Starting phenix.real_space_refine on Tue Jun 17 10:21:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zbh_11155/06_2025/6zbh_11155.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zbh_11155/06_2025/6zbh_11155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zbh_11155/06_2025/6zbh_11155.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zbh_11155/06_2025/6zbh_11155.map" model { file = "/net/cci-nas-00/data/ceres_data/6zbh_11155/06_2025/6zbh_11155.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zbh_11155/06_2025/6zbh_11155.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.036 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 6191 2.51 5 N 1576 2.21 5 O 1841 1.98 5 H 9896 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19523 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 9553 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 14, 'TRANS': 547} Chain breaks: 4 Chain: "B" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1900 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "C" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 4669 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 7, 'TRANS': 276} Chain breaks: 1 Chain: "D" Number of atoms: 3401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3401 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 2, 'TRANS': 198} Chain breaks: 1 Time building chain proxies: 9.55, per 1000 atoms: 0.49 Number of scatterers: 19523 At special positions: 0 Unit cell: (107.3, 137.344, 139.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 O 1841 8.00 N 1576 7.00 C 6191 6.00 H 9896 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=2.08 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 845 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.70 Conformation dependent library (CDL) restraints added in 1.3 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2270 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 0 sheets defined 86.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'A' and resid 21 through 47 Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.596A pdb=" N HIS A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 174 removed outlier: 4.207A pdb=" N ASP A 164 " --> pdb=" O PRO A 160 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N LEU A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 4.279A pdb=" N TYR A 181 " --> pdb=" O HIS A 177 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 184 " --> pdb=" O LYS A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 211 removed outlier: 3.917A pdb=" N GLU A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.619A pdb=" N ASP A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 Processing helix chain 'A' and resid 249 through 281 removed outlier: 4.118A pdb=" N ASP A 255 " --> pdb=" O GLY A 251 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 321 removed outlier: 3.954A pdb=" N SER A 315 " --> pdb=" O HIS A 311 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.508A pdb=" N ILE A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN A 338 " --> pdb=" O LEU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 374 Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 386 through 397 Processing helix chain 'A' and resid 430 through 443 Processing helix chain 'A' and resid 460 through 465 removed outlier: 3.736A pdb=" N ILE A 463 " --> pdb=" O ASN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 495 removed outlier: 3.982A pdb=" N ARG A 470 " --> pdb=" O ASP A 466 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 486 " --> pdb=" O ASP A 482 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 523 removed outlier: 3.728A pdb=" N LEU A 499 " --> pdb=" O ASN A 495 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASP A 501 " --> pdb=" O LYS A 497 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 504 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 512 " --> pdb=" O ASP A 508 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 582 