50 sheet: 0.96 (0.25), residues: 421 loop : -0.90 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 187 HIS 0.004 0.001 HIS C 228 PHE 0.009 0.001 PHE C 150 TYR 0.019 0.001 TYR H 151 ARG 0.004 0.000 ARG H 16 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 1.32154 ( 3) hydrogen bonds : bond 0.03345 ( 289) hydrogen bonds : angle 5.40724 ( 744) SS BOND : bond 0.00364 ( 12) SS BOND : angle 1.10560 ( 24) covalent geometry : bond 0.00258 ( 8205) covalent geometry : angle 0.57400 (11184) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2076 Ramachandran restraints generated. 1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: H 80 TYR cc_start: 0.9029 (m-80) cc_final: 0.8767 (m-10) REVERT: H 123 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8748 (ttmm) REVERT: H 207 LYS cc_start: 0.8784 (mtpt) cc_final: 0.8406 (ttmt) REVERT: L 78 GLU cc_start: 0.8044 (mt-10) cc_final: 0.7587 (mt-10) REVERT: L 110 GLN cc_start: 0.8570 (mm110) cc_final: 0.8061 (mt0) REVERT: C 60 GLU cc_start: 0.8440 (pt0) cc_final: 0.8237 (pt0) REVERT: C 238 LYS cc_start: 0.8112 (tttp) cc_final: 0.7900 (tttp) REVERT: B 17 ASP cc_start: 0.8018 (m-30) cc_final: 0.7365 (m-30) REVERT: B 125 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7832 (mtmm) outliers start: 23 outliers final: 15 residues processed: 160 average time/residue: 0.2456 time to fit residues: 51.0577 Evaluate side-chains 155 residues out of total 886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 405 ASP Chi-restraints excluded: chain H residue 30 ASP Chi-restraints excluded: chain H residue 62 ASP Chi-restraints excluded: chain H residue 147 LEU Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 211 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/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-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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-5687/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-5687/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-5687/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-5687/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: 62.8382 > 50: distance: 41 - 51: 28.188 distance: 51 - 52: 47.200 distance: 52 - 53: 38.730 distance: 52 - 55: 8.089 distance: 53 - 54: 50.328 distance: 53 - 62: 46.486 distance: 55 - 56: 29.957 distance: 56 - 57: 10.785 distance: 56 - 58: 18.411 distance: 57 - 59: 9.080 distance: 58 - 60: 15.357 distance: 59 - 61: 5.780 distance: 62 - 63: 25.154 distance: 62 - 68: 34.531 distance: 63 - 64: 40.666 distance: 63 - 66: 29.955 distance: 64 - 65: 59.392 distance: 64 - 69: 25.974 distance: 66 - 67: 20.727 distance: 67 - 68: 43.602 distance: 69 - 70: 11.000 distance: 70 - 71: 32.207 distance: 70 - 73: 28.218 distance: 71 - 72: 12.911 distance: 71 - 78: 42.610 distance: 73 - 74: 16.742 distance: 74 - 75: 37.907 distance: 75 - 76: 24.683 distance: 75 - 77: 17.274 distance: 78 - 79: 10.628 distance: 78 - 84: 22.943 distance: 79 - 80: 20.075 distance: 79 - 82: 14.796 distance: 80 - 81: 29.172 distance: 80 - 85: 34.014 distance: 82 - 83: 11.396 distance: 83 - 84: 20.365 distance: 85 - 86: 18.635 distance: 86 - 87: 33.493 distance: 86 - 89: 24.159 distance: 87 - 88: 9.731 distance: 87 - 92: 44.357 distance: 89 - 90: 15.583 distance: 89 - 91: 10.364 distance: 92 - 93: 34.706 distance: 92 - 223: 26.071 distance: 93 - 94: 9.784 distance: 93 - 96: 22.393 distance: 94 - 95: 11.624 distance: 94 - 99: 34.016 distance: 95 - 220: 21.676 distance: 96 - 97: 18.231 distance: 96 - 98: 15.119 distance: 99 - 100: 11.052 distance: 100 - 101: 5.054 distance: 100 - 103: 18.133 distance: 101 - 102: 10.700 distance: 101 - 106: 14.651 distance: 103 - 104: 29.427 distance: 103 - 105: 16.238 distance: 106 - 107: 6.818 distance: 106 - 209: 7.861 distance: 107 - 108: 15.517 distance: 107 - 110: 26.111 distance: 108 - 109: 8.543 distance: 108 - 112: 22.489 distance: 109 - 206: 26.599 distance: 110 - 111: 40.528 distance: 112 - 113: 16.891 distance: 113 - 114: 14.695 distance: 113 - 116: 21.973 distance: 114 - 115: 15.577 distance: 114 - 126: 18.900 distance: 116 - 117: 11.273 distance: 117 - 118: 14.374 distance: 117 - 119: 16.491 distance: 118 - 120: 19.904 distance: 119 - 121: 20.070 distance: 119 - 122: 6.994 distance: 120 - 121: 5.735 distance: 121 - 123: 16.259 distance: 122 - 124: 18.222 distance: 123 - 125: 4.486 distance: 124 - 125: 19.131 distance: 126 - 127: 16.618 distance: 127 - 128: 6.739 distance: 127 - 130: 26.483 distance: 128 - 129: 25.147 distance: 128 - 134: 18.159 distance: 130 - 131: 22.838 distance: 131 - 132: 32.859 distance: 131 - 133: 30.665