Starting phenix.real_space_refine on Fri Jul 3 05:11:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9geo_51296/07_2026/9geo_51296.cif Found real_map, /net/cci-nas-00/data/ceres_data/9geo_51296/07_2026/9geo_51296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9geo_51296/07_2026/9geo_51296.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9geo_51296/07_2026/9geo_51296.map" model { file = "/net/cci-nas-00/data/ceres_data/9geo_51296/07_2026/9geo_51296.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9geo_51296/07_2026/9geo_51296.cif" } resolution = 2.79 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= 1.000 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: 5 Type Number sf(0) Gaussians P 290 5.49 5 S 12 5.16 5 C 6598 2.51 5 N 2248 2.21 5 O 3052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12200 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "E" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "F" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "J" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Time building chain proxies: 2.65, per 1000 atoms: 0.22 Number of scatterers: 12200 At special positions: 0 Unit cell: (73.44, 114.24, 121.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 290 15.00 O 3052 8.00 N 2248 7.00 C 6598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 467.8 milliseconds 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1418 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.9% alpha, 3.2% beta 137 base pairs and 269 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.779A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.542A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.527A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.800A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.691A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.510A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.751A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.079A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.763A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.961A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.052A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 411 hydrogen bonds defined for protein. 1206 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 269 stacking parallelities Total time for adding SS restraints: 2.35 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2217 1.33 - 1.45: 4170 1.45 - 1.57: 5762 1.57 - 1.69: 578 1.69 - 1.81: 22 Bond restraints: 12749 Sorted by residual: bond pdb=" C3' DA I -1 " pdb=" C2' DA I -1 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC I 1 " pdb=" C2' DC I 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC I 40 " pdb=" C2' DC I 40 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.72e+00 bond pdb=" C3' DG J 52 " pdb=" C2' DG J 52 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DA J 63 " pdb=" C2' DA J 63 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.77e+00 ... (remaining 12744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 15957 1.00 - 1.99: 1828 1.99 - 2.99: 618 2.99 - 3.99: 48 3.99 - 4.98: 10 Bond angle restraints: 18461 Sorted by residual: angle pdb=" O4' DA I -68 " pdb=" C1' DA I -68 " pdb=" N9 DA I -68 " ideal model delta sigma weight residual 108.00 111.15 -3.15 7.00e-01 2.04e+00 2.02e+01 angle pdb=" N3 DT I -61 " pdb=" C4 DT I -61 " pdb=" O4 DT I -61 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 ... (remaining 18456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.83: 5375 33.83 - 67.67: 1525 67.67 - 101.50: 21 101.50 - 135.33: 1 135.33 - 169.16: 2 Dihedral angle restraints: 6924 sinusoidal: 4728 harmonic: 2196 Sorted by residual: dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 50.84 169.16 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC J 51 " pdb=" C3' DC J 51 " pdb=" O3' DC J 51 " pdb=" P DG J 52 " ideal