Starting phenix.real_space_refine on Sat May 10 13:22:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fjb_29221/05_2025/8fjb_29221.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fjb_29221/05_2025/8fjb_29221.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fjb_29221/05_2025/8fjb_29221.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fjb_29221/05_2025/8fjb_29221.map" model { file = "/net/cci-nas-00/data/ceres_data/8fjb_29221/05_2025/8fjb_29221.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fjb_29221/05_2025/8fjb_29221.cif" } resolution = 3.06 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= 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: 4 Type Number sf(0) Gaussians S 24 5.16 5 C 3980 2.51 5 N 1095 2.21 5 O 1231 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6330 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2230 Classifications: {'peptide': 273} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 829 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Modifications used: {'COO': 1} Link IDs: {'TRANS': 8} Chain: "E" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1555 Classifications: {'peptide': 207} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 196} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PCIS': 4, 'PTRANS': 8, 'TRANS': 201} Time building chain proxies: 4.64, per 1000 atoms: 0.73 Number of scatterers: 6330 At special positions: 0 Unit cell: (139.4, 107.1, 72.25, 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 24 16.00 O 1231 8.00 N 1095 7.00 C 3980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 195 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 884.7 milliseconds 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 17 sheets defined 14.2% alpha, 46.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 56 through 85 removed outlier: 3.773A pdb=" N TRP A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 151 removed outlier: 3.559A pdb=" N LYS A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.656A pdb=" N GLU E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 190 through 197 removed outlier: 3.682A pdb=" N THR E 196 " --> pdb=" O SER E 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 128 removed outlier: 3.991A pdb=" N SER D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 190 removed outlier: 3.818A pdb=" N HIS D 190 " --> pdb=" O ASP D 186 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.752A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG A 111 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N HIS A 114 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ALA A 125 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N TYR A 116 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 194 removed outlier: 5.740A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 194 removed outlier: 5.740A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.814A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45 Processing sheet with id=AA8, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.030A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.892A pdb=" N VAL E 107 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.278A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.278A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 159 removed outlier: 3.543A pdb=" N LYS E 214 " --> pdb=" O CYS E 201 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 4 through 7 removed outlier: 6.283A pdb=" N THR D 69 " --> pdb=" O ALA D 25 " (cutoff:3.500A) removed outlier: 10.552A pdb=" N GLN D 27 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 10.096A pdb=" N SER D 67 " --> pdb=" O GLN D 27 " (cutoff:3.500A) removed outlier: 11.757A pdb=" N ILE D 29 " --> pdb=" O SER D 65 " (cutoff:3.500A) removed outlier: 11.586A pdb=" N SER D 65 " --> pdb=" O ILE D 29 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.775A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 115 through 119 removed outlier: 3.555A pdb=" N VAL D 134 " --> pdb=" O PHE D 119 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N TYR D 174 " --> pdb=" O ASN D 139 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 154 through 155 326 hydrogen bonds defined for protein. 