Starting phenix.real_space_refine on Fri Aug 2 12:30:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/08_2024/7ku5_23034.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/08_2024/7ku5_23034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/08_2024/7ku5_23034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/08_2024/7ku5_23034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/08_2024/7ku5_23034.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ku5_23034/08_2024/7ku5_23034.cif" } resolution = 3.76 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= 0.153 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 Mg 3 5.21 5 S 1 5.16 5 C 512 2.51 5 N 125 2.21 5 O 109 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 750 Number of models: 1 Model: "" Number of chains: 2 Chain: "O" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 655 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 81} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "O" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 95 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 141 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'BCR:plan-2': 1, 'CLA:plan-2': 3, 'CLA:plan-3': 3, 'CLA:plan-4': 3, 'CLA:plan-5': 3, 'CLA:plan-6': 3, 'BCR:plan-5': 1, 'BCR:plan-4': 1, 'BCR:plan-7': 1, 'BCR:plan-6': 1, 'BCR:plan-3': 1, 'BCR:plan-8': 1} Unresolved non-hydrogen planarities: 91 Time building chain proxies: 1.70, per 1000 atoms: 2.27 Number of scatterers: 750 At special positions: 0 Unit cell: (52, 35.36, 62.4, 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 1 16.00 Mg 3 11.99 O 109 8.00 N 125 7.00 C 512 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: 0.38 Conformation dependent library (CDL) restraints added in 128.2 milliseconds 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 150 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 0 sheets defined 56.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'O' and resid 65 through 73 Processing helix chain 'O' and resid 83 through 87 removed outlier: 4.109A pdb=" N SER O 87 " --> pdb=" O ASN O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 101 removed outlier: 3.623A pdb=" N GLU O 99 " --> pdb=" O SER O 95 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 128 removed outlier: 4.374A pdb=" N TRP O 116 " --> pdb=" O PRO O 112 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL O 118 " --> pdb=" O TRP O 114 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL O 122 " --> pdb=" O VAL O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 140 removed outlier: 3.503A pdb=" N ILE O 133 " --> pdb=" O THR O 129 " (cutoff:3.500A) 25 hydrogen bonds defined for protein. 72 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: 0.16 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 335 1.40 - 1.57: 450 1.57 - 1.75: 0 1.75 - 1.92: 2 1.92 - 2.09: 12 Bond restraints: 799 Sorted by residual: bond pdb=" C GLY O 106 " pdb=" N PRO O 107 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.93e+00 bond pdb=" N THR O 105 " pdb=" CA THR O 105 " ideal model delta sigma weight residual 1.462 1.489 -0.027 1.48e-02 4.57e+03 3.42e+00 bond pdb=" N TRP O 114 " pdb=" CA TRP O 114 " ideal model delta sigma weight residual 1.457 1.481 -0.024 1.29e-02 6.01e+03 3.33e+00 bond pdb=" C25 BCR O 301 " pdb=" C30 BCR O 301 " ideal model delta sigma weight residual 1.532 1.496 0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" CB TRP O 114 " pdb=" CG TRP O 114 " ideal model delta sigma weight residual 1.498 1.452 0.046 3.10e-02 1.04e+03 2.25e+00 ... (remaining 794 not shown) Histogram of bond angle deviations from ideal: 86.08 - 104.30: 34 104.30 - 122.52: 916 122.52 - 140.73: 174 140.73 - 158.95: 3 158.95 - 177.17: 6 Bond angle restraints: 1133 Sorted by residual: angle pdb=" C PRO O 104 " pdb=" N THR O 105 " pdb=" CA THR O 105 " ideal model delta sigma weight residual 122.61 129.47 -6.86 1.56e+00 4.11e-01 1.93e+01 angle pdb=" C TRP O 114 " pdb=" CA TRP O 114 " pdb=" CB TRP O 114 " ideal model delta sigma weight residual 110.42 102.99 7.43 1.99e+00 2.53e-01 1.39e+01 angle pdb=" CA LEU O 91 " pdb=" CB LEU O 91 " pdb=" CG LEU O 91 " ideal model delta sigma weight residual 116.30 128.87 -12.57 3.50e+00 8.16e-02 1.29e+01 angle pdb=" N