Starting phenix.real_space_refine (version: 1.21rc1) on Thu May 4 19:14:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/05_2023/6x68_22073.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/05_2023/6x68_22073.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/05_2023/6x68_22073.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/05_2023/6x68_22073.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/05_2023/6x68_22073.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x68_22073/05_2023/6x68_22073.pdb" } resolution = 3.66 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 ------------------------------------------------------------------------------- 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= 0.003 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 124 5.49 5 S 88 5.16 5 C 6063 2.51 5 N 1811 2.21 5 O 2152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 215": "OD1" <-> "OD2" Residue "C PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 423": "OD1" <-> "OD2" Residue "C TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 594": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 10246 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "D" Number of atoms: 3848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3848 Classifications: {'peptide': 478} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 452} Chain: "A" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1517 Classifications: {'DNA': 74} Link IDs: {'rna3p': 73} Chain: "B" Number of atoms: 1025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1025 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 2, ' ZN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3568 SG CYS C 559 43.876 58.830 53.085 1.00101.37 S ATOM 3593 SG CYS C 562 44.008 62.320 53.323 1.00101.18 S ATOM 3747 SG CYS C 582 44.083 60.658 50.274 1.00102.93 S ATOM 3684 SG CYS C 574 50.264 50.434 49.266 1.00157.97 S ATOM 3708 SG CYS C 577 50.090 49.390 52.178 1.00145.09 S ATOM 3815 SG CYS C 590 51.546 52.352 51.479 1.00159.91 S ATOM 3836 SG CYS C 593 52.626 49.806 51.000 1.00172.88 S ATOM 7416 SG CYS D 559 50.389 56.078 28.512 1.00 0.00 S ATOM 7441 SG CYS D 562 47.844 55.761 27.137 1.00319.64 S ATOM 7595 SG CYS D 582 47.770 55.742 30.601 1.00289.96 S ATOM 7532 SG CYS D 574 58.188 55.339 37.702 1.00325.15 S ATOM 7556 SG CYS D 577 60.281 55.493 35.331 1.00356.83 S ATOM 7663 SG CYS D 590 58.020 52.711 36.125 1.00303.36 S ATOM 7684 SG CYS D 593 59.976 53.297 37.650 1.00322.51 S Time building chain proxies: 5.78, per 1000 atoms: 0.56 Number of scatterers: 10246 At special positions: 0 Unit cell: (95.04, 90.72, 149.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 88 16.00 P 124 15.00 O 2152 8.00 N 1811 7.00 C 6063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.48 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 603 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 582 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 562 " pdb="ZN ZN C 603 " - pdb=" SG CYS C 559 " pdb="ZN ZN C 603 " - pdb=" ND1 HIS C 585 " pdb=" ZN C 604 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 577 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 593 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 590 " pdb="ZN ZN C 604 " - pdb=" SG CYS C 574 " pdb=" ZN D 602 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 562 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 582 " pdb="ZN ZN D 602 " - pdb=" SG CYS D 559 " pdb="ZN ZN D 602 " - pdb=" ND1 HIS D 585 " pdb=" ZN D 603 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 574 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 593 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 590 " pdb="ZN ZN D 603 " - pdb=" SG CYS D 577 " Number of angles added : 18 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1820 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 7 sheets defined 46.1% alpha, 11.5% beta 52 base pairs and 103 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'C' and resid 123 through 126 Processing helix chain 'C' and resid 130 through 159 removed outlier: 3.935A pdb=" N PHE C 138 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ASP C 141 " --> pdb=" O LEU C 137 