852 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: 1.75 Time building geometry restraints manager: 1.64 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: 2070 1.34 - 1.46: 1646 1.46 - 1.58: 2739 1.58 - 1.70: 0 1.70 - 1.82: 34 Bond restraints: 6489 Sorted by residual: bond pdb=" CG GLN D 90 " pdb=" CD GLN D 90 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.14e+00 bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.506 1.455 0.051 3.90e-02 6.57e+02 1.74e+00 bond pdb=" CG ARG A 6 " pdb=" CD ARG A 6 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.70e+00 bond pdb=" CG ASP A 137 " pdb=" OD1 ASP A 137 " ideal model delta sigma weight residual 1.249 1.224 0.025 1.90e-02 2.77e+03 1.69e+00 bond pdb=" CB ASP A 137 " pdb=" CG ASP A 137 " ideal model delta sigma weight residual 1.516 1.484 0.032 2.50e-02 1.60e+03 1.64e+00 ... (remaining 6484 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 8625 2.04 - 4.08: 168 4.08 - 6.13: 11 6.13 - 8.17: 5 8.17 - 10.21: 2 Bond angle restraints: 8811 Sorted by residual: angle pdb=" C SER D 93 " pdb=" N THR D 94 " pdb=" CA THR D 94 " ideal model delta sigma weight residual 121.80 132.01 -10.21 2.44e+00 1.68e-01 1.75e+01 angle pdb=" N ASP A 196 " pdb=" CA ASP A 196 " pdb=" C ASP A 196 " ideal model delta sigma weight residual 111.28 114.81 -3.53 1.09e+00 8.42e-01 1.05e+01 angle pdb=" C VAL A 194 " pdb=" N SER A 195 " pdb=" CA SER A 195 " ideal model delta sigma weight residual 121.53 128.72 -7.19 2.25e+00 1.98e-01 1.02e+01 angle pdb=" C TYR D 92 " pdb=" N SER D 93 " pdb=" CA SER D 93 " ideal model delta sigma weight residual 121.54 115.81 5.73 1.91e+00 2.74e-01 9.01e+00 angle pdb=" C ASP A 137 " pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta sigma weight residual 110.45 116.23 -5.78 2.15e+00 2.16e-01 7.22e+00 ... (remaining 8806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 3557 17.89 - 35.79: 245 35.79 - 53.68: 40 53.68 - 71.58: 14 71.58 - 89.47: 6 Dihedral angle restraints: 3862 sinusoidal: 1533 harmonic: 2329 Sorted by residual: dihedral pdb=" CA THR D 94 " pdb=" C THR D 94 " pdb=" N PRO D 95 " pdb=" CA PRO D 95 " ideal model delta harmonic sigma weight residual 0.00 -25.14 25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ILE D 29 " pdb=" C ILE D 29 " pdb=" N SER D 30 " pdb=" CA SER D 30 " ideal model delta harmonic sigma weight residual -180.00 -161.95 -18.05 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" C ASP A 137 " pdb=" N ASP A 137 " pdb=" CA ASP A 137 " pdb=" CB ASP A 137 " ideal model delta harmonic sigma weight residual -122.60 -131.62 9.02 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 3859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 824 0.068 - 0.137: 114 0.137 - 0.205: 9 0.205 - 0.274: 1 0.274 - 0.342: 1 Chirality restraints: 949 Sorted by residual: chirality pdb=" CB ILE B 1 " pdb=" CA ILE B 1 " pdb=" CG1 ILE B 1 " pdb=" CG2 ILE B 1 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA ASP A 137 " pdb=" N ASP A 137 " pdb=" C ASP A 137 " pdb=" CB ASP A 137 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE D 97 " pdb=" N ILE D 97 " pdb=" C ILE D 97 " pdb=" CB ILE D 97 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.52e-01 ... (remaining 946 not shown) Planarity restraints: 1138 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 95 " -0.043 5.00e-02 4.00e+02 6.51e-02 6.78e+00 pdb=" N PRO D 96 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 96 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 96 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 194 " -0.009 2.00e-02 2.50e+03 1.77e-02 3.13e+00 pdb=" C VAL A 194 " 0.031 2.00e-02 2.50e+03 pdb=" O VAL A 194 " -0.012 2.00e-02 2.50e+03 pdb=" N SER A 195 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 94 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO D 95 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 95 " 0.021 5.00e-02 4.00e+02 ... (remaining 1135 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 132 2.69 - 3.24: 5410 3.24 - 3.79: 8981 3.79 - 4.35: 12444 4.35 - 4.90: 22199 Nonbonded interactions: 49166 Sorted by model distance: nonbonded pdb=" OE1 GLU D 188 " pdb=" NH1 ARG D 212 " model vdw 2.135 3.120 nonbonded pdb=" OG1 THR E 200 " pdb=" O LYS E 214 " model vdw 2.257 3.040 nonbonded pdb=" OG SER D 14 " pdb=" OD2 ASP D 17 " model vdw 2.270 3.040 nonbonded pdb=" O LEU D 126 " pdb=" NZ LYS D 184 " model vdw 2.291 3.120 nonbonded pdb=" OE1 GLU C 4 " pdb=" OH TYR E 32 " model vdw 2.296 3.040 ... (remaining 49161 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.670 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.330 Find NCS groups from input model: 0.060 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 0.051 6496 Z= 0.239 Angle : 0.685 10.209 8825 Z= 0.363 Chirality : 0.049 0.342 949 Planarity : 0.005 0.065 1138 Dihedral : 13.228 89.472 2347 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.66 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: -1.47 (0.28), residues: 788 helix: -0.94 (0.47), residues: 96 sheet: 0.03 (0.28), residues: 330 loop : -1.97 (0.28), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 244 HIS 0.005 0.001 HIS C 5 PHE 0.029 0.002 PHE B 70 TYR 0.024 0.002 TYR E 33 ARG 0.008 0.001 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.23165 ( 278) hydrogen bonds : angle 8.99180 ( 852) SS BOND : bond 0.00562 ( 7) SS BOND : angle 1.39339 ( 14) covalent geometry : bond 0.00584 ( 6489) covalent geometry : angle 0.68320 ( 8811) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.684 Fit side-chains REVERT: B 19 LYS cc_start: 0.8774 (mmtt) cc_final: 0.7978 (mtpp) REVERT: B 34 ASP cc_start: 0.8409 (m-30) cc_final: 0.8206 (m-30) REVERT: B 38 ASP cc_start: 0.8283 (m-30) cc_final: 0.7975 (m-30) REVERT: D 82 ASP cc_start: 0.8671 (m-30) cc_final: 0.8433 (m-30) REVERT: D 144 GLU cc_start: 0.8558 (mp0) cc_final: 0.8344 (mp0) REVERT: D 190 HIS cc_start: 0.8933 (m90) cc_final: 0.8649 (m90) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.3028 time to fit residues: 32.4771 Evaluate side-chains 82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.069853 restraints weight = 9333.116| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.81 r_work: 0.2628 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2470 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6496 Z= 0.147 Angle : 0.566 11.565 8825 Z= 0.294 Chirality : 0.044 0.230 949 Planarity : 0.005 0.053 1138 Dihedral : 4.415 17.688 881 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.29 % Allowed : 4.60 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: -0.35 (0.29), residues: 788 helix: 0.19 (0.52), residues: 98 sheet: 0.57 (0.27), residues: 363 loop : -1.27 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 244 HIS 0.003 0.001 HIS B 51 PHE 0.013 0.002 PHE B 70 TYR 0.017 0.001 TYR E 33 ARG 0.008 0.001 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 278) hydrogen bonds : angle 5.76180 ( 852) SS BOND : bond 0.00615 ( 7) SS BOND : angle 1.10683 ( 14) covalent geometry : bond 0.00343 ( 6489) covalent geometry : angle 0.56499 ( 8811) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 0.753 Fit side-chains REVERT: A 108 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.8079 (mmm160) REVERT: B 19 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8021 (mtpp) REVERT: B 34 ASP cc_start: 0.8863 (m-30) cc_final: 0.8642 (m-30) REVERT: B 38 ASP cc_start: 0.8591 (m-30) cc_final: 0.8313 (m-30) REVERT: D 159 ASN cc_start: 0.8841 (p0) cc_final: 0.8454 (p0) REVERT: D 190 HIS cc_start: 0.8790 (m90) cc_final: 0.8480 (m90) outliers start: 2 outliers final: 2 residues processed: 88 average time/residue: 0.2399 time to fit residues: 26.6188 Evaluate side-chains 84 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 82 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 59 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 ASN E 202 ASN D 139 ASN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.112376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.072233 restraints weight = 9371.429| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.99 r_work: 0.2631 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2473 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6496 Z= 0.126 Angle : 0.522 11.545 8825 Z= 0.270 Chirality : 0.043 0.174 949 Planarity : 0.004 0.050 1138 Dihedral : 4.161 16.588 881 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.72 % Allowed : 6.91 % Favored : 92.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 0.33 (0.30), residues: 788 helix: 0.78 (0.53), residues: 98 sheet: 1.13 (0.28), residues: 347 loop : -0.91 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 244 HIS 0.002 0.001 HIS B 51 PHE 0.011 0.001 PHE B 70 TYR 0.016 0.001 TYR E 33 ARG 0.006 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04070 ( 278) hydrogen bonds : angle 5.08370 ( 852) SS BOND : bond 0.00441 ( 7) SS BOND : angle 0.97702 ( 14) covalent geometry : bond 0.00296 ( 6489) covalent geometry : angle 0.52049 ( 8811) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.737 Fit side-chains REVERT: A 108 ARG cc_start: 0.8401 (mmm-85) cc_final: 0.8180 (mmm160) REVERT: A 173 GLU cc_start: 0.8741 (tp30) cc_final: 0.8148 (mt-10) REVERT: B 19 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8005 (mtpp) REVERT: B 34 ASP cc_start: 0.8853 (m-30) cc_final: 0.8638 (m-30) REVERT: B 38 ASP cc_start: 0.8570 (m-30) cc_final: 0.8313 (m-30) REVERT: D 159 ASN cc_start: 0.8806 (p0) cc_final: 0.8499 (p0) REVERT: D 188 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8619 (mm-30) REVERT: D 190 HIS cc_start: 0.8887 (m90) cc_final: 0.8459 (m90) REVERT: D 212 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7742 (ttp80) outliers start: 5 outliers final: 4 residues processed: 85 average time/residue: 0.2438 time to fit residues: 26.1217 Evaluate side-chains 82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 78 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain E residue 194 LEU Chi-restraints excluded: chain E residue 203 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 19 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 30 optimal weight: 0.0070 chunk 7 optimal weight: 2.9990 overall best weight: 1.1204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 253 GLN ** D 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.109107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.069409 restraints weight = 9511.111| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 2.95 r_work: 0.2601 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2444 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8865 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 6496 Z= 0.179 Angle : 0.553 12.292 8825 Z= 0.284 Chirality : 0.044 0.159 949 Planarity : 0.004 0.049 1138 Dihedral : 4.286 18.817 881 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.86 % Allowed : 8.06 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 20.51 % 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: 0.54 (0.30), residues: 788 helix: 0.86 (0.53), residues: 98 sheet: 1.33 (0.28), residues: 341 loop : -0.80 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 47 HIS 0.003 0.001 HIS C 5 PHE 0.012 0.002 PHE D 140 TYR 0.016 0.001 TYR E 33 ARG 0.006 0.000 ARG A 6 Details of bonding type rmsd hydrogen bonds : bond 0.04552 ( 278) hydrogen bonds : angle 5.04385 ( 852) SS BOND : bond 0.00604 ( 7) SS BOND : angle 1.15239 ( 14) covalent geometry : bond 0.00437 ( 6489) covalent geometry : angle 0.55121 ( 8811) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.758 Fit side-chains REVERT: A 108 ARG cc_start: 0.8422 (mmm-85) cc_final: 0.8205 (mmm160) REVERT: A 253 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.8076 (pt0) REVERT: B 19 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8032 (mtpp) REVERT: B 38 ASP cc_start: 0.8649 (m-30) cc_final: 0.8403 (m-30) REVERT: D 159 ASN cc_start: 0.8830 (p0) cc_final: 0.8504 (p0) REVERT: D 190 HIS cc_start: 0.8870 (m90) cc_final: 0.8499 (m90) REVERT: D 212 ARG cc_start: 0.8150 (ttp80) cc_final: 0.7748 (ttp-170) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 0.2700 time to fit residues: 26.7534 Evaluate side-chains 80 residues out of total 695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 GLN Chi-restraints excluded: chain B residue 47 GLU Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 70.2939 > 50: distance: 7 - 99: 32.523 distance: 10 - 96: 9.745 distance: 20 - 84: 22.264 distance: 23 - 81: 27.996 distance: 33 - 74: 30.115 distance: 35 - 41: 15.740 distance: 36 - 71: 32.768 distance: 41 - 42: 45.178 distance: 42 - 43: 40.605 distance: 42 - 45: 7.033 distance: 43 - 44: 5.780 distance: 43 - 46: 25.944 distance: 46 - 47: 15.067 distance: 46 - 52: 39.074 distance: 47 - 50: 36.099 distance: 48 - 49: 40.228 distance: 50 - 51: 28.173 distance: 51 - 52: 44.538 distance: 53 - 54: 20.369 distance: 54 - 55: 20.142 distance: 54 - 57: 17.112 distance: 60 - 61: 11.736 distance: 60 - 63: 35.921 distance: 63 - 64: 35.164 distance: 63 - 165: 21.659 distance: 64 - 65: 26.922 distance: 64 - 67: 14.190 distance: 65 - 66: 35.733 distance: 65 - 71: 35.682 distance: 66 - 162: 16.523 distance: 67 - 68: 48.218 distance: 68 - 69: 13.782 distance: 68 - 70: 6.055 distance: 71 - 72: 43.636 distance: 72 - 73: 42.098 distance: 73 - 74: 14.312 distance: 73 - 75: 44.448 distance: 75 - 76: 10.219 distance: 75 - 154: 23.084 distance: 76 - 77: 30.073 distance: 76 - 79: 25.650 distance: 77 - 78: 36.355 distance: 77 - 81: 15.804 distance: 78 - 151: 23.251 distance: 79 - 80: 27.106 distance: 80 - 193: 27.659 distance: 81 - 82: 5.952 distance: 82 - 83: 20.261 distance: 82 - 85: 18.512 distance: 83 - 84: 12.424 distance: 83 - 89: 16.494 distance: 85 - 86: 32.537 distance: 86 - 87: 31.185 distance: 86 - 88: 28.883 distance: 89 - 90: 19.254 distance: 89 - 141: 29.401 distance: 90 - 93: 15.110 distance: 91 - 92: 16.020 distance: 91 - 96: 17.088 distance: 92 - 138: 26.780 distance: 93 - 94: 31.099 distance: 93 - 95: 30.422 distance: 96 - 97: 22.232 distance: 97 - 98: 16.183 distance: 97 - 100: 31.545 distance: 98 - 99: 44.518 distance: 98 - 105: 16.352 distance: 100 - 101: 19.988 distance: 101 - 102: 40.434 distance: 102 - 103: 9.982 distance: 103 - 104: 43.508