removed outlier: 3.504A pdb=" N PHE A 534 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER A 552 " --> pdb=" O ASN A 548 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N SER A 553 " --> pdb=" O ASN A 549 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N SER A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS A 563 " --> pdb=" O TYR A 559 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASP A 573 " --> pdb=" O SER A 569 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU A 576 " --> pdb=" O GLU A 572 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY A 579 " --> pdb=" O SER A 575 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ILE A 580 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 616 removed outlier: 3.610A pdb=" N ASN A 586 " --> pdb=" O GLU A 582 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS A 601 " --> pdb=" O ALA A 597 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU A 604 " --> pdb=" O LYS A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 666 removed outlier: 4.267A pdb=" N LEU A 637 " --> pdb=" O ASP A 633 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLN A 638 " --> pdb=" O ILE A 634 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 656 " --> pdb=" O ARG A 652 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU A 663 " --> pdb=" O LYS A 659 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS A 664 " --> pdb=" O ASN A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 712 removed outlier: 3.646A pdb=" N ILE A 685 " --> pdb=" O PRO A 681 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LYS A 689 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 696 " --> pdb=" O ASP A 692 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 698 " --> pdb=" O LEU A 694 " (cutoff:3.500A) Proline residue: A 699 - end of helix Processing helix chain 'B' and resid 795 through 822 Processing helix chain 'B' and resid 825 through 831 removed outlier: 3.761A pdb=" N VAL B 831 " --> pdb=" O LYS B 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 840 Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 851 through 856 Processing helix chain 'B' and resid 857 through 891 removed outlier: 3.686A pdb=" N MET B 868 " --> pdb=" O LEU B 864 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 871 " --> pdb=" O SER B 867 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE B 877 " --> pdb=" O GLN B 873 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B 880 " --> pdb=" O PHE B 876 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS B 882 " --> pdb=" O GLU B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 905 removed outlier: 3.952A pdb=" N LEU B 900 " --> pdb=" O HIS B 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 968 Processing helix chain 'C' and resid 970 through 972 No H-bonds generated for 'chain 'C' and resid 970 through 972' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 980 through 982 No H-bonds generated for 'chain 'C' and resid 980 through 982' Processing helix chain 'C' and resid 995 through 1010 removed outlier: 3.763A pdb=" N LYS C1001 " --> pdb=" O THR C 997 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN C1010 " --> pdb=" O ILE C1006 " (cutoff:3.500A) Processing helix chain 'C' and resid 1015 through 1025 removed outlier: 3.597A pdb=" N LYS C1019 " --> pdb=" O ASN C1015 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1031 Processing helix chain 'C' and resid 1033 through 1101 removed outlier: 3.532A pdb=" N GLU C1043 " --> pdb=" O ALA C1039 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C1056 " --> pdb=" O GLN C1052 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C1057 " --> pdb=" O LEU C1053 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C1069 " --> pdb=" O LEU C1065 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASN C1097 " --> pdb=" O GLU C1093 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASN C1100 " --> pdb=" O LEU C1096 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN C1101 " --> pdb=" O ASN C1097 " (cutoff:3.500A) Processing helix chain 'C' and resid 1106 through 1108 No H-bonds generated for 'chain 'C' and resid 1106 through 1108' Processing helix chain 'C' and resid 1109 through 1146 removed outlier: 3.695A pdb=" N PHE C1113 " --> pdb=" O PHE C1109 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C1119 " --> pdb=" O LYS C1115 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA C1122 " --> pdb=" O GLU C1118 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU C1135 " --> pdb=" O THR C1131 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS C1143 " --> pdb=" O LYS C1139 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TYR C1144 " --> pdb=" O GLY C1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 1156 through 1178 removed outlier: 4.040A pdb=" N TYR C1166 " --> pdb=" O THR C1162 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA C1167 " --> pdb=" O GLU C1163 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE C1172 " --> pdb=" O ASN C1168 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU C1175 " --> pdb=" O LYS C1171 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1213 removed outlier: 3.629A pdb=" N LEU C1182 " --> pdb=" O ILE C1178 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP C1184 " --> pdb=" O GLY C1180 " (cutoff:3.500A) Processing helix chain 'C' and resid 1220 through 1235 removed outlier: 3.521A pdb=" N TYR C1235 " --> pdb=" O ALA C1231 " (cutoff:3.500A) Processing helix chain 'C' and resid 1236 through 1239 removed outlier: 3.537A pdb=" N LEU C1239 " --> pdb=" O GLU C1236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1236 through 1239' Processing helix chain 'D' and resid 1342 through 1346 Processing helix chain 'D' and resid 1347 through 1392 removed outlier: 3.617A pdb=" N SER D1357 " --> pdb=" O GLY D1353 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG D1384 " --> pdb=" O ARG D1380 " (cutoff:3.500A) Processing helix chain 'D' and resid 1393 through 1399 removed outlier: 3.643A pdb=" N MET D1396 " --> pdb=" O SER D1393 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLN D1397 " --> pdb=" O ASP D1394 " (cutoff:3.500A) Processing helix chain 'D' and resid 1410 through 1415 removed outlier: 3.603A pdb=" N LEU D1415 " --> pdb=" O PHE D1412 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1473 removed outlier: 3.670A pdb=" N PHE D1440 " --> pdb=" O ASN D1436 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL D1465 " --> pdb=" O SER D1461 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU D1468 " --> pdb=" O LYS D1464 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU D1469 " --> pdb=" O VAL D1465 " (cutoff:3.500A) Processing helix chain 'D' and resid 1496 through 1555 removed outlier: 3.547A pdb=" N LEU D1500 " --> pdb=" O PHE D1496 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE D1519 " --> pdb=" O ASP D1515 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS D1538 " --> pdb=" O GLU D1534 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP D1544 " --> pdb=" O THR D1540 " (cutoff:3.500A) 719 hydrogen bonds defined for protein. 2112 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: 6.55 Time building geometry restraints manager: 6.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 9894 1.04 - 1.23: 264 1.23 - 1.43: 3665 1.43 - 1.62: 5816 1.62 - 1.82: 32 Bond restraints: 19671 Sorted by residual: bond pdb=" N ILE A 218 " pdb=" CA ILE A 218 " ideal model delta sigma weight residual 1.454 1.485 -0.030 7.70e-03 1.69e+04 1.56e+01 bond pdb=" N LYS A 674 " pdb=" CA LYS A 674 " ideal model delta sigma weight residual 1.458 1.485 -0.027 7.40e-03 1.83e+04 1.34e+01 bond pdb=" C ILE A 613 " pdb=" O ILE A 613 " ideal model delta sigma weight residual 1.237 1.193 0.044 1.23e-02 6.61e+03 1.29e+01 bond pdb=" N VAL C1105 " pdb=" CA VAL C1105 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" N VAL B 819 " pdb=" CA VAL B 819 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.23e-02 6.61e+03 1.09e+01 ... (remaining 19666 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 30436 1.59 - 3.18: 4940 3.18 - 4.77: 377 4.77 - 6.36: 75 6.36 - 7.95: 6 Bond angle restraints: 35834 Sorted by residual: angle pdb=" N LYS B 815 " pdb=" CA LYS B 815 " pdb=" C LYS B 815 " ideal model delta sigma weight residual 111.36 104.94 6.42 1.09e+00 8.42e-01 3.47e+01 angle pdb=" N TYR A 215 " pdb=" CA TYR A 215 " pdb=" C TYR A 215 " ideal model delta sigma weight residual 111.28 105.05 6.23 1.09e+00 8.42e-01 3.27e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" C ILE A 321 " ideal model delta sigma weight residual 113.00 105.72 7.28 1.30e+00 5.92e-01 3.14e+01 angle pdb=" CA SER C1026 " pdb=" C SER C1026 " pdb=" O SER C1026 " ideal model delta sigma weight residual 120.92 114.84 6.08 1.12e+00 7.97e-01 2.95e+01 angle pdb=" N ASN A 467 " pdb=" CA ASN A 467 " pdb=" C ASN A 467 " ideal model delta sigma weight residual 111.36 117.25 -5.89 1.09e+00 8.42e-01 2.92e+01 ... (remaining 35829 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 8385 17.83 - 35.66: 542 35.66 - 53.48: 123 53.48 - 71.31: 30 71.31 - 89.14: 13 Dihedral angle restraints: 9093 sinusoidal: 5058 harmonic: 4035 Sorted by residual: dihedral pdb=" CB CYS B 813 " pdb=" SG CYS B 813 " pdb=" SG CYS B 845 " pdb=" CB CYS B 845 " ideal model delta sinusoidal sigma weight residual 93.00 152.93 -59.93 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CA ASP A 466 " pdb=" C ASP A 466 " pdb=" N ASN A 467 " pdb=" CA ASN A 467 " ideal model delta harmonic sigma weight residual -180.00 -163.17 -16.83 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CB GLU A 367 " pdb=" CG GLU A 367 " pdb=" CD GLU A 367 " pdb=" OE1 GLU A 367 " ideal model delta sinusoidal sigma weight residual 0.00 89.00 -89.00 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 9090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 779 0.057 - 0.115: 514 0.115 - 0.172: 151 0.172 - 0.230: 29 0.230 - 0.287: 3 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA VAL C1105 " pdb=" N VAL C1105 " pdb=" C VAL C1105 " pdb=" CB VAL C1105 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ILE D1401 " pdb=" N ILE D1401 " pdb=" C ILE D1401 " pdb=" CB ILE D1401 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA VAL A 39 " pdb=" N VAL A 39 " pdb=" C VAL A 39 " pdb=" CB VAL A 39 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 1473 not shown) Planarity restraints: 2771 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C1099 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C LEU C1099 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU C1099 " -0.022 2.00e-02 2.50e+03 pdb=" N ASN C1100 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 217 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.32e+00 pdb=" C GLN A 217 " -0.050 2.00e-02 2.50e+03 pdb=" O GLN A 217 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 218 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 327 " -0.012 2.00e-02 2.50e+03 2.51e-02 6.32e+00 pdb=" C ASN A 327 " 0.043 2.00e-02 2.50e+03 pdb=" O ASN A 327 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU A 328 " -0.015 2.00e-02 2.50e+03 ... (remaining 2768 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.29: 2661 2.29 - 2.87: 46133 2.87 - 3.45: 48298 3.45 - 4.02: 62136 4.02 - 4.60: 98778 Nonbonded interactions: 258006 Sorted by model distance: nonbonded pdb=" O GLU A 582 " pdb="HD22 ASN A 586 " model vdw 1.717 2.450 nonbonded pdb=" HZ3 LYS C1064 " pdb=" O SER C1150 " model vdw 1.717 2.450 nonbonded pdb=" O THR D1505 " pdb="HD22 ASN D1509 " model vdw 1.722 2.450 nonbonded pdb=" O ASN A 260 " pdb=" HG1 THR A 263 " model vdw 1.732 2.450 nonbonded pdb=" O TYR A 150 " pdb=" HG1 THR A 153 " model vdw 1.736 2.450 ... (remaining 258001 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 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: 2.340 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: 0.360 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.200 Process input