Starting phenix.real_space_refine on Sun Apr 27 20:54:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rl6_19332/04_2025/8rl6_19332.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rl6_19332/04_2025/8rl6_19332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rl6_19332/04_2025/8rl6_19332.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rl6_19332/04_2025/8rl6_19332.map" model { file = "/net/cci-nas-00/data/ceres_data/8rl6_19332/04_2025/8rl6_19332.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rl6_19332/04_2025/8rl6_19332.cif" } resolution = 3.18 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= 0.012 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 S 20 5.16 5 C 2083 2.51 5 N 575 2.21 5 O 597 1.98 5 H 3217 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 6493 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6492 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 17, 'TRANS': 418} Chain breaks: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'GLU:plan': 5, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 88 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5920 SG CYS A 411 26.850 42.159 25.229 1.00 67.90 S ATOM 6155 SG CYS A 427 24.363 42.143 28.158 1.00 94.76 S ATOM 6204 SG CYS A 431 25.319 45.411 26.355 1.00 95.89 S ATOM 6243 SG CYS A 434 23.526 42.902 24.196 1.00 70.28 S Time building chain proxies: 6.00, per 1000 atoms: 0.92 Number of scatterers: 6493 At special positions: 0 Unit cell: (77.7, 81.9, 74.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 20 16.00 O 597 8.00 N 575 7.00 C 2083 6.00 H 3217 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 272 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 649.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 411 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 431 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 434 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 427 " Number of angles added : 6 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 826 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 2 sheets defined 56.0% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 Processing helix chain 'A' and resid 31 through 44 Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.629A pdb=" N CYS A 61 " --> pdb=" O GLY A 57 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 79 through 93 Processing helix chain 'A' and resid 105 through 118 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 137 through 148 removed outlier: 4.452A pdb=" N THR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 170 through 182 removed outlier: 4.039A pdb=" N GLY A 177 " --> pdb=" O TYR A 173 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ALA A 178 " --> pdb=" O LEU A 174 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 Processing helix chain 'A' and resid 237 through 251 removed outlier: 3.834A pdb=" N GLY A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 283 removed outlier: 3.596A pdb=" N GLU A 273 " --> pdb=" O ARG A 269 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 307 Processing helix chain 'A' and resid 339 through 349 removed outlier: 3.929A pdb=" N ARG A 349 " --> pdb=" O GLN A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 385 Processing helix chain 'A' and resid 388 through 407 removed outlier: 3.768A pdb=" N ILE A 396 " --> pdb=" O ASP A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 421 Processing helix chain 'A' and resid 436 through 451 removed outlier: 3.529A pdb=" N VAL A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 100 removed outlier: 6.389A pdb=" N SER A 98 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N THR A 73 " --> pdb=" O LEU A 126 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ILE A 128 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL A 75 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N ILE A 72 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N VAL A 155 " --> pdb=" O ILE A 72 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A 74 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N VAL A 189 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 154 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LEU A 191 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A 156 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA A 214 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 225 through 231 removed