TRP O 114 " pdb=" CA TRP O 114 " pdb=" CB TRP O 114 " ideal model delta sigma weight residual 110.49 116.45 -5.96 1.69e+00 3.50e-01 1.24e+01 angle pdb=" N TRP O 114 " pdb=" CA TRP O 114 " pdb=" C TRP O 114 " ideal model delta sigma weight residual 110.80 118.02 -7.22 2.13e+00 2.20e-01 1.15e+01 ... (remaining 1128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 332 17.20 - 34.39: 36 34.39 - 51.59: 5 51.59 - 68.79: 0 68.79 - 85.98: 1 Dihedral angle restraints: 374 sinusoidal: 136 harmonic: 238 Sorted by residual: dihedral pdb=" CA GLY O 106 " pdb=" C GLY O 106 " pdb=" N PRO O 107 " pdb=" CA PRO O 107 " ideal model delta harmonic sigma weight residual -180.00 -155.26 -24.74 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TRP O 74 " pdb=" C TRP O 74 " pdb=" N LEU O 75 " pdb=" CA LEU O 75 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PHE O 92 " pdb=" C PHE O 92 " pdb=" N LEU O 93 " pdb=" CA LEU O 93 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 371 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 49 0.046 - 0.091: 33 0.091 - 0.137: 10 0.137 - 0.182: 2 0.182 - 0.228: 3 Chirality restraints: 97 Sorted by residual: chirality pdb=" CA TRP O 114 " pdb=" N TRP O 114 " pdb=" C TRP O 114 " pdb=" CB TRP O 114 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LEU O 91 " pdb=" N LEU O 91 " pdb=" C LEU O 91 " pdb=" CB LEU O 91 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA THR O 105 " pdb=" N THR O 105 " pdb=" C THR O 105 " pdb=" CB THR O 105 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 94 not shown) Planarity restraints: 153 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND CLA O 201 " 0.064 2.00e-02 2.50e+03 4.55e-02 3.10e+01 pdb=" C1A CLA O 201 " -0.028 2.00e-02 2.50e+03 pdb=" C3D CLA O 201 " -0.045 2.00e-02 2.50e+03 pdb=" C4D CLA O 201 " -0.039 2.00e-02 2.50e+03 pdb=" CBD CLA O 201 " 0.061 2.00e-02 2.50e+03 pdb=" CHA CLA O 201 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP O 114 " 0.037 2.00e-02 2.50e+03 2.78e-02 1.93e+01 pdb=" CG TRP O 114 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP O 114 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP O 114 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP O 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP O 114 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP O 114 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP O 114 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP O 114 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP O 114 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1A CLA O 203 " -0.019 2.00e-02 2.50e+03 3.56e-02 1.90e+01 pdb=" C2A CLA O 203 " 0.058 2.00e-02 2.50e+03 pdb=" C4A CLA O 203 " -0.032 2.00e-02 2.50e+03 pdb=" CHA CLA O 203 " -0.023 2.00e-02 2.50e+03 pdb=" NA CLA O 203 " -0.026 2.00e-02 2.50e+03 pdb="MG CLA O 203 " 0.041 2.00e-02 2.50e+03 ... (remaining 150 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 252 2.92 - 3.41: 653 3.41 - 3.91: 1118 3.91 - 4.40: 1191 4.40 - 4.90: 1854 Nonbonded interactions: 5068 Sorted by model distance: nonbonded pdb=" NH1 ARG O 61 " pdb=" OE1 GLN O 132 " model vdw 2.420 3.120 nonbonded pdb=" NZ LYS O 136 " pdb=" OD2 ASP O 140 " model vdw 2.502 3.120 nonbonded pdb=" O LEU O 75 " pdb=" OG SER O 79 " model vdw 2.510 3.040 nonbonded pdb=" O LEU O 91 " pdb=" N SER O 95 " model vdw 2.525 3.120 nonbonded pdb=" O ASP O 63 " pdb=" N SER O 65 " model vdw 2.582 3.120 ... (remaining 5063 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 9.000 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:3.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 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 0.052 799 Z= 0.382 Angle : 1.290 12.573 1133 Z= 0.648 Chirality : 0.068 0.228 97 Planarity : 0.013 0.066 153 Dihedral : 14.852 85.984 224 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.79 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -5.41 (0.71), residues: 86 helix: -4.07 (0.40), residues: 40 sheet: None (None), residues: 0 loop : -3.17 (0.90), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.003 TRP O 114 HIS 0.002 0.001 HIS O 121 PHE 0.022 0.002 PHE O 92 TYR 0.008 0.002 TYR O 142 ARG 0.024 0.008 ARG O 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 15 time to