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N GLU C 142 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE C 143 " --> pdb=" O PHE C 139 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA C 153 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 154 " --> pdb=" O TRP C 150 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 172 through 189 Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.838A pdb=" N PHE C 200 " --> pdb=" O THR C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 231 through 235 Processing helix chain 'C' and resid 241 through 243 No H-bonds generated for 'chain 'C' and resid 241 through 243' Processing helix chain 'C' and resid 244 through 258 removed outlier: 4.611A pdb=" N LEU C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN C 258 " --> pdb=" O GLN C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 333 Processing helix chain 'C' and resid 334 through 337 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 379 through 384 Processing helix chain 'C' and resid 433 through 443 Processing helix chain 'C' and resid 443 through 453 removed outlier: 4.831A pdb=" N ASP C 447 " --> pdb=" O LYS C 443 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LEU C 449 " --> pdb=" O GLY C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 491 removed outlier: 4.055A pdb=" N LEU C 469 " --> pdb=" O TRP C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 519 removed outlier: 3.680A pdb=" N SER C 512 " --> pdb=" O MET C 508 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N SER C 513 " --> pdb=" O SER C 509 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N PHE C 514 " --> pdb=" O LEU C 510 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LYS C 517 " --> pdb=" O SER C 513 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 519 " --> pdb=" O MET C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 535 Processing helix chain 'C' and resid 563 through 567 Processing helix chain 'D' and resid 123 through 126 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 140 through 159 removed outlier: 4.075A pdb=" N ALA D 153 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 169 Processing helix chain 'D' and resid 172 through 190 Processing helix chain 'D' and resid 195 through 200 Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 241 through 243 No H-bonds generated for 'chain 'D' and resid 241 through 243' Processing helix chain 'D' and resid 244 through 257 removed outlier: 3.744A pdb=" N GLN D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N CYS D 255 " --> pdb=" O PHE D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 334 through 337 Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.885A pdb=" N THR D 350 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 358 Processing helix chain 'D' and resid 379 through 384 Processing helix chain 'D' and resid 433 through 443 removed outlier: 3.948A pdb=" N GLN D 441 " --> pdb=" O MET D 437 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR D 442 " --> pdb=" O TYR D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 456 Processing helix chain 'D' and resid 464 through 491 removed outlier: 3.542A pdb=" N ALA D 468 " --> pdb=" O ARG D 464 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 470 " --> pdb=" O PRO D 466 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 479 " --> pdb=" O ASN D 475 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE D 482 " --> pdb=" O CYS D 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 519 removed outlier: 5.383A pdb=" N SER D 513 " --> pdb=" O SER D 509 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N PHE D 514 " --> pdb=" O LEU D 510 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 519 " --> pdb=" O MET D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 536 Processing helix chain 'D' and resid 590 through 594 Processing sheet with id=AA1, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AA2, first strand: chain 'C' and resid 306 through 311 removed outlier: 6.828A pdb=" N MET C 298 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLY C 309 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU C 296 " --> pdb=" O GLY C 309 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N