Starting phenix.real_space_refine on Thu Feb 5 14:46:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qn9_53240/02_2026/9qn9_53240.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qn9_53240/02_2026/9qn9_53240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qn9_53240/02_2026/9qn9_53240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qn9_53240/02_2026/9qn9_53240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qn9_53240/02_2026/9qn9_53240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qn9_53240/02_2026/9qn9_53240.map" } resolution = 3.12 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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 168 5.16 5 C 11952 2.51 5 N 2904 2.21 5 O 2988 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18012 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "B" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "C" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "D" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "E" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "F" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "G" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "H" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "I" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "J" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "K" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Chain: "L" Number of atoms: 1501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1501 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 180} Chain breaks: 1 Time building chain proxies: 3.13, per 1000 atoms: 0.17 Number of scatterers: 18012 At special positions: 0 Unit cell: (100.907, 94.3972, 160.801, 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 168 16.00 O 2988 8.00 N 2904 7.00 C 11952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 179 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 179 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 179 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 179 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 179 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 179 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 173 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 179 " distance=2.03 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 173 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 179 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 173 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 179 " distance=2.03 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 173 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 179 " distance=2.03 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 173 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 179 " distance=2.03 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 173 " distance=2.03 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: 1.16 Conformation dependent library (CDL) restraints added in 640.1 milliseconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 12 sheets defined 71.8% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 23 through 41 removed outlier: 3.621A pdb=" N VAL A 27 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 69 removed outlier: 3.609A pdb=" N VAL A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 105 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 128 through 157 Processing helix chain 'A' and resid 183 through 217 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 23 through 41 removed outlier: 3.633A pdb=" N VAL B 27 " --> pdb=" O VAL B 23 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU B 41 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 3.595A pdb=" N VAL B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 105 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 128 through 157 Processing helix chain 'B' and resid 183 through 217 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 23 through 41 removed outlier: 3.621A pdb=" N VAL C 27 " --> pdb=" O VAL C 23 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU C 41 " --> pdb=" O VAL C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 69 removed outlier: 3.619A pdb=" N VAL C 63 " --> pdb=" O GLY