model delta sinusoidal sigma weight residual 220.00 70.41 149.59 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC I 52 " pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " pdb=" P DC I 53 " ideal model delta sinusoidal sigma weight residual 220.00 91.33 128.67 1 3.50e+01 8.16e-04 1.27e+01 ... (remaining 6921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1134 0.030 - 0.060: 624 0.060 - 0.091: 232 0.091 - 0.121: 103 0.121 - 0.151: 10 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CA PRO A 43 " pdb=" N PRO A 43 " pdb=" C PRO A 43 " pdb=" CB PRO A 43 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.71e-01 chirality pdb=" C3' DG I 20 " pdb=" C4' DG I 20 " pdb=" O3' DG I 20 " pdb=" C2' DG I 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.59 -0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" C3' DC I 53 " pdb=" C4' DC I 53 " pdb=" O3' DC I 53 " pdb=" C2' DC I 53 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 2100 not shown) Planarity restraints: 1331 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 43 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.51e+00 pdb=" N9 DG I -35 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I -26 " 0.022 2.00e-02 2.50e+03 1.09e-02 2.66e+00 pdb=" N1 DC I -26 " -0.020 2.00e-02 2.50e+03 pdb=" C2 DC I -26 " 0.002 2.00e-02 2.50e+03 pdb=" O2 DC I -26 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DC I -26 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DC I -26 " 0.003 2.00e-02 2.50e+03 pdb=" N4 DC I -26 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I -26 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I -26 " -0.005 2.00e-02 2.50e+03 ... (remaining 1328 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1131 2.74 - 3.28: 10173 3.28 - 3.82: 24214 3.82 - 4.36: 30965 4.36 - 4.90: 43278 Nonbonded interactions: 109761 Sorted by model distance: nonbonded pdb=" O HIS E 113 " pdb=" O HOH E 201 " model vdw 2.199 3.040 nonbonded pdb=" O HIS B 75 " pdb=" NH2 ARG D 89 " model vdw 2.199 3.120 nonbonded pdb=" NH2 ARG C 32 " pdb=" OE2 GLU D 32 " model vdw 2.204 3.120 nonbonded pdb=" OE2 GLU B 53 " pdb=" O HOH B 201 " model vdw 2.223 3.040 nonbonded pdb=" O LEU B 97 " pdb=" O HOH B 202 " model vdw 2.244 3.040 ... (remaining 109756 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.610 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.680 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 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:8.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 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 0.041 12749 Z= 0.542 Angle : 0.731 4.983 18461 Z= 0.657 Chirality : 0.044 0.151 2103 Planarity : 0.004 0.052 1331 Dihedral : 28.684 169.163 5506 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.23 % Allowed : 20.06 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.65 (0.29), residues: 740 helix: 1.92 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.11 (0.33), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 35 TYR 0.012 0.002 TYR D 34 PHE 0.008 0.002 PHE D 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.54 (12749) covalent geometry : angle 0.73125 / 0.66 (18461) hydrogen bonds : bond 0.11799 / 7.98 ( 761) hydrogen bonds : angle 3.86455 / 2.76 ( 1906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.307 Fit side-chains REVERT: A 115 LYS cc_start: 0.8048 (mtpm) cc_final: 0.7649 (mtmt) REVERT: A 129 ARG cc_start: 0.7656 (ttt180) cc_final: 0.6741 (tmt170) REVERT: B 91 LYS cc_start: 0.8217 (tttt) cc_final: 0.7794 (ttpt) REVERT: C 36 LYS cc_start: 0.8058 (mttt) cc_final: 0.7766 (mtmt) REVERT: C 61 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: C 64 GLU cc_start: 0.7289 (tt0) cc_final: 0.7074 (tt0) REVERT: C 95 LYS cc_start: 0.8308 (tppt) cc_final: 0.7979 (tptp) REVERT: C 99 ARG cc_start: 0.8424 (mmt-90) cc_final: 0.7369 (mtp180) REVERT: C 104 GLN cc_start: 