Starting phenix.real_space_refine on Fri Aug 22 17:57:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dv1_27730/08_2025/8dv1_27730.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dv1_27730/08_2025/8dv1_27730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dv1_27730/08_2025/8dv1_27730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dv1_27730/08_2025/8dv1_27730.map" model { file = "/net/cci-nas-00/data/ceres_data/8dv1_27730/08_2025/8dv1_27730.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dv1_27730/08_2025/8dv1_27730.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.038 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 37 5.16 5 C 4183 2.51 5 N 1074 2.21 5 O 1249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6543 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 11, 'TRANS': 189} Chain: "D" Number of atoms: 4855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4855 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 27, 'TRANS': 567} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 1.44, per 1000 atoms: 0.22 Number of scatterers: 6543 At special positions: 0 Unit cell: (76.311, 87.57, 126.351, 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 37 16.00 O 1249 8.00 N 1074 7.00 C 4183 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.02 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 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D1001 " - " ASN D 322 " " NAG D1002 " - " ASN D 103 " " NAG D1003 " - " ASN D 432 " " NAG D1004 " - " ASN D 546 " " NAG D1005 " - " ASN D 90 " " NAG D1006 " - " ASN D 53 " Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 339.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1498 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 58.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.677A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.589A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.108A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 520 through 522 No H-bonds generated for 'chain 'A' and resid 520 through 522' Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.969A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N TYR D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 81 Processing helix chain 'D' and resid 82 through 83 No H-bonds generated for 'chain 'D' and resid 82 through 83' Processing helix chain 'D' and resid 84 through 88 Processing helix chain 'D' and resid 90 through 101 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 137 through 141 Processing helix chain 'D' and resid 147 through 155 removed outlier: 3.736A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix removed outlier: 4.486A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 220 through 252 Proline residue: D 235 - end of helix removed outlier: 3.996A pdb=" N ASN D 250 " --> pdb=" O ALA D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 399 through 413 Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 4.078A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.881A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 598 Proline residue: D 590 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.915A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.072A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 347 through 350 323 hydrogen bonds defined for protein. 906 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: 0.66 Time building geometry restraints manager: 0.