model: 42.790 Find NCS groups from input model: 0.120 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: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.010 0.054 9777 Z= 0.725 Angle : 1.215 35.748 13115 Z= 0.865 Chirality : 0.076 0.287 1476 Planarity : 0.006 0.043 1647 Dihedral : 13.653 89.139 3843 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % 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: 0.82 (0.24), residues: 1139 helix: 0.84 (0.16), residues: 900 sheet: None (None), residues: 0 loop : -0.25 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D1400 PHE 0.015 0.003 PHE C1238 TYR 0.026 0.003 TYR A 683 ARG 0.003 0.001 ARG A 546 Details of bonding type rmsd hydrogen bonds : bond 0.17231 ( 719) hydrogen bonds : angle 5.82594 ( 2112) SS BOND : bond 0.03461 ( 2) SS BOND : angle 18.17792 ( 4) covalent geometry : bond 0.01006 ( 9775) covalent geometry : angle 1.17283 (13111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLN cc_start: 0.9249 (tt0) cc_final: 0.9000 (tp40) REVERT: A 662 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7857 (tm-30) REVERT: C 972 ASP cc_start: 0.8440 (m-30) cc_final: 0.7282 (t0) REVERT: D 1377 LEU cc_start: 0.9148 (mp) cc_final: 0.8904 (mt) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.6194 time to fit residues: 179.3437 Evaluate side-chains 95 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 ASN A 365 HIS B 821 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.061979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.052671 restraints weight = 163970.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.054527 restraints weight = 64657.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.055663 restraints weight = 35764.726| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9777 Z= 0.142 Angle : 0.565 5.711 13115 Z= 0.313 Chirality : 0.034 0.138 1476 Planarity : 0.004 0.040 1647 Dihedral : 4.234 24.860 1231 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.91 % Allowed : 7.25 % Favored : 91.85 % 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: 1.78 (0.24), residues: 1139 helix: 1.57 (0.17), residues: 904 sheet: None (None), residues: 0 loop : -0.14 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 896 PHE 0.011 0.001 PHE C1014 TYR 0.016 0.001 TYR D1455 ARG 0.002 0.000 ARG D1384 Details of bonding type rmsd hydrogen bonds : bond 0.05843 ( 719) hydrogen bonds : angle 4.11317 ( 2112) SS BOND : bond 0.01092 ( 2) SS BOND : angle 2.42284 ( 4) covalent geometry : bond 0.00284 ( 9775) covalent geometry : angle 0.56341 (13111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 ASP cc_start: 0.8834 (t0) cc_final: 0.8414 (m-30) REVERT: A 662 GLN cc_start: 0.8224 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 840 ASN cc_start: 0.8775 (p0) cc_final: 0.8567 (p0) REVERT: B 846 ASP cc_start: 0.7464 (t0) cc_final: 0.6910 (t0) REVERT: C 1053 LEU cc_start: 0.9017 (tt) cc_final: 0.8577 (mt) REVERT: C 1078 ASP cc_start: 0.8717 (m-30) cc_final: 0.8368 (m-30) outliers start: 10 outliers final: 5 residues processed: 115 average time/residue: 0.5634 time to fit residues: 89.2047 Evaluate side-chains 89 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 637 LEU Chi-restraints excluded: chain A residue 680 GLU Chi-restraints excluded: chain C residue 1066 ASP Chi-restraints excluded: chain C residue 1081 GLN Chi-restraints excluded: chain D residue 1452 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.8984 > 50: distance: 71 - 83: 11.732 distance: 83 - 84: 21.822 distance: 83 - 95: 18.541 distance: 84 - 85: 16.902 distance: 84 - 87: 16.447 distance: 85 - 86: 30.764 distance: 85 - 104: 19.490 distance: 87 - 88: 15.465 distance: 87 - 97: 27.335 distance: 87 - 98: 4.515 distance: 88 - 89: 15.386 distance: 88 - 90: 14.288 distance: 89 - 91: 4.968 distance: 89 - 99: 6.265 distance: 90 - 92: 6.200 distance: 90 - 100: 6.302 distance: 91 - 93: 9.392 distance: 91 - 101: 7.736 distance: 92 - 93: 19.847 distance: 92 - 102: 8.574 distance: 93 - 94: 7.159 