Starting phenix.real_space_refine on Thu Dec 7 22:24:46 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/12_2023/7sax_24958.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/12_2023/7sax_24958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/12_2023/7sax_24958.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/12_2023/7sax_24958.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/12_2023/7sax_24958.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sax_24958/12_2023/7sax_24958.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 28 5.16 5 C 3431 2.51 5 N 882 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 194": "OE1" <-> "OE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5305 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1627 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 6, 'TRANS': 206} Chain: "B" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1614 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain: "C" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 473 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "D" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 430 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "E" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "F" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "G" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Time building chain proxies: 3.21, per 1000 atoms: 0.61 Number of scatterers: 5305 At special positions: 0 Unit cell: (66.56, 58.24, 129.792, 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 28 16.00 O 964 8.00 N 882 7.00 C 3431 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 972.7 milliseconds 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1232 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 7 through 25 removed outlier: 3.823A pdb=" N ALA A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 69 removed outlier: 5.074A pdb=" N LEU A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N LYS A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 69 " --> pdb=" O LYS A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 104 Proline residue: A 75 - end of helix removed outlier: 3.592A pdb=" N VAL A 87 " --> pdb=" O ALA A 83 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN A 88 " --> pdb=" O GLN A 84 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 132 through 153 removed outlier: 3.690A pdb=" N GLU A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 185 through 215 removed outlier: 4.253A pdb=" N MET A 215 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 28 removed outlier: 5.295A pdb=" N LEU B 18 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 19 " --> pdb=" O ILE B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 63 Processing helix chain 'B' and resid 69 through 104 Proline residue: B 75 - end of helix removed outlier: 3.716A pdb=" N LEU B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 128 Processing helix chain 'B' and resid 132 through 153 removed outlier: 3.519A pdb=" N LEU B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 152 " --> pdb=" O LEU B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 185 through 214 Processing helix chain 'C' and resid 10 through 31 removed outlier: 4.013A pdb=" N LEU C 14 " --> pdb=" O GLY C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 58 removed outlier: 3.869A pdb=" N ILE C 40 " --> pdb=" O GLY C 36 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLY C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 31 removed outlier: 3.804A pdb=" N LEU D 14 " --> pdb=" O GLY D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 55 removed outlier: 4.277A pdb=" N MET D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 31 removed outlier: 3.750A pdb=" N LEU E 14 " --> pdb=" O GLY E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.899A pdb=" N GLY E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'F' and resid 10 through 31 removed outlier: 4.125A pdb=" N LEU F 14 " --> pdb=" O GLY F 10 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 15 " --> pdb=" O ILE F 11 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA F 19 " --> pdb=" O ILE F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 55 Processing helix chain 'G' and resid 10 through 31 removed outlier: 4.011A pdb=" N LEU G 14 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA G 19 " --> pdb=" O ILE G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 55 removed outlier: 4.193A pdb=" N MET G 39 " --> pdb=" O GLY G 35 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) 405 hydrogen bonds defined for protein. 