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1266 1.32 - 1.45: 2072 1.45 - 1.58: 3320 1.58 - 1.71: 9 1.71 - 1.84: 58 Bond restraints: 6725 Sorted by residual: bond pdb=" CD2 TRP D 477 " pdb=" CE3 TRP D 477 " ideal model delta sigma weight residual 1.398 1.306 0.092 1.60e-02 3.91e+03 3.28e+01 bond pdb=" CB SER D 44 " pdb=" OG SER D 44 " ideal model delta sigma weight residual 1.417 1.313 0.104 2.00e-02 2.50e+03 2.69e+01 bond pdb=" CB TYR A 421 " pdb=" CG TYR A 421 " ideal model delta sigma weight residual 1.512 1.402 0.110 2.20e-02 2.07e+03 2.48e+01 bond pdb=" CB ASN A 422 " pdb=" CG ASN A 422 " ideal model delta sigma weight residual 1.516 1.392 0.124 2.50e-02 1.60e+03 2.45e+01 bond pdb=" CB HIS D 540 " pdb=" CG HIS D 540 " ideal model delta sigma weight residual 1.497 1.430 0.067 1.40e-02 5.10e+03 2.29e+01 ... (remaining 6720 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 7553 2.16 - 4.32: 1363 4.32 - 6.47: 181 6.47 - 8.63: 35 8.63 - 10.79: 8 Bond angle restraints: 9140 Sorted by residual: angle pdb=" C GLY D 537 " pdb=" N PRO D 538 " pdb=" CA PRO D 538 " ideal model delta sigma weight residual 119.78 128.55 -8.77 1.03e+00 9.43e-01 7.24e+01 angle pdb=" C ALA A 520 " pdb=" N PRO A 521 " pdb=" CA PRO A 521 " ideal model delta sigma weight residual 119.47 129.12 -9.65 1.16e+00 7.43e-01 6.93e+01 angle pdb=" C ASN D 137 " pdb=" N PRO D 138 " pdb=" CA PRO D 138 " ideal model delta sigma weight residual 119.56 127.64 -8.08 1.02e+00 9.61e-01 6.28e+01 angle pdb=" C VAL D 283 " pdb=" N PRO D 284 " pdb=" CA PRO D 284 " ideal model delta sigma weight residual 119.24 127.24 -8.00 1.04e+00 9.25e-01 5.91e+01 angle pdb=" C SER D 611 " pdb=" N PRO D 612 " pdb=" CA PRO D 612 " ideal model delta sigma weight residual 119.82 127.13 -7.31 9.80e-01 1.04e+00 5.57e+01 ... (remaining 9135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3870 17.80 - 35.59: 146 35.59 - 53.39: 29 53.39 - 71.19: 12 71.19 - 88.98: 5 Dihedral angle restraints: 4062 sinusoidal: 1727 harmonic: 2335 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -140.80 54.80 1 1.00e+01 1.00e-02 4.07e+01 dihedral pdb=" C TYR A 421 " pdb=" N TYR A 421 " pdb=" CA TYR A 421 " pdb=" CB TYR A 421 " ideal model delta harmonic sigma weight residual -122.60 -135.05 12.45 0 2.50e+00 1.60e-01 2.48e+01 dihedral pdb=" CA ALA D 153 " pdb=" C ALA D 153 " pdb=" N ASN D 154 " pdb=" CA ASN D 154 " ideal model delta harmonic sigma weight residual -180.00 -157.26 -22.74 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 4059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 838 0.137 - 0.274: 124 0.274 - 0.412: 10 0.412 - 0.549: 3 0.549 - 0.686: 1 Chirality restraints: 976 Sorted by residual: chirality pdb=" CA TYR A 421 " pdb=" N TYR A 421 " pdb=" C TYR A 421 " pdb=" CB TYR A 421 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG D1002 " pdb=" ND2 ASN D 103 " pdb=" C2 NAG D1002 " pdb=" O5 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.93 0.53 2.00e-01 2.50e+01 6.96e+00 chirality pdb=" C2 NAG D1002 " pdb=" C1 NAG D1002 " pdb=" C3 NAG D1002 " pdb=" N2 NAG D1002 " both_signs ideal model delta sigma weight residual False -2.49 -3.00 0.50 2.00e-01 2.50e+01 6.35e+00 ... (remaining 973 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 90 " 0.217 2.00e-02 2.50e+03 2.54e-01 8.05e+02 pdb=" CG ASN D 90 " -0.123 2.00e-02 2.50e+03 pdb=" OD1 ASN D 90 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN D 90 " -0.403 2.00e-02 2.50e+03 pdb=" C1 NAG D1005 " 0.312 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 163 " 0.287 2.00e-02 2.50e+03 1.39e-01 4.80e+02 pdb=" CG TRP D 163 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP D 163 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 TRP D 163 " -0.148 2.00e-02 2.50e+03 pdb=" NE1 TRP D 163 " -0.046 2.00e-02 2.50e+03 pdb=" CE2 TRP D 163 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP D 163 " -0.174 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 163 " 0.148 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 163 " -0.037 2.00e-02 2.50e+03 pdb=" CH2 TRP D 163 " 0.139 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.135 2.00e-02 2.50e+03 1.44e-01 2.59e+02 pdb=" CG ASN A 343 " 0.075 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.225 