evaluate : 0.077 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.1610 time to fit residues: 2.6466 Evaluate side-chains 12 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 overall best weight: 1.9485 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 799 Z= 0.286 Angle : 0.766 6.362 1133 Z= 0.380 Chirality : 0.053 0.157 97 Planarity : 0.007 0.054 153 Dihedral : 7.104 23.742 99 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 1.67 % Allowed : 10.00 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.83), residues: 86 helix: -2.70 (0.61), residues: 45 sheet: None (None), residues: 0 loop : -2.93 (1.04), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP O 116 HIS 0.002 0.001 HIS O 121 PHE 0.016 0.002 PHE O 92 TYR 0.006 0.002 TYR O 142 ARG 0.003 0.001 ARG O 138 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.084 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 16 average time/residue: 0.1163 time to fit residues: 2.0819 Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.8730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6796 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 799 Z= 0.160 Angle : 0.638 6.260 1133 Z= 0.308 Chirality : 0.048 0.148 97 Planarity : 0.006 0.045 153 Dihedral : 6.574 21.766 99 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 3.33 % Allowed : 8.33 % Favored : 88.33 % 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: -3.54 (0.86), residues: 86 helix: -1.94 (0.62), residues: 45 sheet: None (None), residues: 0 loop : -2.83 (1.10), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP O 74 HIS 0.001 0.001 HIS O 121 PHE 0.015 0.001 PHE O 92 TYR 0.004 0.001 TYR O 142 ARG 0.004 0.001 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 12 time to evaluate : 0.077 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 12 average time/residue: 0.0591 time to fit residues: 0.9321 Evaluate side-chains 13 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 overall best weight: 1.0733 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 799 Z= 0.177 Angle : 0.624 5.939 1133 Z= 0.307 Chirality : 0.049 0.120 97 Planarity : 0.006 0.043 153 Dihedral : 6.368 19.138 99 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 3.33 % Allowed : 8.33 % Favored : 88.33 % 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: -2.95 (0.90), residues: 86 helix: -1.16 (0.69), residues: 45 sheet: None (None), residues: 0 loop : -2.94 (1.10), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.013 0.001 PHE O 92 TYR 0.005 0.001 TYR O 142 ARG 0.002 0.001 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 13 time to evaluate : 0.076 Fit side-chains REVERT: O 114 TRP cc_start: 0.7156 (m-90) cc_final: 0.6371 (m-10) REVERT: O 142 TYR cc_start: 0.7951 (m-80) cc_final: 0.7394 (m-80) outliers start: 2 outliers final: 0 residues processed: 13 average time/residue: 0.0642 time to fit residues: 1.0384 Evaluate side-chains 13 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.0010 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 0.6488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6837 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 799 Z= 0.144 Angle : 0.600 5.952 1133 Z= 0.286 Chirality : 0.049 0.170 97 Planarity : 0.006 0.042 153 Dihedral : 6.166 19.489 99 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 5.00 % Allowed : 13.33 % Favored : 81.67 % 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: -2.38 (0.93), residues: 86 helix: -0.63 (0.71), residues: 46 sheet: None (None), residues: 0 loop : -2.79 (1.12), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 74 HIS 0.000 0.000 HIS O 102 PHE 0.010 0.001 PHE O 92 TYR 0.003 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 15 time to evaluate : 0.070 Fit side-chains REVERT: O 114 TRP cc_start: 0.7120 (m-90) cc_final: 0.6619 (m-10) REVERT: O 142 TYR cc_start: 0.7874 (m-80) cc_final: 0.7406 (m-80) outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 0.0581 time to fit residues: 1.1550 Evaluate side-chains 16 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 14 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 75 LEU Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 0.9485 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 799 Z= 0.171 