0.8645 (mt0) cc_final: 0.7799 (mm110) REVERT: D 109 SER cc_start: 0.8182 (t) cc_final: 0.7751 (m) REVERT: E 56 LYS cc_start: 0.8576 (tttt) cc_final: 0.8128 (ttpp) REVERT: E 59 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7726 (pt0) REVERT: E 76 GLN cc_start: 0.7134 (mt0) cc_final: 0.6654 (pt0) REVERT: E 129 ARG cc_start: 0.7932 (ttt180) cc_final: 0.6644 (tpt90) REVERT: E 131 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.6537 (mtp85) REVERT: F 93 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.7736 (mm-40) REVERT: G 95 LYS cc_start: 0.8084 (ttmt) cc_final: 0.7502 (tmtt) REVERT: G 99 ARG cc_start: 0.8107 (mmt180) cc_final: 0.7088 (mmm160) REVERT: G 104 GLN cc_start: 0.8223 (mt0) cc_final: 0.7409 (mm110) REVERT: H 31 LYS cc_start: 0.7955 (tptt) cc_final: 0.7291 (tptm) REVERT: H 113 LYS cc_start: 0.8164 (ttpt) cc_final: 0.7703 (ttmm) outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 0.8610 time to fit residues: 88.0698 Evaluate side-chains 94 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.165966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121508 restraints weight = 10346.613| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 0.65 r_work: 0.3046 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12749 Z= 0.171 Angle : 0.624 6.791 18461 Z= 0.371 Chirality : 0.045 0.244 2103 Planarity : 0.005 0.055 1331 Dihedral : 31.200 168.687 4032 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.87 % Allowed : 17.83 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.29), residues: 740 helix: 2.16 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -1.03 (0.34), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 78 TYR 0.011 0.001 TYR B 51 PHE 0.008 0.002 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.17 (12749) covalent geometry : angle 0.62411 / 0.37 (18461) hydrogen bonds : bond 0.05260 / 3.60 ( 761) hydrogen bonds : angle 3.10567 / 2.23 ( 1906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.372 Fit side-chains REVERT: A 129 ARG cc_start: 0.7854 (ttt180) cc_final: 0.7479 (tmt170) REVERT: C 92 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: C 99 ARG cc_start: 0.8300 (mmt-90) cc_final: 0.7777 (mtp180) REVERT: C 104 GLN cc_start: 0.8570 (mt0) cc_final: 0.7988 (mm110) REVERT: C 118 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.5767 (mptt) REVERT: D 102 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6650 (mp0) REVERT: E 56 LYS cc_start: 0.8793 (tttt) cc_final: 0.8527 (ttpp) REVERT: E 76 GLN cc_start: 0.7477 (mt0) cc_final: 0.7235 (pt0) REVERT: E 129 ARG cc_start: 0.7989 (ttt180) cc_final: 0.7356 (tpt90) REVERT: G 95 LYS cc_start: 0.8289 (ttmt) cc_final: 0.8024 (tmtt) REVERT: G 99 ARG cc_start: 0.8159 (mmt180) cc_final: 0.7839 (mmm160) REVERT: G 104 GLN cc_start: 0.8323 (mt0) cc_final: 0.7828 (mm110) REVERT: H 31 LYS cc_start: 0.7959 (tptt) cc_final: 0.7466 (tptm) REVERT: H 113 LYS cc_start: 0.8485 (ttpt) cc_final: 0.8137 (ttmm) outliers start: 18 outliers final: 7 residues processed: 102 average time/residue: 0.7974 time to fit residues: 86.3303 Evaluate side-chains 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 20.0000 chunk 59 optimal weight: 0.5980 chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 56 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.166316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.122662 restraints weight = 10454.163| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 0.63 r_work: 0.3069 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12749 Z= 0.145 Angle : 0.598 6.631 18461 Z= 0.360 Chirality : 0.045 0.248 2103 Planarity : 0.004 0.051 1331 Dihedral : 31.180 168.307 4015 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.03 % Allowed : 18.95 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.38 (0.29), residues: 740 helix: 2.45 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.98 (0.35), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.017 0.001 TYR D 34 PHE 0.008 0.001 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (12749) covalent geometry : angle 0.59837 / 0.36 (18461) hydrogen bonds : bond 0.04759 / 3.27 ( 761) hydrogen bonds : angle 2.99803 / 2.15 ( 1906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.316 Fit side-chains REVERT: A 120 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7623 (mtt) REVERT: A 129 ARG cc_start: 0.7832 (ttt180) cc_final: 0.7439 (tmt170) REVERT: B 59 LYS cc_start: 0.8429 (tttm) cc_final: 0.8132 (tttt) REVERT: C 92 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: C 99 ARG cc_start: 0.8251 (mmt-90) cc_final: 0.7749 (mtp180) REVERT: C 104 GLN cc_start: 0.8556 (mt0) cc_final: 0.7955 (mm110) REVERT: C 108 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8587 (mp) REVERT: C 118 LYS cc_start: 0.6805 (OUTLIER) cc_final: 0.5754 (mptt) REVERT: D 102 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: E 56 LYS cc_start: 0.8774 (tttt) cc_final: 0.8515 (ttpp) REVERT: E 76 GLN cc_start: 0.7474 (mt0) cc_final: 0.7214 (pt0) REVERT: E 129 ARG cc_start: 0.7948 (ttt180) cc_final: 0.7325 (tpt90) REVERT: F 92 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7600 (mtp85) REVERT: G 95 LYS cc_start: 0.8254 (ttmt) cc_final: 0.8007 (tmtt) REVERT: G 99 ARG cc_start: 0.8122 (mmt180) cc_final: 0.7804 (mmm160) REVERT: G 104 GLN cc_start: 0.8308 (mt0) cc_final: 0.7813 (mm110) REVERT: H 31 LYS cc_start: 0.7959 (tptt) cc_final: 0.7473 (tptm) REVERT: H 113 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8188 (ttmm) outliers start: 19 outliers final: 7 residues processed: 100 average time/residue: 0.7503 time to fit residues: 79.3091 Evaluate side-chains 96 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 98 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 71 optimal weight: 30.0000 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN G 110 ASN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.167005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.122660 restraints weight = 10472.143| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.65 r_work: 0.3079 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12749 Z= 0.140 Angle : 0.573 6.340 18461 Z= 0.347 Chirality : 0.043 0.250 2103 Planarity : 0.004 0.049 1331 Dihedral : 31.139 167.439 4015 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.71 % Allowed : 19.11 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.70 (0.30), residues: 740 helix: 2.69 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.89 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 35 TYR 0.010 0.001 TYR B 51 PHE 0.008 0.001 PHE E 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.14 (12749) covalent geometry : angle 0.57317 / 0.35 (18461) hydrogen bonds : bond 0.04482 / 3.08 ( 761) hydrogen bonds : angle 2.81459 / 2.02 ( 1906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.294 Fit side-chains REVERT: A 129 ARG cc_start: 0.7819 (ttt180) cc_final: 0.7436 (tmt170) REVERT: B 92 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.8134 (mtp-110) REVERT: C 61 GLU cc_start: 0.7469 (OUTLIER) cc_final: 0.7250 (mm-30) REVERT: C 92 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8201 (mt-10) REVERT: C 99 ARG cc_start: 0.8252 (mmt-90) cc_final: 0.7727 (mtp180) REVERT: C 104 GLN cc_start: 0.8567 (mt0) cc_final: 0.7957 (mm110) REVERT: C 108 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8622 (mp) REVERT: C 118 LYS cc_start: 0.6825 (OUTLIER) cc_final: 0.5778 (mptt) REVERT: D 102 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6556 (mp0) REVERT: E 56 LYS cc_start: 0.8787 (tttt) cc_final: 0.8447 (ttpp) REVERT: E 76 GLN cc_start: 0.7468 (mt0) cc_final: 0.7222 (pt0) REVERT: E 129 ARG cc_start: 0.7962 (ttt180) cc_final: 0.7351 (tpt90) REVERT: F 92 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7591 (mtp85) REVERT: G 95 