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " -0.171 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1716 2.80 - 3.33: 6477 3.33 - 3.85: 11592 3.85 - 4.38: 14234 4.38 - 4.90: 22417 Nonbonded interactions: 56436 Sorted by model distance: nonbonded pdb=" O4 NAG D1004 " pdb=" O6 NAG D1004 " model vdw 2.277 3.040 nonbonded pdb=" N ASN D 103 " pdb=" OD1 ASN D 103 " model vdw 2.318 3.120 nonbonded pdb=" N ASN D 432 " pdb=" OD1 ASN D 432 " model vdw 2.327 3.120 nonbonded pdb=" N ASN D 546 " pdb=" OD1 ASN D 546 " model vdw 2.356 3.120 nonbonded pdb=" N ASN D 322 " pdb=" OD1 ASN D 322 " model vdw 2.411 3.120 ... (remaining 56431 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.940 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: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.480 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 : 0.018 0.125 6739 Z= 0.970 Angle : 1.726 12.104 9175 Z= 1.170 Chirality : 0.101 0.686 976 Planarity : 0.011 0.139 1177 Dihedral : 10.891 88.982 2543 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.43 % Allowed : 1.57 % Favored : 98.00 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.28), residues: 792 helix: -0.33 (0.23), residues: 378 sheet: 0.33 (0.67), residues: 58 loop : 0.18 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 177 TYR 0.070 0.011 TYR D 180 PHE 0.069 0.008 PHE D 32 TRP 0.287 0.015 TRP D 163 HIS 0.010 0.002 HIS D 241 Details of bonding type rmsd covalent geometry : bond 0.01796 ( 6725) covalent geometry : angle 1.70873 ( 9140) SS BOND : bond 0.00792 ( 7) SS BOND : angle 1.59109 ( 14) hydrogen bonds : bond 0.17554 ( 323) hydrogen bonds : angle 7.51538 ( 906) link_NAG-ASN : bond 0.08250 ( 7) link_NAG-ASN : angle 5.45673 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 198 time to evaluate : 0.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 360 ASN cc_start: 0.7661 (m-40) cc_final: 0.7098 (p0) REVERT: A 472 ILE cc_start: 0.7249 (mm) cc_final: 0.7040 (mm) REVERT: A 500 THR cc_start: 0.8413 (p) cc_final: 0.8103 (p) REVERT: D 476 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8347 (mptt) outliers start: 3 outliers final: 1 residues processed: 200 average time/residue: 0.0873 time to fit residues: 22.0912 Evaluate side-chains 119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 322 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 61 ASN D 96 GLN D 401 HIS D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.111640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.098372 restraints weight = 15187.037| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 3.01 r_work: 0.3334 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6739 Z= 0.178 Angle : 0.781 20.076 9175 Z= 0.376 Chirality : 0.054 0.664 976 Planarity : 0.005 0.037 1177 Dihedral : 7.500 89.119 1013 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.86 % Allowed : 9.44 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.30), residues: 792 helix: 1.27 (0.27), residues: 377 sheet: 0.04 (0.66), residues: 60 loop : 0.41 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 466 TYR 0.022 0.002 TYR D 183 PHE 0.018 0.002 PHE D 369 TRP 0.016 0.002 TRP D 165 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 6725) covalent geometry : angle 0.68821 ( 9140) SS BOND : bond 0.00457 ( 7) SS BOND : angle 1.61190 ( 14) hydrogen bonds : bond 0.05299 ( 323) hydrogen bonds : angle 5.42007 ( 906) link_NAG-ASN : bond 0.00731 ( 7) link_NAG-ASN : angle 7.65830 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 332 ILE cc_start: 0.7884 (pt) cc_final: 0.7400 (pt) REVERT: A 355 ARG cc_start: 0.8628 (tpt170) cc_final: 0.8170 (tpt170) REVERT: A 414 GLN cc_start: 0.8010 (mm110) cc_final: 0.7783 (mt0) REVERT: A 523 THR cc_start: 0.7970 (m) cc_final: 0.7724 (p) REVERT: D 26 