outlier: 5.801A pdb=" N PHE A 226 " --> pdb=" O CYS A 359 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N LEU A 361 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ASP A 228 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N TYR A 363 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLN A 230 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 331 " --> pdb=" O ARG A 360 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N TYR A 362 " --> pdb=" O VAL A 331 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N HIS A 333 " --> pdb=" O TYR A 362 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ILE A 263 " --> pdb=" O ALA A 332 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLY A 262 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ALA A 315 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N VAL A 264 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N TYR A 289 " --> pdb=" O THR A 316 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 162 hydrogen bonds defined for protein. 477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3208 1.03 - 1.23: 10 1.23 - 1.42: 1369 1.42 - 1.62: 1944 1.62 - 1.81: 25 Bond restraints: 6556 Sorted by residual: bond pdb=" CG LEU A 176 " pdb=" CD1 LEU A 176 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.35e+00 bond pdb=" CB CYS A 427 " pdb=" HB2 CYS A 427 " ideal model delta sigma weight residual 0.970 0.954 0.016 2.00e-02 2.50e+03 6.46e-01 bond pdb=" N LEU A 176 " pdb=" CA LEU A 176 " ideal model delta sigma weight residual 1.457 1.467 -0.009 1.29e-02 6.01e+03 5.13e-01 bond pdb=" CB LEU A 183 " pdb=" CG LEU A 183 " ideal model delta sigma weight residual 1.530 1.543 -0.013 2.00e-02 2.50e+03 4.05e-01 bond pdb=" CB GLU A 407 " pdb=" CG GLU A 407 " ideal model delta sigma weight residual 1.520 1.502 0.018 3.00e-02 1.11e+03 3.68e-01 ... (remaining 6551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 11079 1.01 - 2.02: 717 2.02 - 3.03: 34 3.03 - 4.04: 12 4.04 - 5.06: 9 Bond angle restraints: 11851 Sorted by residual: angle pdb=" CB LEU A 279 " pdb=" CG LEU A 279 " pdb=" CD1 LEU A 279 " ideal model delta sigma weight residual 110.70 114.97 -4.27 3.00e+00 1.11e-01 2.03e+00 angle pdb=" CA LEU A 183 " pdb=" CB LEU A 183 " pdb=" CG LEU A 183 " ideal model delta sigma weight residual 116.30 120.89 -4.59 3.50e+00 8.16e-02 1.72e+00 angle pdb=" CB LEU A 176 " pdb=" CG LEU A 176 " pdb=" CD1 LEU A 176 " ideal model delta sigma weight residual 110.70 114.51 -3.81 3.00e+00 1.11e-01 1.61e+00 angle pdb=" CA TYR A 173 " pdb=" CB TYR A 173 " pdb=" CG TYR A 173 " ideal model delta sigma weight residual 113.90 111.64 2.26 1.80e+00 3.09e-01 1.57e+00 angle pdb=" CB MET A 132 " pdb=" CG MET A 132 " pdb=" SD MET A 132 " ideal model delta sigma weight residual 112.70 116.43 -3.73 3.00e+00 1.11e-01 1.55e+00 ... (remaining 11846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 2784 15.53 - 31.06: 224 31.06 - 46.59: 56 46.59 - 62.11: 30 62.11 - 77.64: 8 Dihedral angle restraints: 3102 sinusoidal: 1636 harmonic: 1466 Sorted by residual: dihedral pdb=" CB CYS A 266 " pdb=" SG CYS A 266 " pdb=" SG CYS A 272 " pdb=" CB CYS A 272 " ideal model delta sinusoidal sigma weight residual 93.00 55.80 37.20 1 1.00e+01 1.00e-02 1.95e+01 dihedral pdb=" CA TYR A 363 " pdb=" C TYR A 363 " pdb=" N SER A 364 " pdb=" CA SER A 364 " ideal model delta harmonic sigma weight residual 180.00 163.55 16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG A 412 " pdb=" CD ARG A 412 " pdb=" NE ARG A 412 " pdb=" CZ ARG A 412 " ideal model delta sinusoidal sigma weight residual -90.00 -49.78 -40.22 2 1.50e+01 4.44e-03 8.90e+00 ... (remaining 3099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 332 0.024 - 0.047: 102 0.047 - 0.071: 49 0.071 - 0.094: 21 0.094 - 0.118: 21 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA VAL A 314 " pdb=" N VAL A 314 " pdb=" C VAL A 314 " pdb=" CB VAL A 314 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE A 74 " pdb=" N ILE A 74 " pdb=" C ILE A 74 " pdb=" CB ILE A 74 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.38e-01 ... (remaining 522 not shown) Planarity restraints: 996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 363 " 0.013 2.00e-02 2.50e+03 9.54e-03 2.73e+00 pdb=" CG TYR A 363 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 363 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 363 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 