LYS C 294 " --> pdb=" O PRO C 311 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU C 265 " --> pdb=" O THR C 344 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 572 through 574 removed outlier: 3.539A pdb=" N LYS C 579 " --> pdb=" O CYS C 574 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 120 through 121 Processing sheet with id=AA5, first strand: chain 'D' and resid 282 through 283 removed outlier: 6.457A pdb=" N ASP D 300 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N MET D 306 " --> pdb=" O ASP D 300 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 282 through 283 removed outlier: 5.029A pdb=" N ILE D 367 " --> pdb=" O SER D 419 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 572 through 573 332 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 129 hydrogen bonds 258 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 103 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 4.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2084 1.33 - 1.45: 3323 1.45 - 1.58: 4912 1.58 - 1.71: 247 1.71 - 1.83: 136 Bond restraints: 10702 Sorted by residual: bond pdb=" O3' DA A 33 " pdb=" P DT A 34 " ideal model delta sigma weight residual 1.607 1.516 0.091 1.50e-02 4.44e+03 3.72e+01 bond pdb=" N SER D 289 " pdb=" CA SER D 289 " ideal model delta sigma weight residual 1.458 1.392 0.066 1.19e-02 7.06e+03 3.10e+01 bond pdb=" N ASN C 384 " pdb=" CA ASN C 384 " ideal model delta sigma weight residual 1.454 1.392 0.061 1.23e-02 6.61e+03 2.47e+01 bond pdb=" CA ASN C 384 " pdb=" C ASN C 384 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.21e-02 6.83e+03 2.33e+01 bond pdb=" C4' DT A 34 " pdb=" C3' DT A 34 " ideal model delta sigma weight residual 1.523 1.617 -0.094 2.00e-02 2.50e+03 2.23e+01 ... (remaining 10697 not shown) Histogram of bond angle deviations from ideal: 90.81 - 100.23: 16 100.23 - 109.64: 2855 109.64 - 119.06: 6629 119.06 - 128.47: 5301 128.47 - 137.89: 169 Bond angle restraints: 14970 Sorted by residual: angle pdb=" CA ASN C 384 " pdb=" C ASN C 384 " pdb=" N SER C 385 " ideal model delta sigma weight residual 115.36 93.39 21.97 1.56e+00 4.11e-01 1.98e+02 angle pdb=" N VAL C 552 " pdb=" CA VAL C 552 " pdb=" C VAL C 552 " ideal model delta sigma weight residual 113.47 101.80 11.67 1.01e+00 9.80e-01 1.33e+02 angle pdb=" N ASN C 384 " pdb=" CA ASN C 384 " pdb=" C ASN C 384 " ideal model delta sigma weight residual 109.85 125.80 -15.95 1.58e+00 4.01e-01 1.02e+02 angle pdb=" CA ASN C 384 " pdb=" C ASN C 384 " pdb=" O ASN C 384 " ideal model delta sigma weight residual 121.46 132.88 -11.42 1.17e+00 7.31e-01 9.53e+01 angle pdb=" CA ARG D 315 " pdb=" C ARG D 315 " pdb=" N GLY D 316 " ideal model delta sigma weight residual 116.84 100.98 15.86 1.71e+00 3.42e-01 8.60e+01 ... (remaining 14965 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 5575 33.95 - 67.90: 529 67.90 - 101.85: 6 101.85 - 135.80: 0 135.80 - 169.75: 2 Dihedral angle restraints: 6112 sinusoidal: 3296 harmonic: 2816 Sorted by residual: dihedral pdb=" C PRO D 408 " pdb=" N PRO D 408 " pdb=" CA PRO D 408 " pdb=" CB PRO D 408 " ideal model delta harmonic sigma weight residual -120.70 -107.37 -13.33 0 2.50e+00 1.60e-01 2.84e+01 dihedral pdb=" C TYR D 527 " pdb=" N TYR D 527 " pdb=" CA TYR D 527 " pdb=" CB TYR D 527 " ideal model delta harmonic sigma weight residual -122.60 -110.50 -12.10 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" C PRO C 541 " pdb=" N PRO C 541 " pdb=" CA PRO C 541 " pdb=" CB PRO C 541 " ideal model delta harmonic sigma weight residual -120.70 -108.72 -11.98 0 2.50e+00 1.60e-01 2.29e+01 ... (remaining 6109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1311 0.098 - 0.196: 290 0.196 - 0.294: 44 0.294 - 0.393: 10 0.393 - 0.491: 3 Chirality restraints: 1658 Sorted by residual: chirality pdb=" CA ASN C 384 " pdb=" N ASN C 384 " pdb=" C ASN C 384 " pdb=" CB ASN C 384 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CA PRO D 551 " pdb=" N PRO D 551 " pdb=" C PRO D 551 " pdb=" CB PRO D 551 " both_signs ideal model delta sigma weight residual False 2.72 2.31 0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA PRO D 410 " pdb=" N PRO D 410 " pdb=" C PRO D 410 " pdb=" CB PRO D 410 " both_signs ideal model delta