LYS cc_start: 0.8262 (ttmt) cc_final: 0.8017 (tmtt) REVERT: G 99 ARG cc_start: 0.8138 (mmt180) cc_final: 0.7792 (mmm160) REVERT: G 104 GLN cc_start: 0.8364 (mt0) cc_final: 0.7846 (mm110) REVERT: H 31 LYS cc_start: 0.7943 (tptt) cc_final: 0.7463 (tptm) REVERT: H 113 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8205 (ttmm) outliers start: 17 outliers final: 7 residues processed: 101 average time/residue: 0.7767 time to fit residues: 82.7159 Evaluate side-chains 99 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 3 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN G 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.166613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.122035 restraints weight = 10491.048| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 0.65 r_work: 0.3070 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12749 Z= 0.144 Angle : 0.574 6.369 18461 Z= 0.345 Chirality : 0.043 0.248 2103 Planarity : 0.004 0.050 1331 Dihedral : 31.128 167.843 4015 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.82 % Allowed : 18.63 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.76 (0.30), residues: 740 helix: 2.73 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.86 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.011 0.001 TYR D 34 PHE 0.008 0.001 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (12749) covalent geometry : angle 0.57392 / 0.35 (18461) hydrogen bonds : bond 0.04542 / 3.11 ( 761) hydrogen bonds : angle 2.80238 / 2.02 ( 1906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 0.245 Fit side-chains REVERT: A 129 ARG cc_start: 0.7833 (ttt180) cc_final: 0.7435 (tmt170) REVERT: C 61 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.7281 (mm-30) REVERT: C 99 ARG cc_start: 0.8264 (mmt-90) cc_final: 0.7720 (mtp180) REVERT: C 104 GLN cc_start: 0.8566 (mt0) cc_final: 0.7956 (mm110) REVERT: C 108 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8617 (mp) REVERT: C 118 LYS cc_start: 0.6836 (OUTLIER) cc_final: 0.5767 (mptt) REVERT: D 102 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: E 56 LYS cc_start: 0.8785 (tttt) cc_final: 0.8446 (ttpp) REVERT: E 76 GLN cc_start: 0.7490 (mt0) cc_final: 0.7234 (pt0) REVERT: E 129 ARG cc_start: 0.7968 (ttt180) cc_final: 0.7347 (tpt90) REVERT: F 92 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7583 (mtp85) REVERT: G 95 LYS cc_start: 0.8271 (ttmt) cc_final: 0.8012 (tmtt) REVERT: G 99 ARG cc_start: 0.8155 (mmt180) cc_final: 0.7790 (mmm160) REVERT: G 104 GLN cc_start: 0.8360 (mt0) cc_final: 0.7836 (mm110) REVERT: H 31 LYS cc_start: 0.7917 (tptt) cc_final: 0.7441 (tptm) REVERT: H 113 LYS cc_start: 0.8496 (ttpt) cc_final: 0.8198 (ttmm) outliers start: 24 outliers final: 12 residues processed: 106 average time/residue: 0.8187 time to fit residues: 91.5821 Evaluate side-chains 104 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 64 optimal weight: 0.9990 chunk 53 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 110 ASN H 44 GLN H 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.166611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.121806 restraints weight = 10369.831| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 0.66 r_work: 0.3055 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12749 Z= 0.154 Angle : 0.583 6.474 18461 Z= 0.347 Chirality : 0.044 0.250 2103 Planarity : 0.004 0.050 1331 Dihedral : 31.163 167.652 4015 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.34 % Allowed : 19.11 % Favored : 77.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.68 (0.30), residues: 740 helix: 2.68 (0.21), residues: 542 sheet: None (None), residues: 0 loop : -0.90 (0.36), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 42 TYR 0.010 0.001 TYR D 34 PHE 0.008 0.001 PHE A 67 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.15 (12749) covalent geometry : angle 0.58259 / 0.35 (18461) hydrogen bonds : bond 0.04698 / 3.22 ( 761) hydrogen bonds : angle 2.81349 / 2.03 ( 1906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1480 Ramachandran restraints generated. 