363 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A 363 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 363 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 363 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR A 363 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 TYR A 363 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 TYR A 363 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 TYR A 363 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 412 " -0.128 9.50e-02 1.11e+02 4.29e-02 2.17e+00 pdb=" NE ARG A 412 " 0.009 2.00e-02 2.50e+03 pdb=" CZ ARG A 412 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 412 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 412 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG A 412 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG A 412 " -0.000 2.00e-02 2.50e+03 pdb="HH21 ARG A 412 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 412 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 196 " -0.019 5.00e-02 4.00e+02 2.91e-02 1.35e+00 pdb=" N PRO A 197 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 197 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 197 " -0.016 5.00e-02 4.00e+02 ... (remaining 993 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 600 2.22 - 2.81: 14437 2.81 - 3.41: 18983 3.41 - 4.00: 24217 4.00 - 4.60: 37030 Nonbonded interactions: 95267 Sorted by model distance: nonbonded pdb=" O ASP A 157 " pdb=" HH TYR A 173 " model vdw 1.621 2.450 nonbonded pdb=" H ALA A 159 " pdb=" O LEU A 191 " model vdw 1.652 2.450 nonbonded pdb=" HE2 HIS A 333 " pdb=" OE1 GLU A 346 " model vdw 1.666 2.450 nonbonded pdb=" O ARG A 175 " pdb=" H ALA A 178 " model vdw 1.681 2.450 nonbonded pdb=" O LEU A 382 " pdb=" H GLY A 387 " model vdw 1.739 2.450 ... (remaining 95262 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.680 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: 0.120 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 25.710 Find NCS groups from input model: 0.050 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5880 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3344 Z= 0.113 Angle : 0.552 12.648 4537 Z= 0.254 Chirality : 0.037 0.118 525 Planarity : 0.004 0.056 580 Dihedral : 13.535 77.642 1194 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.86 (0.43), residues: 432 helix: 2.14 (0.35), residues: 226 sheet: -0.90 (0.62), residues: 74 loop : 1.17 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 334 HIS 0.003 0.001 HIS A 433 PHE 0.009 0.001 PHE A 216 TYR 0.027 0.002 TYR A 363 ARG 0.007 0.001 ARG A 349 Details of bonding type rmsd hydrogen bonds : bond 0.12246 ( 162) hydrogen bonds : angle 6.06628 ( 477) metal coordination : bond 0.01832 ( 4) metal coordination : angle 6.81760 ( 6) SS BOND : bond 0.00247 ( 1) SS BOND : angle 0.78293 ( 2) covalent geometry : bond 0.00243 ( 3339) covalent geometry : angle 0.49378 ( 4529) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 CYS cc_start: 0.6830 (m) cc_final: 0.6624 (m) REVERT: A 407 GLU cc_start: 0.6589 (mp0) cc_final: 0.6319 (mp0) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.2727 time to fit residues: 27.7604 Evaluate side-chains 78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.0670 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.207986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.188638 restraints weight = 15734.417| |-----------------------------------------------------------------------------| r_work (start): 0.4408 rms_B_bonded: 3.20 r_work: 0.4281 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3344 Z= 0.215 Angle : 0.618 11.363 4537 Z= 0.308 Chirality : 0.039 0.137 525 Planarity : 0.004 0.040 580 Dihedral : 4.085 14.991 469 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.60 % Allowed : 8.41 % Favored : 90.99 % 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: 1.19 (0.42), residues: 432 helix: 1.79 (0.35), residues: 228 sheet: -1.88 (0.55), residues: 75 loop : 0.94 (0.59), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 305 HIS 0.005 0.002 HIS A 89 PHE 0.017 0.002 PHE A 49 TYR 0.023 0.002 TYR A 363 ARG 0.005 0.001 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.04101 ( 162) hydrogen bonds : angle 5.08400 ( 477) metal coordination : bond 0.01318 ( 4) metal coordination : angle 6.50026 ( 6) SS BOND : bond 0.00321 ( 1) SS BOND : angle 0.44485 ( 2) covalent geometry : bond 0.00443 ( 