1215 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: 1.37 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1709 1.34 - 1.46: 681 1.46 - 1.57: 2938 1.57 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 5384 Sorted by residual: bond pdb=" CG1 ILE D 15 " pdb=" CD1 ILE D 15 " ideal model delta sigma weight residual 1.513 1.428 0.085 3.90e-02 6.57e+02 4.74e+00 bond pdb=" CB MET A 12 " pdb=" CG MET A 12 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.60e+00 bond pdb=" CB MET E 54 " pdb=" CG MET E 54 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.33e+00 bond pdb=" CG1 ILE B 15 " pdb=" CD1 ILE B 15 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00 bond pdb=" CG1 ILE D 23 " pdb=" CD1 ILE D 23 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.26e+00 ... (remaining 5379 not shown) Histogram of bond angle deviations from ideal: 96.15 - 103.72: 56 103.72 - 111.29: 2357 111.29 - 118.86: 2097 118.86 - 126.43: 2673 126.43 - 134.00: 72 Bond angle restraints: 7255 Sorted by residual: angle pdb=" CB MET D 54 " pdb=" CG MET D 54 " pdb=" SD MET D 54 " ideal model delta sigma weight residual 112.70 100.94 11.76 3.00e+00 1.11e-01 1.54e+01 angle pdb=" C ILE E 53 " pdb=" N MET E 54 " pdb=" CA MET E 54 " ideal model delta sigma weight residual 122.31 115.73 6.58 2.00e+00 2.50e-01 1.08e+01 angle pdb=" CB MET E 54 " pdb=" CG MET E 54 " pdb=" SD MET E 54 " ideal model delta sigma weight residual 112.70 103.40 9.30 3.00e+00 1.11e-01 9.62e+00 angle pdb=" C ARG A 11 " pdb=" N MET A 12 " pdb=" CA MET A 12 " ideal model delta sigma weight residual 122.06 116.31 5.75 1.86e+00 2.89e-01 9.55e+00 angle pdb=" CA ARG A 9 " pdb=" CB ARG A 9 " pdb=" CG ARG A 9 " ideal model delta sigma weight residual 114.10 118.91 -4.81 2.00e+00 2.50e-01 5.79e+00 ... (remaining 7250 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 2882 17.57 - 35.14: 267 35.14 - 52.71: 38 52.71 - 70.28: 8 70.28 - 87.85: 2 Dihedral angle restraints: 3197 sinusoidal: 1279 harmonic: 1918 Sorted by residual: dihedral pdb=" CA MET E 54 " pdb=" C MET E 54 " pdb=" N GLY E 55 " pdb=" CA GLY E 55 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA VAL A 115 " pdb=" C VAL A 115 " pdb=" N LYS A 116 " pdb=" CA LYS A 116 " ideal model delta harmonic sigma weight residual 180.00 161.41 18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET A 12 " pdb=" C MET A 12 " pdb=" N ILE A 13 " pdb=" CA ILE A 13 " ideal model delta harmonic sigma weight residual 180.00 161.76 18.24 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 3194 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 589 0.043 - 0.086: 234 0.086 - 0.130: 24 0.130 - 0.173: 5 0.173 - 0.216: 2 Chirality restraints: 854 Sorted by residual: chirality pdb=" CB VAL F 22 " pdb=" CA VAL F 22 " pdb=" CG1 VAL F 22 " pdb=" CG2 VAL F 22 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE B 156 " pdb=" CA ILE B 156 " pdb=" CG1 ILE B 156 " pdb=" CG2 ILE B 156 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA MET E 54 " pdb=" N MET E 54 " pdb=" C MET E 54 " pdb=" CB MET E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.43e-01 ... (remaining 851 not shown) Planarity restraints: 908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 52 " 0.011 2.00e-02 2.50e+03 1.13e-02 2.24e+00 pdb=" CG PHE C 52 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE C 52 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 52 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 52 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE C 52 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 52 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 12 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C MET A 12 " -0.021 2.00e-02 2.50e+03 pdb=" O MET A 12 " 0.008 2.00e-02 2.50e+03 pdb=" N ILE A 13 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 9 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.09e+00 pdb=" C ARG A 9 " -0.018 2.00e-02 2.50e+03 pdb=" O ARG A 9 " 0.007 2.00e-02 2.50e+03 pdb=" N GLN A 10 " 0.006 2.00e-02 2.50e+03 ... (remaining 905 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 234 2.72 - 3.26: 5640 3.26 - 3.81: 8814 3.81 - 4.35: 10573 4.35 - 4.90: 18257 Nonbonded interactions: 43518 Sorted by model distance: nonbonded pdb=" NH1 ARG B 9 " pdb=" OE2 GLU C 47 " model vdw 2.174 2.520 nonbonded pdb=" O ALA B 60 " pdb=" OG1 THR B 64 " model vdw 2.232 2.440 nonbonded pdb=" NE2 GLN A 51 " pdb=" OD1 ASP A 55 " model vdw 2.240 2.520 nonbonded pdb=" OG1 THR A 112 " pdb=" OD1 ASP A 114 " model vdw 2.262 2.440 nonbonded pdb=" OE1 GLU A 131 " pdb=" NH1 ARG A 133 " model vdw 2.283 2.520 ... (remaining 43513 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 5 through 215) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 9 through 60) selection = (chain 'D' and resid 9 through 60) } ncs_group { reference = (chain 'E' and resid 9 through 57) selection = (chain 'F' and resid 9 through 57) selection = (chain 'G' and resid 9 through 57) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 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: 3.930 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.870 Find NCS groups from input model: 0.310 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.007 0.085 5384 Z= 0.469 Angle : 0.660 11.764 7255 Z= 0.344 Chirality : 0.044 0.216 854 Planarity : 0.003 0.018 908 Dihedral : 13.544 87.846 1965 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.33), residues: 675 helix: 1.69 (0.23), residues: 507 sheet: None (None), residues: 0 loop : -2.01 (0.46), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 38 HIS 0.002 0.001 HIS D 32 PHE 0.026 0.002 PHE C 52 TYR 0.017 0.003 TYR A 117 ARG 0.014 0.001 ARG A 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 0.549 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 1.1090 time to fit residues: 168.9196 Evaluate side-chains 122 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 53 optimal weight: 0.0270 chunk 20 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5384 Z= 0.142 Angle : 0.453 6.024 7255 Z= 0.241 Chirality : 0.036 0.151 854 Planarity : 0.003 0.017 908 Dihedral : 3.920 15.939 705 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.13 % Allowed : 13.82 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.33), residues: 675 helix: 2.49 (0.23), residues: 513 sheet: None (None), residues: 0 loop : -1.71 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 38 HIS 0.011 0.001 HIS A 210 PHE 0.017 0.001 PHE A 61 TYR 0.009 0.002 TYR A 117 ARG 0.003 0.000 ARG B 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.548 Fit side-chains outliers start: 23 outliers final: 5 residues processed: 133 average time/residue: 1.0897 time to fit residues: 151.4754 Evaluate side-chains 126 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 0.611 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 1 residues processed: 4 average time/residue: 0.3586 time to fit residues: 2.4886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 78 GLN B 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5384 Z= 0.179 Angle : 0.467 6.527 7255 Z= 0.246 Chirality : 0.037 0.153 854 Planarity : 0.003 0.018 908 Dihedral : 3.861 14.447 705 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 4.49 % Allowed : 17.06 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.33), residues: 675 helix: 2.68 (0.22), residues: 512 sheet: None (None), residues: 0 loop : -1.91 (0.46), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 38 HIS 0.008 0.001 HIS A 210 PHE 0.027 0.001 PHE C 52 TYR 0.011 0.002 TYR B 17 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 0.614 Fit side-chains outliers start: 25 outliers final: 9 residues processed: 131 average time/residue: 1.1242 time to fit residues: 154.0141 Evaluate side-chains 128 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.663 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 5 residues processed: 4 average time/residue: 0.0969 time to fit residues: 1.4327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 0.0770 chunk 0 optimal weight: 5.9990 overall best weight: 1.