sigma weight residual False 2.72 2.32 0.40 2.00e-01 2.50e+01 3.92e+00 ... (remaining 1655 not shown) Planarity restraints: 1472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE D 594 " -0.034 2.00e-02 2.50e+03 6.58e-02 4.33e+01 pdb=" C PHE D 594 " 0.114 2.00e-02 2.50e+03 pdb=" O PHE D 594 " -0.041 2.00e-02 2.50e+03 pdb=" OXT PHE D 594 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 594 " -0.030 2.00e-02 2.50e+03 5.78e-02 3.34e+01 pdb=" C PHE C 594 " 0.100 2.00e-02 2.50e+03 pdb=" O PHE C 594 " -0.035 2.00e-02 2.50e+03 pdb=" OXT PHE C 594 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 507 " -0.061 2.00e-02 2.50e+03 3.40e-02 2.31e+01 pdb=" CG TYR D 507 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR D 507 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR D 507 " 0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR D 507 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR D 507 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR D 507 " -0.008 2.00e-02 2.50e+03 pdb=" OH TYR D 507 " -0.046 2.00e-02 2.50e+03 ... (remaining 1469 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 9 2.30 - 2.95: 4458 2.95 - 3.60: 13893 3.60 - 4.25: 25472 4.25 - 4.90: 37684 Nonbonded interactions: 81516 Sorted by model distance: nonbonded pdb=" OP1 DT A -3 " pdb="CA CA A 101 " model vdw 1.652 2.510 nonbonded pdb=" OD2 ASP D 346 " pdb="CA CA A 101 " model vdw 1.905 2.510 nonbonded pdb=" OD2 ASP C 218 " pdb="CA CA C 602 " model vdw 2.030 2.510 nonbonded pdb=" OD2 ASP C 346 " pdb="CA CA C 601 " model vdw 2.075 2.510 nonbonded pdb=" OP1 DT B -3 " pdb="CA CA C 601 " model vdw 2.105 2.510 ... (remaining 81511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'C' and (resid 117 through 594 or resid 601 or resid 603)) selection = (chain 'D' and (resid 117 through 594 or resid 601 or resid 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 2.540 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 35.280 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.012 0.094 10702 Z= 0.746 Angle : 1.744 21.974 14970 Z= 1.196 Chirality : 0.087 0.491 1658 Planarity : 0.005 0.066 1472 Dihedral : 20.684 169.750 4292 Min Nonbonded Distance : 1.652 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.52 % Favored : 97.16 % Rotamer Outliers : 0.57 % Cbeta Deviations : 1.10 % 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: -0.38 (0.26), residues: 952 helix: -1.14 (0.24), residues: 366 sheet: 1.50 (0.50), residues: 108 loop : 0.25 (0.28), residues: 478 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 354 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 357 average time/residue: 0.2706 time to fit residues: 127.4661 Evaluate side-chains 224 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1151 time to fit residues: 1.6578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.0570 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 357 ASN C 440 ASN C 441 GLN C 571 ASN D 253 HIS D 264 HIS D 347 ASN D 480 ASN D 531 ASN D 538 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 10702 Z= 0.259 Angle : 0.787 9.316 14970 Z= 0.440 Chirality : 0.044 0.161 1658 Planarity : 0.005 0.047 1472 Dihedral : 24.381 162.199 2306 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.73 % Favored : 97.16 % Rotamer Outliers : 3.85 % 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: 0.45 (0.28), residues: 952 helix: 0.50 (0.28), residues: 360 sheet: 1.37 (0.50), residues: 111 loop : 0.00 (0.29), residues: 481 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 246 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 267 average time/residue: 0.2382 time to fit residues: 87.2378 Evaluate side-chains 239 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 217 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1189 time to fit residues: 5.7167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 77 optimal weight: 0.0770 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 488 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 571 ASN D 347 ASN D 434 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 10702 Z= 0.232 Angle : 0.699 6.732 14970 Z= 0.390 Chirality : 0.041 0.150 1658 Planarity : 0.005 0.042 1472 Dihedral : 24.586 159.299 