740 Oldfield, 0 Emsley, 740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 0.332 Fit side-chains REVERT: A 129 ARG cc_start: 0.7850 (ttt180) cc_final: 0.7445 (tmt170) REVERT: C 61 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7298 (mm-30) REVERT: C 99 ARG cc_start: 0.8283 (mmt-90) cc_final: 0.7725 (mtp180) REVERT: C 104 GLN cc_start: 0.8589 (mt0) cc_final: 0.7971 (mm110) REVERT: C 108 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8636 (mp) REVERT: C 118 LYS cc_start: 0.6838 (OUTLIER) cc_final: 0.5751 (mptt) REVERT: D 102 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: E 56 LYS cc_start: 0.8795 (tttt) cc_final: 0.8551 (ttpp) REVERT: E 76 GLN cc_start: 0.7502 (mt0) cc_final: 0.7240 (pt0) REVERT: E 129 ARG cc_start: 0.7970 (ttt180) cc_final: 0.7349 (tpt90) REVERT: F 92 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7587 (mtp85) REVERT: G 92 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7814 (mt-10) REVERT: G 95 LYS cc_start: 0.8278 (ttmt) cc_final: 0.8023 (tmtt) REVERT: G 99 ARG cc_start: 0.8180 (mmt180) cc_final: 0.7785 (mmm160) REVERT: G 104 GLN cc_start: 0.8347 (mt0) cc_final: 0.7832 (mm110) REVERT: H 31 LYS cc_start: 0.7935 (tptt) cc_final: 0.7454 (tptm) REVERT: H 113 LYS cc_start: 0.8498 (ttpt) cc_final: 0.8205 (ttmm) outliers start: 21 outliers final: 10 residues processed: 101 average time/residue: 0.8710 time to fit residues: 93.0664 Evaluate side-chains 100 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 84 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 88 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/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-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.9187 > 50: distance: 9 - 33: 37.216 distance: 13 - 44: 29.124 distance: 29 - 33: 34.266 distance: 33 - 34: 55.308 distance: 34 - 35: 54.146 distance: 34 - 37: 41.443 distance: 35 - 44: 59.917 distance: 37 - 38: 13.742 distance: 38 - 39: 34.386 distance: 39 - 40: 10.531 distance: 40 - 41: 30.976 distance: 41 - 42: 16.776 distance: 41 - 43: 29.399 distance: 44 - 45: 14.605 distance: 45 - 46: 19.821 distance: 45 - 48: 17.404 distance: 46 - 47: 22.803 distance: 46 - 49: 38.555 distance: 49 - 50: 15.569 distance: 50 - 51: 21.263 distance: 51 - 53: 69.910 distance: 54 - 55: 17.845 distance: 54 - 57: 39.187 distance: 55 - 56: 17.880 distance: 55 - 61: 44.619 distance: 57 - 58: 28.853 distance: 58 - 59: 29.443 distance: 58 - 60: 30.966 distance: 61 - 62: 15.048 distance: 62 - 63: 43.034 distance: 62 - 65: 23.714 distance: 63 - 64: 56.272 distance: 66 - 67: 39.063 distance: 67 - 69: 15.546 distance: 70 - 71: 4.498 distance: 71 - 72: 4.404 distance: 71 - 74: 40.331 distance: 72 - 73: 36.866 distance: 72 - 81: 51.882 distance: 74 - 75: 39.756 distance: 75 - 76: 50.569 distance: 75 - 77: 13.627 distance: 76 - 78: 10.316 distance: 77 - 79: 23.025 distance: 79 - 80: 25.964 distance: 81 - 82: 5.310 distance: 81 - 87: 14.236 distance: 82 - 83: 19.056 distance: 82 - 85: 3.705 distance: 83 - 84: 38.741 distance: 83 - 88: 8.685 distance: 84 - 110: 19.180 distance: 85 - 86: 25.214 distance: 86 - 87: 17.818 distance: 88 - 89: 25.766 distance: 89 - 90: 8.633 distance: 89 - 92: 11.784 distance: 90 - 91: 14.230 distance: 90 - 95: 28.068 distance: 91 - 117: 28.680 distance: 92 - 93: 25.957 distance: 92 - 94: 30.500 distance: 95 - 96: 38.585 distance: 96 - 97: 40.913 distance: 97 - 98: 16.741 distance: 97 - 99: 30.635 distance: 98 - 123: 23.732 distance: 99 - 100: 32.173 distance: 100 - 103: 7.762 distance: 101 - 110: 21.142 distance: 102 - 133: 19.805 distance: 103 - 104: 13.645 distance: 104 - 105: 3.213 distance: 105 - 106: 8.439 distance: 106 - 107: 17.821 distance: 107 - 108: 26.482 distance: 107 - 109: 25.724