C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 105 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 128 through 157 Processing helix chain 'C' and resid 183 through 217 Processing helix chain 'D' and resid 18 through 23 Processing helix chain 'D' and resid 23 through 41 removed outlier: 3.639A pdb=" N VAL D 27 " --> pdb=" O VAL D 23 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N GLU D 41 " --> pdb=" O VAL D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 69 removed outlier: 3.613A pdb=" N VAL D 63 " --> pdb=" O GLY D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 105 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 128 through 157 Processing helix chain 'D' and resid 183 through 217 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 23 through 41 removed outlier: 3.640A pdb=" N VAL E 27 " --> pdb=" O VAL E 23 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLU E 41 " --> pdb=" O VAL E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 69 removed outlier: 3.597A pdb=" N VAL E 63 " --> pdb=" O GLY E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 72 through 105 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 128 through 157 Processing helix chain 'E' and resid 183 through 217 Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 23 through 41 removed outlier: 3.623A pdb=" N VAL F 27 " --> pdb=" O VAL F 23 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N GLU F 41 " --> pdb=" O VAL F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 69 removed outlier: 3.616A pdb=" N VAL F 63 " --> pdb=" O GLY F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 105 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 128 through 157 Processing helix chain 'F' and resid 183 through 217 Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 23 through 41 removed outlier: 3.644A pdb=" N VAL G 27 " --> pdb=" O VAL G 23 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU G 41 " --> pdb=" O VAL G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.598A pdb=" N VAL G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 105 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 128 through 157 Processing helix chain 'G' and resid 183 through 217 Processing helix chain 'H' and resid 18 through 23 Processing helix chain 'H' and resid 23 through 41 removed outlier: 3.640A pdb=" N VAL H 27 " --> pdb=" O VAL H 23 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU H 41 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 69 removed outlier: 3.608A pdb=" N VAL H 63 " --> pdb=" O GLY H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 105 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 128 through 157 Processing helix chain 'H' and resid 183 through 217 Processing helix chain 'I' and resid 18 through 23 Processing helix chain 'I' and resid 23 through 41 removed outlier: 3.633A pdb=" N VAL I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N GLU I 41 " --> pdb=" O VAL I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 59 through 69 removed outlier: 3.617A pdb=" N VAL I 63 " --> pdb=" O GLY I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 72 through 105 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 128 through 157 Processing helix chain 'I' and resid 183 through 217 Processing helix chain 'J' and resid 18 through 23 Processing helix chain 'J' and resid 23 through 41 removed outlier: 3.658A pdb=" N VAL J 27 " --> pdb=" O VAL J 23 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLU J 41 " --> pdb=" O VAL J 37 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 69 removed outlier: 3.599A pdb=" N VAL J 63 " --> pdb=" O GLY J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 105 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 128 through 157 Processing helix chain 'J' and resid 183 through 217 Processing helix chain 'K' and resid 18 through 23 Processing helix chain 'K' and resid 23 through 41 removed outlier: 3.633A pdb=" N VAL K 27 " --> pdb=" O VAL K 23 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU K 41 " --> pdb=" O VAL K 37 " (cutoff:3.500A) Processing helix chain 'K' and resid 59 through 69 removed outlier: 3.595A pdb=" N VAL K 63 " --> pdb=" O GLY K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 