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8338 (ttmt) REVERT: D 56 GLU cc_start: 0.8122 (pm20) cc_final: 0.7673 (pm20) REVERT: D 60 GLN cc_start: 0.8531 (mm-40) cc_final: 0.8222 (mm-40) REVERT: D 115 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.7896 (mmm-85) REVERT: D 168 TRP cc_start: 0.6876 (t-100) cc_final: 0.6342 (t-100) REVERT: D 174 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7978 (ttmm) REVERT: D 206 ASP cc_start: 0.9108 (t70) cc_final: 0.8714 (t0) REVERT: D 210 ASN cc_start: 0.7671 (m-40) cc_final: 0.7394 (m110) REVERT: D 270 MET cc_start: 0.7677 (mmt) cc_final: 0.7353 (tpp) REVERT: D 472 GLN cc_start: 0.7188 (mt0) cc_final: 0.6645 (mp10) REVERT: D 476 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8086 (tppt) REVERT: D 577 LYS cc_start: 0.7429 (mttt) cc_final: 0.7146 (mtpt) outliers start: 13 outliers final: 6 residues processed: 155 average time/residue: 0.0836 time to fit residues: 16.8352 Evaluate side-chains 126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 233 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 25 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 0.0970 chunk 32 optimal weight: 2.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN D 61 ASN D 373 HIS D 437 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.108197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.095006 restraints weight = 15177.805| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.96 r_work: 0.3287 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6739 Z= 0.192 Angle : 0.769 19.698 9175 Z= 0.362 Chirality : 0.052 0.608 976 Planarity : 0.004 0.029 1177 Dihedral : 7.028 78.305 1011 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.00 % Allowed : 10.01 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.30), residues: 792 helix: 1.35 (0.27), residues: 380 sheet: -0.40 (0.65), residues: 61 loop : 0.23 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 518 TYR 0.019 0.001 TYR D 385 PHE 0.017 0.002 PHE A 374 TRP 0.014 0.001 TRP D 478 HIS 0.007 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 6725) covalent geometry : angle 0.67561 ( 9140) SS BOND : bond 0.00688 ( 7) SS BOND : angle 1.56581 ( 14) hydrogen bonds : bond 0.05158 ( 323) hydrogen bonds : angle 5.07975 ( 906) link_NAG-ASN : bond 0.00829 ( 7) link_NAG-ASN : angle 7.63918 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.268 Fit side-chains REVERT: A 469 SER cc_start: 0.8717 (t) cc_final: 0.8438 (p) REVERT: A 498 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8181 (mt0) REVERT: D 26 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8541 (ttmt) REVERT: D 56 GLU cc_start: 0.8134 (pm20) cc_final: 0.7663 (pm20) REVERT: D 60 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8191 (mm-40) REVERT: D 115 ARG cc_start: 0.8427 (mmm-85) cc_final: 0.8050 (mmm-85) REVERT: D 168 TRP cc_start: 0.6880 (t-100) cc_final: 0.6193 (t-100) REVERT: D 206 ASP cc_start: 0.9081 (t70) cc_final: 0.8742 (t0) REVERT: D 210 ASN cc_start: 0.7901 (m-40) cc_final: 0.7665 (m110) REVERT: D 401 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.7662 (t-90) REVERT: D 472 GLN cc_start: 0.7297 (mt0) cc_final: 0.6756 (mp10) REVERT: D 476 LYS cc_start: 0.8055 (mmmt) cc_final: 0.7844 (tppt) REVERT: D 494 ASP cc_start: 0.8699 (t70) cc_final: 0.8352 (t0) outliers start: 21 outliers final: 10 residues processed: 133 average time/residue: 0.0728 time to fit residues: 12.9604 Evaluate side-chains 129 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 26 LYS Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 401 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 16 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 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 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.107106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093779 