Angle : 0.605 6.114 1133 Z= 0.295 Chirality : 0.049 0.147 97 Planarity : 0.006 0.041 153 Dihedral : 6.114 18.849 99 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 1.67 % Allowed : 16.67 % Favored : 81.67 % 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: -2.25 (0.94), residues: 86 helix: -0.60 (0.70), residues: 46 sheet: None (None), residues: 0 loop : -2.61 (1.16), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.009 0.001 PHE O 92 TYR 0.004 0.001 TYR O 142 ARG 0.001 0.000 ARG O 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.078 Fit side-chains REVERT: O 114 TRP cc_start: 0.7128 (m-90) cc_final: 0.4541 (p-90) REVERT: O 142 TYR cc_start: 0.7904 (m-80) cc_final: 0.7479 (m-80) outliers start: 1 outliers final: 1 residues processed: 15 average time/residue: 0.0634 time to fit residues: 1.1792 Evaluate side-chains 15 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 14 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.2980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 1.2485 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 799 Z= 0.184 Angle : 0.613 5.846 1133 Z= 0.304 Chirality : 0.050 0.139 97 Planarity : 0.006 0.040 153 Dihedral : 6.218 18.870 99 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 3.33 % Allowed : 13.33 % Favored : 83.33 % 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: -2.31 (0.93), residues: 86 helix: -0.57 (0.70), residues: 46 sheet: None (None), residues: 0 loop : -2.76 (1.13), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 74 HIS 0.001 0.000 HIS O 121 PHE 0.008 0.001 PHE O 135 TYR 0.005 0.001 TYR O 142 ARG 0.001 0.000 ARG O 138 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 17 time to evaluate : 0.072 Fit side-chains REVERT: O 114 TRP cc_start: 0.7175 (m-90) cc_final: 0.4639 (p-90) REVERT: O 142 TYR cc_start: 0.8008 (m-80) cc_final: 0.7494 (m-80) outliers start: 2 outliers final: 1 residues processed: 17 average time/residue: 0.0662 time to fit residues: 1.3531 Evaluate side-chains 17 residues out of total 72 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 16 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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-dev-5409/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-dev-5409/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: 53.2465 > 50: distance: 12 - 22: 28.680 distance: 22 - 23: 27.836 distance: 23 - 24: 20.679 distance: 23 - 26: 25.490 distance: 24 - 25: 35.073 distance: 24 - 30: 21.526 distance: 26 - 27: 19.113 distance: 27 - 28: 27.795 distance: 27 - 29: 14.459 distance: 30 - 31: 23.569 distance: 31 - 32: 21.985 distance: 31 - 34: 20.556 distance: 32 - 33: 21.952 distance: 32 - 35: 46.995 distance: 35 - 36: 26.421 distance: 35 - 41: 31.310 distance: 36 - 37: 26.064 distance: 36 - 39: 30.105 distance: 37 - 38: 32.388 distance: 37 - 42: 38.548 distance: 39 - 40: 17.152 distance: 40 - 41: 11.868 distance: 42 - 43: 14.927 distance: 43 - 44: 20.764 distance: 43 - 46: 18.644 distance: 44 - 45: 20.655 distance: 44 - 48: 21.318 distance: 46 - 47: 30.226 distance: 48 - 49: 10.258 distance: 49 - 50: 31.172 distance: 49 - 52: 18.834 distance: 50 - 51: 28.501 distance: 50 - 54: 3.667 distance: 52 - 53: 4.954 distance: 54 - 55: 8.676 distance: 55 - 56: 14.991 distance: 55 - 58: 25.909 distance: 56 - 57: 13.146 distance: 56 - 62: 10.070 distance: 58 - 59: 27.655 distance: 59 - 60: 28.829 distance: 59 - 61: 6.916 distance: 62 - 63: 10.364 distance: 62 - 68: 27.522 distance: 63 - 64: 26.065 distance: 63 - 66: 8.927 distance: 64 - 65: 24.084 distance: 64 - 69: 10.784 distance: 66 - 67: 14.731 distance: 67 - 68: 22.228 distance: 69 - 70: 16.903 distance: 70 - 71: 35.376 distance: 70 - 73: 16.044 distance: 71 - 72: 20.860 distance: 71 - 76: 26.372 distance: 73 - 74: 25.724 distance: 73 - 75: 15.449 distance: 76 - 77: 29.877 distance: 77 - 78: 20.175 distance: 77 - 80: 27.635 distance: 78 - 79: 16.745 distance: 78 - 84: 19.154 distance: 79 - 96: 26.368 distance: 80 - 81: 31.658 distance: 80 - 82: 15.851 distance: 81 - 83: 4.487 distance: 84 - 85: 23.852 distance: 85 - 86: 19.304 distance: 85 - 88: 13.991 distance: 86 - 87: 25.158 distance: 86 - 92: 29.208 distance: 88 - 89: 21.645 distance: 89 - 90: 26.147 distance: 89 - 91: 15.509