3339) covalent geometry : angle 0.57129 ( 4529) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 76 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6639 (mm-40) cc_final: 0.6379 (mm-40) REVERT: A 151 LEU cc_start: 0.7732 (tp) cc_final: 0.7437 (tt) REVERT: A 407 GLU cc_start: 0.6820 (mp0) cc_final: 0.6511 (mp0) outliers start: 2 outliers final: 2 residues processed: 77 average time/residue: 0.2857 time to fit residues: 28.1650 Evaluate side-chains 76 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 8 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 38 optimal weight: 0.5980 chunk 30 optimal weight: 0.3980 chunk 29 optimal weight: 0.1980 chunk 20 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 32 optimal weight: 0.0870 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.208072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.187617 restraints weight = 15834.068| |-----------------------------------------------------------------------------| r_work (start): 0.4398 rms_B_bonded: 3.44 r_work: 0.4270 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3344 Z= 0.151 Angle : 0.545 9.140 4537 Z= 0.264 Chirality : 0.037 0.128 525 Planarity : 0.004 0.035 580 Dihedral : 4.031 15.366 469 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.60 % Allowed : 8.71 % Favored : 90.69 % 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: 1.20 (0.42), residues: 432 helix: 1.74 (0.35), residues: 228 sheet: -1.87 (0.56), residues: 75 loop : 1.06 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.004 0.001 HIS A 89 PHE 0.012 0.001 PHE A 204 TYR 0.029 0.002 TYR A 363 ARG 0.003 0.000 ARG A 329 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 162) hydrogen bonds : angle 4.88120 ( 477) metal coordination : bond 0.01118 ( 4) metal coordination : angle 6.01450 ( 6) SS BOND : bond 0.00475 ( 1) SS BOND : angle 0.42560 ( 2) covalent geometry : bond 0.00314 ( 3339) covalent geometry : angle 0.49952 ( 4529) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6637 (mm-40) cc_final: 0.6379 (mm-40) REVERT: A 346 GLU cc_start: 0.7279 (mt-10) cc_final: 0.7031 (mt-10) outliers start: 2 outliers final: 2 residues processed: 74 average time/residue: 0.4178 time to fit residues: 39.8050 Evaluate side-chains 74 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 318 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 19 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 3 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 31 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 39 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 overall best weight: 0.2358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.207740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.187512 restraints weight = 16003.187| |-----------------------------------------------------------------------------| r_work (start): 0.4405 rms_B_bonded: 3.36 r_work: 0.4280 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6044 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3344 Z= 0.123 Angle : 0.517 8.318 4537 Z= 0.250 Chirality : 0.037 0.125 525 Planarity : 0.004 0.037 580 Dihedral : 3.935 15.810 469 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.90 % Allowed : 11.41 % Favored : 87.69 % 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: 1.23 (0.42), residues: 432 helix: 1.78 (0.35), residues: 228 sheet: -1.87 (0.56), residues: 75 loop : 1.06 (0.58), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.003 0.001 HIS A 290 PHE 0.012 0.001 PHE A 204 TYR 0.014 0.001 TYR A 363 ARG 0.004 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03256 ( 162) hydrogen bonds : angle 4.64938 ( 477) metal coordination : bond 0.00937 ( 4) metal coordination : angle 5.13485 ( 6) SS BOND : bond 0.00361 ( 1) SS BOND : angle 0.48687 ( 2) covalent geometry : bond 0.00261 ( 3339) covalent geometry : angle 0.48288 ( 4529) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 864 Ramachandran restraints generated. 