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN B 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5384 Z= 0.249 Angle : 0.514 6.627 7255 Z= 0.268 Chirality : 0.039 0.153 854 Planarity : 0.003 0.021 908 Dihedral : 4.016 15.769 705 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.46 % Allowed : 17.06 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.33), residues: 675 helix: 2.60 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.87 (0.47), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 38 HIS 0.006 0.001 HIS A 210 PHE 0.026 0.001 PHE C 52 TYR 0.011 0.002 TYR B 17 ARG 0.002 0.000 ARG B 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 0.636 Fit side-chains outliers start: 36 outliers final: 16 residues processed: 133 average time/residue: 1.0807 time to fit residues: 150.4193 Evaluate side-chains 134 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 0.6151 time to fit residues: 6.7342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 33 optimal weight: 0.0370 chunk 58 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 10 GLN A 74 GLN B 27 ASN B 44 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 5384 Z= 0.145 Angle : 0.450 5.789 7255 Z= 0.239 Chirality : 0.036 0.141 854 Planarity : 0.002 0.017 908 Dihedral : 3.758 14.868 705 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.49 % Allowed : 20.29 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.33), residues: 675 helix: 2.83 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.79 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 38 HIS 0.005 0.001 HIS A 210 PHE 0.024 0.001 PHE C 52 TYR 0.009 0.001 TYR B 17 ARG 0.002 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 124 time to evaluate : 0.635 Fit side-chains outliers start: 25 outliers final: 11 residues processed: 132 average time/residue: 1.1001 time to fit residues: 151.8853 Evaluate side-chains 128 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 6 residues processed: 5 average time/residue: 0.3053 time to fit residues: 2.5106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 5 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN B 27 ASN B 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5384 Z= 0.217 Angle : 0.496 6.008 7255 Z= 0.261 Chirality : 0.038 0.146 854 Planarity : 0.003 0.018 908 Dihedral : 3.901 15.672 705 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.21 % Allowed : 21.01 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.33), residues: 675 helix: 2.75 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -1.85 (0.48), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 38 HIS 0.011 0.002 HIS A 210 PHE 0.022 0.001 PHE C 52 TYR 0.014 0.002 TYR B 17 ARG 0.002 0.000 ARG A 11 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1350 Ramachandran restraints generated. 675 Oldfield, 0 Emsley, 675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 122 time to evaluate : 0.627 Fit side-chains outliers start: 29 outliers final: 12 residues processed: 135 average time/residue: 1.0064 time to fit residues: 142.5491 Evaluate side-chains 131 residues out of total 557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.9102 time to fit residues: 4.6288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.8833 > 50: distance: 50 - 69: 34.212 distance: 54 - 77: 35.281 distance: 60 - 88: 24.212 distance: 63 - 69: 34.556 distance: 64 - 97: 37.298 distance: 69 - 70: 42.667 distance: 70 - 71: 42.642 distance: 70 - 73: 29.235 distance: 72 - 105: 39.223 distance: 73 - 74: 29.066 distance: 74 - 75: 6.985 distance: 75 - 76: 32.869 distance: 77 - 78: 40.681 distance: 78 - 79: 43.084 distance: 78 - 81: 55.375 distance: 79 - 80: 13.738 distance: 79 - 88: 9.168 distance: 84 - 86: 22.557 distance: 85 - 87: 24.294 distance: 86 - 87: 4.208 distance: 88 - 89: 39.178 distance: 89 - 90: 57.912 distance: 90 - 91: 39.782 distance: 90 - 97: 40.464 distance: 92 - 93: 9.048 distance: 93 - 94: 10.410 distance: 95 - 96: 40.399 distance: 97 - 98: 55.998 distance: 98 - 99: 57.889 distance: 98 - 101: 40.332 distance: 99 - 100: 68.087 distance: 99 - 105: 57.351 distance: 105 - 106: 40.133 distance: 106 - 107: 39.941 distance: 106 - 109: 47.885 distance: 107 - 108: 57.768 distance: 107 - 113: 68.669 distance: 109 - 110: 27.380 distance: 110 - 112: 56.937 distance: 113 - 114: 39.846 distance: 114 - 115: 38.687 distance: 114 - 117: 3.896 distance: 117 - 118: 54.394 distance: 118 - 119: 40.897 distance: 118 - 120: 56.114 distance: 120 - 122: 38.644 distance: 124 - 127: 56.952 distance: 125 - 131: 57.244 distance: 128 - 129: 40.007 distance: 128 - 130: 57.477 distance: 132 - 133: 23.677 distance: 132 - 135: 40.540 distance: 133 - 134: 21.613 distance: 133 - 140: 17.650 distance: 135 - 136: 30.311 distance: 136 - 137: 40.434 distance: 137 - 138: 14.768 distance: 140 - 141: 55.789 distance: 142 - 143: 40.575 distance: 143 - 169: 35.102 distance: 145 - 146: 39.545 distance: 146 - 147: 39.185 distance: 146 - 148: 35.990 distance: 147 - 176: 33.739