2306 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.47 % Favored : 96.43 % Rotamer Outliers : 2.26 % 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: 0.47 (0.28), residues: 952 helix: 0.95 (0.28), residues: 360 sheet: 1.11 (0.51), residues: 112 loop : -0.32 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 236 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 245 average time/residue: 0.2192 time to fit residues: 75.2499 Evaluate side-chains 214 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 1.002 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1347 time to fit residues: 3.8632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 0.1980 chunk 85 optimal weight: 5.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 463 ASN C 571 ASN D 254 GLN D 480 ASN D 488 ASN ** D 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 10702 Z= 0.271 Angle : 0.704 6.612 14970 Z= 0.391 Chirality : 0.042 0.143 1658 Planarity : 0.005 0.049 1472 Dihedral : 24.535 160.872 2306 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.57 % Favored : 96.32 % Rotamer Outliers : 2.94 % 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: 0.27 (0.28), residues: 952 helix: 1.03 (0.28), residues: 356 sheet: 0.79 (0.50), residues: 115 loop : -0.60 (0.29), residues: 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1904 Ramachandran restraints generated. 952 Oldfield, 0 Emsley, 952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 211 time to evaluate : 1.045 Fit side-chains revert: symmetry clash outliers start: 26 outliers final: 19 residues processed: 222 average time/residue: 0.2094 time to fit residues: 66.6517 Evaluate side-chains 213 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 1.058 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0976 time to fit residues: 4.8786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/iotbx/cli_parser.py", line 872, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.5073 > 50: distance: 7 - 11: 9.931 distance: 11 - 12: 10.257 distance: 12 - 13: 24.466 distance: 12 - 15: 24.276 distance: 13 - 14: 19.639 distance: 13 - 22: 25.384 distance: 15 - 16: 17.184 distance: 16 - 17: 12.453 distance: 17 - 18: 13.327 distance: 18 - 19: 3.966 distance: 19 - 20: 6.567 distance: 22 - 23: 10.282 distance: 23 - 24: 13.347 distance: 24 - 25: 12.263 distance: 24 - 29: 16.119 distance: 26 - 27: 10.243 distance: 26 - 28: 17.286 distance: 29 - 30: 22.050 distance: 30 - 31: 18.553 distance: 30 - 33: 14.950 distance: 31 - 32: 34.186 distance: 31 - 41: 23.621 distance: 33 - 34: 9.329 distance: 34 - 35: 11.879 distance: 34 - 36: 8.382 distance: 35 - 37: 11.829 distance: 36 - 38: 8.150 distance: 37 - 39: 10.355 distance: 38 - 39: 14.452 distance: 39 - 40: 5.055 distance: 41 - 42: 16.298 distance: 42 - 43: 14.513 distance: 42 - 45: 34.363 distance: 43 - 44: 20.149 distance: 43 - 47: 11.027 distance: 45 - 46: 25.263 distance: 46 - 224: 14.319 distance: 47 - 48: 13.804 distance: 48 - 49: 11.303 distance: 48 - 51: 44.308 distance: 49 - 50: 5.622 distance: 49 - 54: 11.553 distance: 51 - 52: 20.918 distance: 51 - 53: 34.369 distance: 54 - 55: 19.750 distance: 55 - 56: 15.082 distance: 55 - 58: 11.216 distance: 56 - 57: 17.093 distance: 56 - 66: 26.165 distance: 58 - 59: 15.733 distance: 59 - 60: 4.722 distance: 59 - 61: 11.191 distance: 60 - 62: 4.950 distance: 61 - 63: 4.029 distance: 62 - 64: 9.071 distance: 63 - 64: 11.703 distance: 64 - 65: 11.247 distance: 66 - 67: 16.730 distance: 67 - 68: 37.618 distance: 67 - 70: 28.604 distance: 68 - 69: 26.383 distance: 68 - 72: 41.863 distance: 70 - 71: 28.951 distance: 71 - 224: 24.243 distance: 72 - 73: 40.863 distance: 72 - 78: 34.527 distance: 73 - 74: 47.404 distance: 73 - 76: 43.920 distance: 74 - 75: 39.625 distance: 74 - 79: 12.072 distance: 76 - 77: 25.280 distance: 77 - 78: 18.371 distance: 79 - 80: 21.507 distance: 80 - 81: 17.144 distance: 80 - 83: 11.214 distance: 81 - 82: 23.315 distance: 81 - 85: 17.207 distance: 83 - 84: 19.344 distance: 85 - 86: 8.634 distance: 86 - 87: 20.428 distance: 86 - 89: 17.873 distance: 87 - 88: 17.968 distance: 87 - 94: 23.387 distance: 89 - 90: 11.476 distance: 90 - 91: 12.880 distance: 91 - 92: 7.548 distance: 92 - 93: 21.705