432 Oldfield, 0 Emsley, 432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 22 is missing expected H atoms. Skipping. Residue LEU 68 is missing expected H atoms. Skipping. Residue SER 259 is missing expected H atoms. Skipping. Residue LYS 287 is missing expected H atoms. Skipping. Residue LYS 309 is missing expected H atoms. Skipping. Residue LYS 338 is missing expected H atoms. Skipping. Residue LYS 389 is missing expected H atoms. Skipping. Residue SER 391 is missing expected H atoms. Skipping. Residue LYS 393 is missing expected H atoms. Skipping. Residue MET 397 is missing expected H atoms. Skipping. Residue VAL 440 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLN cc_start: 0.6595 (mm-40) cc_final: 0.6368 (mm-40) REVERT: A 346 GLU cc_start: 0.7263 (mt-10) cc_final: 0.6891 (mt-10) outliers start: 3 outliers final: 1 residues processed: 74 average time/residue: 0.2316 time to fit residues: 22.7134 Evaluate side-chains 73 residues out of total 366 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 70.5744 > 50: distance: 40 - 50: 22.284 distance: 50 - 51: 8.912 distance: 50 - 54: 13.313 distance: 51 - 52: 27.748 distance: 51 - 55: 30.453 distance: 51 - 56: 10.498 distance: 52 - 53: 44.424 distance: 52 - 57: 20.490 distance: 57 - 58: 32.784 distance: 57 - 65: 29.390 distance: 58 - 59: 24.108 distance: 58 - 61: 32.193 distance: 58 - 66: 24.718 distance: 59 - 60: 37.278 distance: 59 - 76: 20.164 distance: 61 - 62: 40.360 distance: 61 - 63: 57.926 distance: 61 - 67: 13.555 distance: 62 - 68: 7.610 distance: 62 - 69: 12.883 distance: 63 - 71: 40.096 distance: 63 - 72: 44.607 distance: 64 - 73: 6.026 distance: 64 - 74: 4.988 distance: 64 - 75: 40.515 distance: 76 - 77: 37.474 distance: 76 - 83: 37.882 distance: 77 - 78: 16.008 distance: 77 - 80: 4.892 distance: 77 - 84: 39.786 distance: 78 - 79: 28.623 distance: 78 - 90: 49.884 distance: 82 - 87: 10.975 distance: 82 - 88: 40.941 distance: 82 - 89: 20.156 distance: 90 - 91: 19.687 distance: 90 - 98: 21.282 distance: 91 - 92: 26.560 distance: 91 - 94: 29.822 distance: 91 - 99: 40.243 distance: 92 - 93: 28.963 distance: 92 - 109: 36.542 distance: 94 - 95: 48.900 distance: 94 - 96: 41.825 distance: 94 - 100: 43.721 distance: 95 - 97: 40.766 distance: 95 - 101: 3.431 distance: 95 - 102: 13.349 distance: 96 - 103: 15.124 distance: 96 - 105: 28.094 distance: 97 - 106: 23.779 distance: 97 - 107: 4.917 distance: 109 - 110: 33.157 distance: 109 - 116: 8.080 distance: 110 - 111: 24.682 distance: 110 - 113: 18.863 distance: 110 - 117: 22.315 distance: 111 - 112: 30.460 distance: 111 - 125: 55.116 distance: 113 - 118: 6.360 distance: 114 - 119: 4.709 distance: 114 - 120: 3.975 distance: 114 - 121: 36.352 distance: 125 - 126: 10.922 distance: 125 - 132: 49.430 distance: 126 - 127: 45.626 distance: 126 - 129: 41.511 distance: 126 - 133: 39.711 distance: 127 - 128: 10.331 distance: 127 - 141: 16.721 distance: 129 - 130: 4.190 distance: 129 - 134: 39.128 distance: 130 - 135: 52.289 distance: 130 - 136: 35.547 distance: 130 - 137: 34.921 distance: 131 - 138: 39.340 distance: 131 - 139: 19.163 distance: 131 - 140: 26.020 distance: 141 - 142: 22.347 distance: 141 - 147: 21.960 distance: 142 - 143: 51.720 distance: 142 - 145: 11.024 distance: 142 - 148: 49.369 distance: 143 - 144: 40.803 distance: 143 - 152: 55.971 distance: 145 - 146: 55.910 distance: 145 - 149: 4.216 distance: 146 - 151: 39.427 distance: 152 - 153: 40.871 distance: 152 - 158: 46.893 distance: 153 - 156: 14.056 distance: 153 - 159: 39.750 distance: 154 - 155: 39.712 distance: 154 - 166: 42.611 distance: 156 - 157: 59.877 distance: 156 - 160: 42.127 distance: 156 - 161: 44.148 distance: 157 - 158: 58.611 distance: 157 - 162: 24.487 distance: 157 - 163: 26.647 distance: 158 - 164: 34.381 distance: 158 - 165: 35.761 distance: 166 - 167: 40.087 distance: 166 - 174: 34.492 distance: 167 - 168: 30.438 distance: 167 - 170: 28.769 distance: 167 - 175: 33.178 distance: 168 - 169: 29.375 distance: 168 - 185: 15.132 distance: 169 - 233: 21.115 distance: 170 - 171: 3.134 distance: 170 - 176: 23.528 distance: 170 - 177: 17.475 distance: 171 - 172: 25.717 distance: 171 - 173: 19.518 distance: 171 - 178: 20.719 distance: 172 - 179: 29.910 distance: 172 - 180: 21.406 distance: 172 - 181: 19.955 distance: 173 - 184: 23.738 distance: 185 - 186: 18.951 distance: 185 - 193: 32.342 distance: 186 - 187: 58.494 distance: 186 - 189: 42.584 distance: 186 - 194: 49.109 distance: 187 - 188: 16.716 distance: 187 - 204: 28.566 distance: 188 - 251: 18.383 distance: 189 - 190: 27.105 distance: 189 - 191: 13.584 distance: 189 - 195: 4.751 distance: 190 - 192: 11.944 distance: 190 - 196: 13.517 distance: 190 - 197: 42.778 distance: 191 - 198: 16.741 distance: 191 - 199: 14.848 distance: 191 - 200: 30.383 distance: 192 - 201: 10.304 distance: 192 - 202: 25.320 distance: 192 - 203: 31.106 distance: 207 - 257: 3.175