72 through 105 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 128 through 157 Processing helix chain 'K' and resid 183 through 217 Processing helix chain 'L' and resid 18 through 23 Processing helix chain 'L' and resid 23 through 41 removed outlier: 3.575A pdb=" N VAL L 27 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU L 41 " --> pdb=" O VAL L 37 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 69 removed outlier: 3.617A pdb=" N VAL L 63 " --> pdb=" O GLY L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 72 through 105 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 128 through 157 Processing helix chain 'L' and resid 183 through 217 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 removed outlier: 3.822A pdb=" N ILE A 52 " --> pdb=" O PHE A 180 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 removed outlier: 3.824A pdb=" N ILE B 52 " --> pdb=" O PHE B 180 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 removed outlier: 3.822A pdb=" N ILE C 52 " --> pdb=" O PHE C 180 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 removed outlier: 3.820A pdb=" N ILE D 52 " --> pdb=" O PHE D 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 removed outlier: 3.827A pdb=" N ILE E 52 " --> pdb=" O PHE E 180 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 removed outlier: 3.809A pdb=" N ILE F 52 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 removed outlier: 3.822A pdb=" N ILE G 52 " --> pdb=" O PHE G 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 removed outlier: 3.829A pdb=" N ILE H 52 " --> pdb=" O PHE H 180 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 removed outlier: 3.818A pdb=" N ILE I 52 " --> pdb=" O PHE I 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 removed outlier: 3.830A pdb=" N ILE J 52 " --> pdb=" O PHE J 180 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 removed outlier: 3.825A pdb=" N ILE K 52 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 3.820A pdb=" N ILE L 52 " --> pdb=" O PHE L 180 " (cutoff:3.500A) 1320 hydrogen bonds defined for protein. 3924 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: 2.45 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5376 1.34 - 1.46: 4695 1.46 - 1.58: 8181 1.58 - 1.70: 0 1.70 - 1.81: 240 Bond restraints: 18492 Sorted by residual: bond pdb=" CA THR L 86 " pdb=" C THR L 86 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.79e-01 bond pdb=" CA THR J 86 " pdb=" C THR J 86 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.79e-01 bond pdb=" CA THR C 86 " pdb=" C THR C 86 " ideal model delta sigma weight residual 1.520 1.528 -0.008 1.23e-02 6.61e+03 3.72e-01 bond pdb=" CA THR D 86 " pdb=" C THR D 86 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.68e-01 bond pdb=" CA THR G 86 " pdb=" C THR G 86 " ideal model delta sigma weight residual 1.520 1.528 -0.007 1.23e-02 6.61e+03 3.57e-01 ... (remaining 18487 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.09: 24394 1.09 - 2.18: 596 2.18 - 3.26: 168 3.26 - 4.35: 42 4.35 - 5.44: 24 Bond angle restraints: 25224 Sorted by residual: angle pdb=" N ARG K 15 " pdb=" CA ARG K 15 " pdb=" CB ARG K 15 " ideal model delta sigma weight residual 113.65 110.31 3.34 1.47e+00 4.63e-01 5.16e+00 angle pdb=" N ARG B 15 " pdb=" CA ARG B 15 " pdb=" CB ARG B 15 " ideal model delta sigma weight residual 113.65 110.33 3.32 1.47e+00 4.63e-01 5.10e+00 angle pdb=" N ARG J 15 " pdb=" CA ARG J 15 " pdb=" CB ARG J 15 " ideal model delta sigma weight residual 113.65 110.35 3.30 1.47e+00 4.63e-01 5.03e+00 angle pdb=" N ARG C 15 " pdb=" CA ARG C 15 " pdb=" CB ARG C 15 " ideal model delta sigma weight residual 113.65 110.38 3.27 1.47e+00 4.63e-01 4.96e+00 angle pdb=" N ARG L 15 " pdb=" CA ARG L 15 " pdb=" CB ARG L 15 " ideal model delta sigma weight residual 113.65 110.38 3.27 1.47e+00 4.63e-01 4.95e+00 ... (remaining 25219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.32: 9614 12.32 - 24.64: 857 24.64 - 36.95: 213 36.95 - 49.27: 97 49.27 - 61.59: 19 Dihedral angle restraints: 10800 sinusoidal: 4128 harmonic: 6672 Sorted by residual: dihedral pdb=" SG CYS D 53 " pdb=" CB CYS D 179 " pdb=" SG CYS D 179 " pdb=" CA CYS D 179 " ideal model delta sinusoidal sigma weight residual -73.00 -11.41 -61.59 1 2.00e+01 2.50e-03 1.26e+01 dihedral pdb=" SG CYS K 53 " pdb=" CB CYS K 179 " pdb=" SG CYS K 179 " pdb=" CA CYS K 179 " ideal model delta sinusoidal sigma weight residual -73.00 -11.71 -61.29 1 2.00e+01 2.50e-03 1.25e+01 dihedral pdb=" SG CYS A 53 " pdb=" CB CYS A 179 " pdb=" SG CYS A 179 " pdb=" CA CYS A 179 " ideal model delta sinusoidal sigma weight residual -73.00 -11.79 -61.21 1 2.00e+01 2.50e-03 1.24e+01 ... (remaining 10797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 1638 0.023 - 0.047: 781 0.047 - 0.070: 398 0.070 - 0.093: 144 0.093 - 0.117: 63 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA THR F 86 " pdb=" N THR F 86 " pdb=" C THR F 86 " pdb=" CB THR F 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA THR D 86 " pdb=" N THR D 86 " pdb=" C THR D 86 " pdb=" CB THR D 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA THR C 86 " pdb=" N THR C 86 " pdb=" C THR C 86 " pdb=" CB THR C 86 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 3021 not shown) Planarity restraints: 3012 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 183 " -0.015 5.00e-02 4.00e+02 2.21e-02 7.80e-01 pdb=" N PRO K 184 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO K 184 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO K 184 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 183 " -0.014 5.00e-02 4.00e+02 2.09e-02 6.98e-01 pdb=" N PRO F 184 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO F 184 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO F 184 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG I 183 " -0.012 5.00e-02 4.00e+02 1.86e-02 5.53e-01 pdb=" N PRO I 184 " 0.032 5.00e-02 4.00e+02 pdb=" CA PRO I 184 " -0.009 5.00e-02 4.00e+02 pdb=" CD PRO I 184 " -0.010 5.00e-02 4.00e+02 ... (remaining 3009 not shown) Histogram of nonbonded interaction distances: 2.64 - 3.09: 12811 3.09 - 3.54: 20650 3.54 - 3.99: 26497 3.99 - 4.45: 32718 4.45 - 4.90: 52119 Nonbonded interactions: 144795 Sorted by model distance: nonbonded pdb=" N ASN E 175 " pdb=" CG ASN E 175 " model vdw 2.636 2.680 nonbonded pdb=" N ASN I 175 " pdb=" CG ASN I 175 " model vdw 2.637 2.680 nonbonded pdb=" N ASN A 175 " pdb=" CG ASN A 175 " model vdw 2.637 2.680 nonbonded pdb=" N ASN D 175 " pdb=" CG ASN D 175 " model vdw 2.639 2.680 nonbonded pdb=" N ASN L 175 " pdb=" CG ASN L 175 " model vdw 2.649 2.680 ... (remaining 144790 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 5.010 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.790 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: 0.010 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 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 : 0.003 0.019 18516 Z= 0.116 Angle : 0.479 5.438 25272 Z= 0.254 Chirality : 0.036 0.117 3024 Planarity : 0.003 0.024 3012 Dihedral : 10.746 58.481 6384 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.96 % Allowed : 4.49 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.70 (0.18), residues: 2208 helix: 3.97 (0.11), residues: 1488 sheet: 1.49 (0.49), residues: 132 loop : -1.73 (0.24), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG F 164 TYR 0.005 0.001 TYR I 135 PHE 0.008 0.001 PHE C 51 TRP 0.005 0.001 TRP C 132 HIS 0.002 0.000 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00256 (18492) covalent geometry : angle 0.47482 (25224) SS BOND : bond 0.00208 ( 24) SS BOND : angle 1.46362 ( 48) hydrogen bonds : bond 0.06407 ( 1320) hydrogen bonds : angle 3.28556 ( 3924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 374 time to evaluate : 0.550 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6001 (pp) REVERT: A 22 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8304 (ttm-80) REVERT: A 41 GLU cc_start: 0.8553 (mm-30) cc_final: 0.8239 (mm-30) REVERT: A 211 TYR cc_start: 0.8426 (t80) cc_final: 0.7924 (t80) REVERT: B 10 LEU cc_start: 0.6646 (OUTLIER) cc_final: 0.6070 (pp) REVERT: B 41 GLU cc_start: 0.8654 (mm-30) cc_final: 0.8313 (mm-30) REVERT: B 211 TYR cc_start: 0.8424 (t80) cc_final: 0.7908 (t80) REVERT: C 10 LEU cc_start: 0.6345 (OUTLIER) cc_final: 0.5841 (pp) REVERT: C 22 ARG cc_start: 0.8523 (ttm-80) cc_final: 0.8288 (ttm-80) REVERT: C 41 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8244 (mm-30) REVERT: D 10 LEU cc_start: 0.6380 (OUTLIER) cc_final: 0.5851 (pp) REVERT: D 22 ARG cc_start: 0.8535 (ttm-80) cc_final: 0.8293 (ttm-80) REVERT: D 41 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8228 (mm-30) REVERT: D 211 TYR cc_start: 0.8451 (t80) cc_final: 0.8009 (t80) REVERT: E 10 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5832 (pp) REVERT: E 22 ARG cc_start: 0.8541 (ttm-80) cc_final: 0.8296 (ttm-80) REVERT: E 41 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8311 (mm-30) REVERT: E 211 TYR cc_start: 0.8403 (t80) cc_final: 0.7841 (t80) REVERT: F 10 LEU cc_start: 0.6236 (OUTLIER) cc_final: 0.5722 (pp) REVERT: F 22 ARG cc_start: 0.8551 (ttm-80) cc_final: 0.8325 (ttm-80) REVERT: F 41 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8241 (mm-30) REVERT: G 10 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.5997 (pp) REVERT: G 22 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8308 (ttm-80) REVERT: G 41 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8268 (mm-30) REVERT: G 211 TYR cc_start: 0.8415 (t80) cc_final: 0.7831 (t80) REVERT: H 10 LEU cc_start: 0.6320 (OUTLIER) cc_final: 0.5813 (pp) REVERT: H 22 ARG cc_start: 0.8623 (ttm-80) cc_final: 0.8383 (ttm-80) REVERT: H 211 TYR cc_start: 0.8361 (t80) cc_final: 0.7544 (t80) REVERT: I 10 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6297 (pp) REVERT: I 41 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8181 (mm-30) REVERT: I 211 TYR cc_start: 0.8396 (t80) cc_final: 0.8107 (t80) REVERT: J 10 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6017 (pp) REVERT: J 22 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8246 (ttm-80) REVERT: J 41 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8247 (mm-30) REVERT: K 10 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5829 (pp) REVERT: K 22 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.8309 (ttm-80) REVERT: K 211 TYR cc_start: 0.8369 (t80) cc_final: 0.7906 (t80) REVERT: L 10 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.5781 (pp) REVERT: L 22 ARG cc_start: 0.8536 (ttm-80) cc_final: 0.8276 (ttm-80) REVERT: L 41 GLU cc_start: 0.8558 (mm-30) cc_final: 0.8224 (mm-30) outliers start: 60 outliers final: 17 residues processed: 414 average time/residue: 0.1288 time to fit residues: 79.2205 Evaluate side-chains 314 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 285 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 175 ASN Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 8.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 175 ASN ** H 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.085853 restraints weight = 23604.473| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.81 r_work: 0.2837 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18516 Z= 0.151 Angle : 0.514 5.450 25272 Z= 0.254 Chirality : 0.039 0.125 3024 Planarity : 0.003 0.029 3012 Dihedral : 5.666 53.399 2470 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.66 % Allowed : 9.86 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.98 (0.18), residues: 2208 helix: 4.18 (0.11), residues: 1488 sheet: 1.92 (0.49), residues: 132 loop : -1.71 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 183 TYR 0.008 0.001 TYR L 65 PHE 0.011 0.001 PHE C 68 TRP 0.005 0.001 TRP J 132 HIS 0.005 0.001 HIS K 16 Details of bonding type rmsd covalent geometry : bond 0.00382 (18492) covalent geometry : angle 0.51069 (25224) SS BOND : bond 0.00326 ( 24) SS BOND : angle 1.37628 ( 48) hydrogen bonds : bond 0.03653 ( 1320) hydrogen bonds : angle 2.84315 ( 3924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 272 time to evaluate : 0.766 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.6557 (OUTLIER) cc_final: 0.6020 (pp) REVERT: A 22 ARG cc_start: 0.8516 (ttm-80) cc_final: 0.8289 (ttm-80) REVERT: A 41 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8252 (mm-30) REVERT: A 211 TYR cc_start: 0.8458 (t80) cc_final: 0.7949 (t80) REVERT: B 10 LEU cc_start: 0.6513 (OUTLIER) cc_final: 0.5929 (pp) REVERT: B 22 ARG cc_start: 0.8398 (ttm-80) cc_final: 0.8005 (ttm-80) REVERT: B 41 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8302 (mm-30) REVERT: B 211 TYR cc_start: 0.8481 (t80) cc_final: 0.7985 (t80) REVERT: C 10 LEU cc_start: 0.6303 (OUTLIER) cc_final: 0.5791 (pp) REVERT: C 22 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8318 (ttm-80) REVERT: C 41 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8228 (mm-30) REVERT: C 211 TYR cc_start: 0.8309 (t80) cc_final: 0.7939 (t80) REVERT: D 10 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.5888 (pp) REVERT: D 22 ARG cc_start: 0.8540 (ttm-80) cc_final: 0.8298 (ttm-80) REVERT: D 41 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8248 (mm-30) REVERT: D 211 TYR cc_start: 0.8472 (t80) cc_final: 0.8027 (t80) REVERT: E 10 LEU cc_start: 0.6349 (OUTLIER) cc_final: 0.5814 (pp) REVERT: E 22 ARG cc_start: 0.8505 (ttm-80) cc_final: 0.8282 (ttm-80) REVERT: E 41 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8293 (mm-30) REVERT: E 211 TYR cc_start: 0.8437 (t80) cc_final: 0.7856 (t80) REVERT: F 10 LEU cc_start: 0.6301 (OUTLIER) cc_final: 0.5761 (pp) REVERT: F 22 ARG cc_start: 0.8552 (ttm-80) cc_final: 0.8338 (ttm-80) REVERT: F 41 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8227 (mm-30) REVERT: F 211 TYR cc_start: 0.8278 (t80) cc_final: 0.7902 (t80) REVERT: G 10 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.5894 (pp) REVERT: G 22 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8270 (ttm-80) REVERT: G 41 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8258 (mm-30) REVERT: G 211 TYR cc_start: 0.8460 (t80) cc_final: 0.7854 (t80) REVERT: H 10 LEU cc_start: 0.6282 (OUTLIER) cc_final: 0.5781 (pp) REVERT: H 22 ARG cc_start: 0.8593 (ttm-80) cc_final: 0.8355 (ttm-80) REVERT: H 211 TYR cc_start: 0.8340 (t80) cc_final: 0.7589 (t80) REVERT: I 10 LEU cc_start: 0.6658 (OUTLIER) cc_final: 0.6206 (pp) REVERT: I 41 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8210 (mm-30) REVERT: I 211 TYR cc_start: 0.8446 (t80) cc_final: 0.8146 (t80) REVERT: J 10 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5979 (pp) REVERT: J 22 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8239 (ttm-80) REVERT: J 41 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8279 (mm-30) REVERT: K 10 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5791 (pp) REVERT: K 22 ARG cc_start: 0.8507 (ttm-80) cc_final: 0.8296 (ttm-80) REVERT: K 41 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8282 (mm-30) REVERT: K 211 TYR cc_start: 0.8437 (t80) cc_final: 0.7962 (t80) REVERT: L 10 LEU cc_start: 0.6267 (OUTLIER) cc_final: 0.5756 (pp) REVERT: L 22 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8211 (ttm-80) REVERT: L 41 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8229 (mm-30) outliers start: 54 outliers final: 40 residues processed: 305 average time/residue: 0.1513 time to fit residues: 68.2153 Evaluate side-chains 311 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 259 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 210 VAL Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 89 LEU Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 210 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain E residue 210 VAL Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain F residue 175 ASN Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 175 ASN Chi-restraints excluded: chain G residue 210 VAL Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 175 ASN Chi-restraints excluded: chain I residue 210 VAL Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 95 VAL Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain J residue 210 VAL Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 89 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 158 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 185 optimal weight: 0.1980 chunk 202 optimal weight: 2.9990 chunk 210 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 0.4980 chunk 195 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN D 14 ASN ** E 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 14 ASN ** K 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 175 ASN ** L 14 ASN ** 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 = 0.3529 r_free = 0.3529 target = 0.123369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.087866 restraints weight = 23899.463| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.81 r_work: 0.2878 