restraints weight = 15436.825| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.01 r_work: 0.3277 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6739 Z= 0.191 Angle : 0.749 19.969 9175 Z= 0.350 Chirality : 0.051 0.605 976 Planarity : 0.004 0.027 1177 Dihedral : 6.238 49.969 1011 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.58 % Allowed : 11.30 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.30), residues: 792 helix: 1.35 (0.26), residues: 380 sheet: -0.42 (0.66), residues: 61 loop : 0.10 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 582 TYR 0.017 0.001 TYR D 385 PHE 0.014 0.002 PHE D 230 TRP 0.012 0.001 TRP D 478 HIS 0.006 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00421 ( 6725) covalent geometry : angle 0.64969 ( 9140) SS BOND : bond 0.00543 ( 7) SS BOND : angle 1.76576 ( 14) hydrogen bonds : bond 0.04886 ( 323) hydrogen bonds : angle 4.96993 ( 906) link_NAG-ASN : bond 0.00856 ( 7) link_NAG-ASN : angle 7.68096 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.246 Fit side-chains REVERT: A 469 SER cc_start: 0.8679 (t) cc_final: 0.8320 (p) REVERT: A 498 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: D 56 GLU cc_start: 0.8217 (pm20) cc_final: 0.7684 (pm20) REVERT: D 60 GLN cc_start: 0.8514 (mm-40) cc_final: 0.8284 (mm-40) REVERT: D 63 ASN cc_start: 0.8566 (m-40) cc_final: 0.8177 (m-40) REVERT: D 163 TRP cc_start: 0.5851 (t60) cc_final: 0.5514 (t60) REVERT: D 174 LYS cc_start: 0.8312 (ttmm) cc_final: 0.8032 (mttp) REVERT: D 206 ASP cc_start: 0.9076 (t70) cc_final: 0.8766 (t0) REVERT: D 210 ASN cc_start: 0.7913 (m-40) cc_final: 0.7667 (m110) REVERT: D 249 MET cc_start: 0.7804 (tpt) cc_final: 0.7472 (tpt) REVERT: D 401 HIS cc_start: 0.8744 (OUTLIER) cc_final: 0.7760 (t-90) REVERT: D 494 ASP cc_start: 0.8755 (t70) cc_final: 0.8382 (t70) outliers start: 18 outliers final: 9 residues processed: 132 average time/residue: 0.0806 time to fit residues: 14.1884 Evaluate side-chains 128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 117 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 496 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 60 optimal weight: 0.0040 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 37 optimal weight: 0.4980 chunk 20 optimal weight: 0.5980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 437 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.109392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096767 restraints weight = 15526.559| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.75 r_work: 0.3363 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6739 Z= 0.155 Angle : 0.722 20.028 9175 Z= 0.331 Chirality : 0.050 0.580 976 Planarity : 0.003 0.027 1177 Dihedral : 5.677 51.299 1011 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.15 % Allowed : 13.45 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.30), residues: 792 helix: 1.43 (0.27), residues: 381 sheet: -0.65 (0.63), residues: 61 loop : 0.07 (0.35), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 115 TYR 0.018 0.001 TYR D 385 PHE 0.013 0.001 PHE A 377 TRP 0.011 0.001 TRP D 477 HIS 0.005 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 6725) covalent geometry : angle 0.62167 ( 9140) SS BOND : bond 0.00393 ( 7) SS BOND : angle 1.82264 ( 14) hydrogen bonds : bond 0.04615 ( 323) hydrogen bonds : angle 4.95031 ( 906) link_NAG-ASN : bond 0.00856 ( 7) link_NAG-ASN : angle 7.56918 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.254 Fit side-chains REVERT: A 469 SER cc_start: 0.8678 (t) cc_final: 0.8364 (p) REVERT: A 498 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7955 (mt0) REVERT: D 63 ASN cc_start: 0.8491 (m-40) cc_final: 0.8098 (m-40) REVERT: D 115 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7206 (tpt-90) REVERT: D 174 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.8166 (mttp) REVERT: D 206 ASP cc_start: 0.9068 (t70) cc_final: 0.8838 (t0) REVERT: D 367 ASP cc_start: 0.8083 (m-30) cc_final: 0.7782 (m-30) REVERT: D 494 ASP cc_start: 0.8704 (t70) cc_final: 0.8388 (t70) outliers start: 15 outliers final: 11 residues processed: 131 average time/residue: 0.0776 time to fit residues: 13.4535 Evaluate side-chains 121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 108 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 530 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 75 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 71 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN D 81 GLN D 493 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.108555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.095911 restraints weight = 15644.740| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.76 r_work: 0.3348 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6739 Z= 0.172 Angle : 0.712 20.081 9175 Z= 0.332 Chirality : 0.050 0.584 976 Planarity : 0.004 0.028 1177 Dihedral : 5.582 50.797 1011 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 2.86 % Allowed : 13.30 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.31), residues: 792 helix: 1.44 (0.26), residues: 381 sheet: -0.70 (0.64), residues: 61 loop : 0.03 (0.36), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 582 TYR 0.018 0.001 TYR D 385 PHE 0.012 0.001 PHE D 230 TRP 0.014 0.001 TRP D 168 HIS 0.004 0.001 HIS D 378 Details of bonding type rmsd covalent geometry : bond 0.00380 ( 6725) covalent geometry : angle 0.61263 ( 9140) SS BOND : bond 0.00292 ( 7) SS BOND : angle 1.59878 ( 14) hydrogen bonds : bond 0.04637 ( 323) hydrogen bonds : angle 4.98722 ( 906) link_NAG-ASN : bond 0.00860 ( 7) link_NAG-ASN : angle 7.51918 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.249 Fit side-chains REVERT: A 364 ASP cc_start: 0.6933 (t70) cc_final: 0.6022 (m-30) REVERT: A 469 SER cc_start: 0.8659 (t) cc_final: 0.8351 (p) REVERT: A 498 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: D 56 GLU cc_start: 0.8130 (pm20) cc_final: 0.7681 (pm20) REVERT: D 63 ASN cc_start: 0.8544 (m-40) cc_final: 0.8183 (m-40) REVERT: D 79 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8599 (mm) REVERT: D 174 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8323 (mttp) REVERT: D 249 MET cc_start: 0.8029 (tpt) cc_final: 0.7578 (tpp) REVERT: D 310 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7859 (mm-30) REVERT: D 401 HIS cc_start: 0.8628 (OUTLIER) cc_final: 0.7693 (t-90) REVERT: D 494 ASP cc_start: 0.8655 (t70) cc_final: 0.8347 (t70) outliers start: 20 outliers final: 12 residues processed: 128 average time/residue: 0.0790 time to fit residues: 13.5467 Evaluate side-chains 125 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 174 LYS Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 69 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 493 HIS ** 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 = 0.3659 r_free = 0.3659 target = 0.108770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.096408 restraints weight = 15406.971| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.71 r_work: 0.3358 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.5378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6739 Z= 0.156 Angle : 0.723 20.185 9175 Z= 0.335 Chirality : 0.049 0.569 976 Planarity : 0.003 0.027 1177 Dihedral : 5.571 51.491 1011 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.72 % Allowed : 14.31 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.87 (0.31), residues: 792 helix: 1.42 (0.27), residues: 383 sheet: -0.71 (0.64), residues: 61 loop : -0.03 (0.36), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 115 TYR 0.018 0.001 TYR D 385 PHE 0.012 0.001 PHE A 377 TRP 0.014 0.001 TRP D 168 HIS 0.004 0.001 HIS D 535 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6725) covalent geometry : angle 0.62840 ( 9140) SS BOND : bond 0.00254 ( 7) SS BOND : angle 1.51561 ( 14) hydrogen bonds : bond 0.04505 ( 323) hydrogen bonds : angle 4.97757 ( 906) link_NAG-ASN : bond 0.00906 ( 7) link_NAG-ASN : angle 7.42097 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1584 Ramachandran restraints generated. 