distance: 94 - 103: 8.371 distance: 104 - 105: 9.478 distance: 104 - 110: 34.046 distance: 105 - 106: 24.529 distance: 105 - 108: 23.913 distance: 105 - 111: 13.624 distance: 106 - 107: 6.727 distance: 106 - 118: 59.368 distance: 108 - 109: 15.687 distance: 108 - 113: 12.833 distance: 109 - 110: 3.520 distance: 110 - 116: 23.491 distance: 110 - 117: 43.819 distance: 118 - 119: 19.502 distance: 118 - 126: 33.916 distance: 119 - 120: 41.581 distance: 119 - 122: 41.032 distance: 119 - 127: 18.694 distance: 120 - 121: 27.843 distance: 120 - 137: 22.156 distance: 122 - 123: 33.018 distance: 122 - 128: 19.822 distance: 122 - 129: 17.442 distance: 123 - 124: 19.602 distance: 123 - 125: 18.609 distance: 123 - 130: 5.333 distance: 124 - 131: 18.357 distance: 124 - 132: 15.400 distance: 124 - 133: 29.772 distance: 125 - 134: 22.791 distance: 125 - 135: 23.639 distance: 125 - 136: 27.446 distance: 137 - 138: 31.473 distance: 137 - 143: 18.584 distance: 138 - 139: 14.099 distance: 138 - 144: 12.664 distance: 139 - 140: 14.266 distance: 139 - 151: 13.322 distance: 140 - 196: 25.332 distance: 141 - 142: 29.125 distance: 141 - 145: 19.310 distance: 141 - 146: 21.904 distance: 142 - 143: 9.330 distance: 142 - 147: 7.861 distance: 142 - 148: 13.398 distance: 143 - 149: 26.044 distance: 143 - 150: 26.835 distance: 151 - 152: 18.816 distance: 151 - 159: 25.033 distance: 152 - 153: 16.803 distance: 152 - 155: 16.116 distance: 152 - 160: 27.901 distance: 153 - 154: 17.777 distance: 153 - 170: 17.669 distance: 154 - 215: 57.283 distance: 155 - 156: 16.137 distance: 155 - 161: 23.640 distance: 155 - 162: 19.486 distance: 156 - 157: 25.394 distance: 156 - 158: 23.310 distance: 156 - 163: 29.320 distance: 157 - 164: 21.326 distance: 157 - 165: 14.509 distance: 157 - 166: 12.412 distance: 158 - 167: 35.816 distance: 158 - 168: 5.147 distance: 158 - 169: 6.218 distance: 170 - 171: 31.466 distance: 170 - 177: 19.983 distance: 171 - 172: 8.903 distance: 171 - 174: 14.860 distance: 171 - 178: 11.361 distance: 172 - 184: 30.512 distance: 173 - 232: 35.103 distance: 174 - 175: 44.321 distance: 174 - 176: 9.296 distance: 174 - 179: 6.187 distance: 175 - 180: 56.558 distance: 176 - 181: 25.852 distance: 176 - 182: 21.552 distance: 176 - 183: 20.266 distance: 184 - 185: 33.505 distance: 184 - 192: 34.313 distance: 185 - 186: 26.684 distance: 185 - 188: 23.278 distance: 185 - 193: 26.111 distance: 186 - 187: 20.273 distance: 186 - 196: 17.204 distance: 187 - 246: 19.230 distance: 188 - 189: 15.747 distance: 188 - 194: 41.577 distance: 188 - 195: 37.947 distance: 189 - 190: 36.064 distance: 189 - 191: 56.098 distance: 196 - 197: 17.986 distance: 196 - 204: 39.396 distance: 197 - 205: 21.937 distance: 198 - 199: 19.028 distance: 199 - 257: 22.376 distance: 200 - 201: 24.653 distance: 200 - 202: 24.707 distance: 200 - 206: 25.156 distance: 201 - 203: 23.608 distance: 201 - 207: 20.153 distance: 201 - 208: 5.099 distance: 202 - 209: 5.656 distance: 202 - 210: 16.382 distance: 202 - 211: 7.078 distance: 203 - 212: 4.461 distance: 203 - 213: 27.292 distance: 203 - 214: 19.922 distance: 215 - 216: 17.246 distance: 215 - 225: 26.056 distance: 216 - 217: 19.978 distance: 216 - 219: 21.429 distance: 216 - 226: 3.094 distance: 217 - 218: 7.835 distance: 217 - 232: 6.256 distance: 218 - 271: 19.057 distance: 219 - 220: 22.838 distance: 219 - 227: 29.681 distance: 219 - 228: 16.804 distance: 220 - 221: 13.903 distance: 220 - 222: 26.044 distance: 221 - 223: 12.234 distance: 222 - 224: 12.747 distance: 222 - 229: 13.203 distance: 223 - 224: 16.094 distance: 223 - 230: 8.332 distance: 224 - 231: 18.614 distance: 232 - 233: 9.554 distance: 232 - 240: 26.628 distance: 233 - 234: 13.432 distance: 233 - 236: 19.750 distance: 233 - 241: 24.290 distance: 234 - 235: 8.837 distance: 234 - 246: 10.336 distance: 235 - 281: 16.812 distance: 236 - 237: 18.558 distance: 236 - 242: 17.981 distance: 236 - 243: 17.833 distance: 237 - 238: 3.924 distance: 239 - 244: 11.702 distance: 239 - 245: 13.386