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18516 Z= 0.092 Angle : 0.446 5.296 25272 Z= 0.220 Chirality : 0.037 0.121 3024 Planarity : 0.003 0.021 3012 Dihedral : 5.739 59.020 2470 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.47 % Allowed : 13.95 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.22 (0.18), residues: 2208 helix: 4.38 (0.11), residues: 1488 sheet: 1.88 (0.49), residues: 132 loop : -1.64 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 22 TYR 0.005 0.001 TYR G 135 PHE 0.009 0.001 PHE F 51 TRP 0.005 0.001 TRP J 132 HIS 0.002 0.000 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00206 (18492) covalent geometry : angle 0.44384 (25224) SS BOND : bond 0.00182 ( 24) SS BOND : angle 1.17875 ( 48) hydrogen bonds : bond 0.03227 ( 1320) hydrogen bonds : angle 2.70954 ( 3924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 0.729 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6013 (pp) REVERT: A 22 ARG cc_start: 0.8520 (ttm-80) cc_final: 0.8300 (ttm-80) REVERT: A 41 GLU cc_start: 0.8515 (mm-30) cc_final: 0.8201 (mm-30) REVERT: A 211 TYR cc_start: 0.8483 (t80) cc_final: 0.7942 (t80) REVERT: B 10 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.5915 (pp) REVERT: B 22 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.7969 (ttm-80) REVERT: B 41 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8240 (mm-30) REVERT: B 211 TYR cc_start: 0.8478 (t80) cc_final: 0.7950 (t80) REVERT: C 10 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.5777 (pp) REVERT: C 22 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.8311 (ttm-80) REVERT: C 41 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8209 (mm-30) REVERT: C 65 TYR cc_start: 0.9140 (t80) cc_final: 0.8923 (t80) REVERT: C 211 TYR cc_start: 0.8349 (t80) cc_final: 0.7916 (t80) REVERT: D 10 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.5948 (pp) REVERT: D 22 ARG cc_start: 0.8545 (ttm-80) cc_final: 0.8316 (ttm-80) REVERT: D 41 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8174 (mm-30) REVERT: D 211 TYR cc_start: 0.8483 (t80) cc_final: 0.8016 (t80) REVERT: E 10 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5798 (pp) REVERT: E 22 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8279 (ttm-80) REVERT: E 41 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8266 (mm-30) REVERT: E 211 TYR cc_start: 0.8453 (t80) cc_final: 0.7891 (t80) REVERT: F 10 LEU cc_start: 0.6276 (OUTLIER) cc_final: 0.5761 (pp) REVERT: F 22 ARG cc_start: 0.8538 (ttm-80) cc_final: 0.8330 (ttm-80) REVERT: F 41 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8191 (mm-30) REVERT: F 65 TYR cc_start: 0.9142 (t80) cc_final: 0.8921 (t80) REVERT: F 105 MET cc_start: 0.3426 (mmp) cc_final: 0.3216 (mmm) REVERT: F 211 TYR cc_start: 0.8317 (t80) cc_final: 0.7950 (t80) REVERT: G 10 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6050 (pp) REVERT: G 22 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8285 (ttm-80) REVERT: G 41 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8214 (mm-30) REVERT: G 211 TYR cc_start: 0.8465 (t80) cc_final: 0.7895 (t80) REVERT: H 10 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.5774 (pp) REVERT: H 22 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8360 (ttm-80) REVERT: H 211 TYR cc_start: 0.8345 (t80) cc_final: 0.7569 (t80) REVERT: I 10 LEU cc_start: 0.6781 (OUTLIER) cc_final: 0.6301 (pp) REVERT: I 41 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8164 (mm-30) REVERT: I 65 TYR cc_start: 0.9156 (t80) cc_final: 0.8936 (t80) REVERT: I 211 TYR cc_start: 0.8454 (t80) cc_final: 0.8153 (t80) REVERT: J 10 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6012 (pp) REVERT: J 22 ARG cc_start: 0.8512 (ttm-80) cc_final: 0.8259 (ttm-80) REVERT: J 41 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8279 (mm-30) REVERT: K 10 LEU cc_start: 0.6368 (OUTLIER) cc_final: 0.5860 (pp) REVERT: K 41 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8273 (mm-30) REVERT: K 211 TYR cc_start: 0.8452 (t80) cc_final: 0.7938 (t80) REVERT: L 10 LEU cc_start: 0.6270 (OUTLIER) cc_final: 0.5774 (pp) REVERT: L 22 ARG cc_start: 0.8575 (ttm-80) cc_final: 0.8220 (ttm-80) REVERT: L 41 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8151 (mm-30) outliers start: 50 outliers