792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.180 Fit side-chains revert: symmetry clash REVERT: A 356 LYS cc_start: 0.8889 (tptp) cc_final: 0.8688 (tptp) REVERT: A 469 SER cc_start: 0.8657 (t) cc_final: 0.8344 (p) REVERT: A 498 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.7895 (mt0) REVERT: D 63 ASN cc_start: 0.8534 (m-40) cc_final: 0.8189 (m-40) REVERT: D 249 MET cc_start: 0.7939 (tpt) cc_final: 0.7504 (tpp) REVERT: D 310 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7793 (mm-30) REVERT: D 401 HIS cc_start: 0.8534 (OUTLIER) cc_final: 0.7538 (t-90) outliers start: 19 outliers final: 13 residues processed: 126 average time/residue: 0.0692 time to fit residues: 11.7257 Evaluate side-chains 127 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 519 HIS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 79 LEU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.168 > 50: distance: 69 - 92: 31.602 distance: 73 - 100: 21.903 distance: 81 - 87: 22.479 distance: 82 - 112: 32.072 distance: 87 - 88: 13.287 distance: 88 - 89: 24.991 distance: 88 - 91: 51.544 distance: 89 - 90: 46.242 distance: 89 - 92: 5.032 distance: 92 - 93: 21.876 distance: 93 - 94: 17.544 distance: 93 - 96: 30.992 distance: 94 - 95: 31.027 distance: 94 - 100: 19.336 distance: 96 - 97: 17.353 distance: 97 - 98: 25.947 distance: 97 - 99: 25.313 distance: 100 - 101: 14.942 distance: 101 - 102: 10.386 distance: 101 - 104: 41.220 distance: 102 - 103: 26.194 distance: 102 - 112: 51.252 distance: 104 - 105: 22.870 distance: 105 - 106: 11.426 distance: 105 - 107: 20.451 distance: 106 - 108: 23.548 distance: 107 - 109: 18.749 distance: 108 - 110: 20.043 distance: 109 - 110: 15.555 distance: 110 - 111: 23.264 distance: 112 - 113: 25.442 distance: 113 - 114: 40.298 distance: 113 - 116: 16.200 distance: 114 - 115: 20.626 distance: 114 - 120: 38.645 distance: 116 - 117: 15.401 distance: 117 - 118: 30.722 distance: 117 - 119: 13.097 distance: 120 - 121: 3.823 distance: 121 - 122: 22.816 distance: 121 - 124: 16.413 distance: 122 - 123: 20.738 distance: 122 - 132: 18.605 distance: 124 - 125: 8.504 distance: 125 - 126: 14.092 distance: 125 - 127: 11.251 distance: 126 - 128: 3.163 distance: 127 - 129: 19.558 distance: 128 - 130: 18.664 distance: 129 - 130: 6.032 distance: 130 - 131: 11.319 distance: 132 - 133: 37.802 distance: 133 - 134: 25.234 distance: 133 - 136: 21.977 distance: 134 - 135: 27.064 distance: 134 - 141: 29.142 distance: 136 - 137: 21.583 distance: 137 - 138: 11.651 distance: 138 - 139: 12.807 distance: 139 - 140: 17.255 distance: 141 - 142: 40.108 distance: 142 - 143: 44.920 distance: 142 - 145: 6.455 distance: 143 - 144: 26.516 distance: 143 - 149: 23.751 distance: 145 - 146: 5.936 distance: 146 - 147: 57.778 distance: 146 - 148: 42.852 distance: 149 - 150: 22.271 distance: 149 - 155: 16.745 distance: 150 - 151: 33.978 distance: 150 - 153: 30.242 distance: 151 - 152: 26.507 distance: 151 - 156: 13.786 distance: 153 - 154: 33.459 distance: 154 - 155: 19.346 distance: 156 - 157: 7.490 distance: 157 - 158: 37.286 distance: 157 - 160: 28.954 distance: 158 - 159: 14.286 distance: 158 - 164: 28.103 distance: 160 - 161: 37.241 distance: 161 - 162: 24.866 distance: 161 - 163: 25.779 distance: 164 - 165: 24.496 distance: 165 - 166: 13.663 distance: 165 - 168: 36.147 distance: 166 - 167: 22.519 distance: 166 - 172: 15.879 distance: 168 - 169: 50.541 distance: 169 - 170: 5.384 distance: 169 - 171: 42.405