final: 28 residues processed: 299 average time/residue: 0.1534 time to fit residues: 68.1892 Evaluate side-chains 304 residues out of total 2028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 175 ASN Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 34 MET Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain E residue 10 LEU Chi-restraints excluded: chain E residue 53 CYS Chi-restraints excluded: chain E residue 175 ASN Chi-restraints excluded: chain F residue 10 LEU Chi-restraints excluded: chain F residue 53 CYS Chi-restraints excluded: chain F residue 85 SER Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain H residue 10 LEU Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 175 ASN Chi-restraints excluded: chain I residue 10 LEU Chi-restraints excluded: chain I residue 53 CYS Chi-restraints excluded: chain I residue 175 ASN Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 34 MET Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain J residue 85 SER Chi-restraints excluded: chain J residue 175 ASN Chi-restraints excluded: chain K residue 10 LEU Chi-restraints excluded: chain K residue 53 CYS Chi-restraints excluded: chain K residue 175 ASN Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 53 CYS Chi-restraints excluded: chain L residue 175 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.2358 > 50: distance: 53 - 76: 20.063 distance: 57 - 87: 24.215 distance: 71 - 76: 22.744 distance: 76 - 77: 34.272 distance: 77 - 78: 13.595 distance: 77 - 80: 32.591 distance: 78 - 79: 19.472 distance: 78 - 87: 13.988 distance: 80 - 81: 15.502 distance: 81 - 82: 14.719 distance: 81 - 83: 27.988 distance: 82 - 84: 9.431 distance: 83 - 85: 7.988 distance: 84 - 86: 17.677 distance: 85 - 86: 25.718 distance: 87 - 88: 10.701 distance: 88 - 89: 34.041 distance: 88 - 91: 10.930 distance: 89 - 90: 16.257 distance: 89 - 98: 35.376 distance: 92 - 93: 20.523 distance: 92 - 94: 36.570 distance: 93 - 95: 14.331 distance: 95 - 97: 41.780 distance: 96 - 97: 17.678 distance: 98 - 99: 15.662 distance: 98 - 104: 9.836 distance: 99 - 100: 7.960 distance: 99 - 102: 15.230 distance: 100 - 101: 37.032 distance: 100 - 105: 7.869 distance: 102 - 103: 13.403 distance: 103 - 104: 5.926 distance: 105 - 106: 19.480 distance: 106 - 107: 20.325 distance: 106 - 109: 40.164 distance: 107 - 108: 13.634 distance: 107 - 113: 22.356 distance: 109 - 110: 28.338 distance: 109 - 111: 24.267 distance: 110 - 112: 30.906 distance: 113 - 114: 33.274 distance: 114 - 115: 20.632 distance: 114 - 117: 24.968 distance: 115 - 116: 31.365 distance: 115 - 119: 10.056 distance: 116 - 147: 38.123 distance: 117 - 118: 3.953 distance: 119 - 120: 25.528 distance: 120 - 121: 17.749 distance: 120 - 123: 23.176 distance: 121 - 122: 19.339 distance: 121 - 129: 20.998 distance: 122 - 155: 30.203 distance: 123 - 124: 15.116 distance: 124 - 125: 8.566 distance: 124 - 126: 12.310 distance: 125 - 127: 10.812 distance: 126 - 128: 6.358 distance: 127 - 128: 9.060 distance: 129 - 130: 10.764 distance: 130 - 131: 21.834 distance: 130 - 133: 5.254 distance: 131 - 132: 13.772 distance: 131 - 136: 18.718 distance: 132 - 169: 23.272 distance: 133 - 134: 16.881 distance: 133 - 135: 24.389 distance: 136 - 137: 6.444 distance: 137 - 138: 21.733 distance: 137 - 140: 17.862 distance: 138 - 139: 18.481 distance: 138 - 147: 20.418 distance: 139 - 175: 34.256 distance: 140 - 141: 3.341 distance: 141 - 142: 9.105 distance: 142 - 143: 4.615 distance: 143 - 144: 19.047 distance: 144 - 145: 6.942 distance: 144 - 146: 5.516 distance: 147 - 148: 22.200 distance: 148 - 149: 21.754 distance: 148 - 151: 24.497 distance: 149 - 150: 11.651 distance: 149 - 155: 23.000 distance: 150 - 183: 19.102 distance: 151 - 152: 20.301 distance: 152 - 153: 28.862 distance: 152 - 154: 16.188 distance: 155 - 156: 10.018 distance: 156 - 157: 3.257 distance: 156 - 159: 12.961 distance: 157 - 158: 31.398 distance: 157 - 169: 4.943 distance: 158 - 191: 27.647 distance: 159 - 160: 17.228 distance: 160 - 161: 7.397 distance: 160 - 162: 8.077 distance: 161 - 163: 3.395 distance: 162 - 164: 5.775 distance: 162 - 165: 5.584 distance: 163 - 164: 5.364 distance: 164 - 166: 7.449 distance: 165 - 167: 10.081 distance: 166 - 168: 9.302 distance: 167 - 168: 5.084