Starting phenix.real_space_refine on Thu Sep 26 19:01:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/09_2024/8sny_40642.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/09_2024/8sny_40642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/09_2024/8sny_40642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/09_2024/8sny_40642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/09_2024/8sny_40642.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sny_40642/09_2024/8sny_40642.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 P 8 5.49 5 S 75 5.16 5 C 8733 2.51 5 N 2333 2.21 5 O 2595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13744 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1388, 11317 Classifications: {'peptide': 1388} Link IDs: {'PTRANS': 47, 'TRANS': 1340} Chain breaks: 3 Chain: "B" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "C" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "D" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 496 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain breaks: 1 Chain: "E" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 885 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "T" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 163 Classifications: {'RNA': 8} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 5} Time building chain proxies: 7.96, per 1000 atoms: 0.58 Number of scatterers: 13744 At special positions: 0 Unit cell: (123.786, 108.974, 108.974, 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 75 16.00 P 8 15.00 O 2595 8.00 N 2333 7.00 C 8733 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 - 3.00 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: 3.41 Conformation dependent library (CDL) restraints added in 1.7 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 8 sheets defined 62.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 Processing helix chain 'A' and resid 44 through 53 removed outlier: 3.725A pdb=" N LEU A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.679A pdb=" N LEU A 64 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 98 through 132 removed outlier: 3.813A pdb=" N VAL A 122 " --> pdb=" O GLU A 118 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 201 through 228 Processing helix chain 'A' and resid 265 through 296 removed outlier: 3.782A pdb=" N LEU A 295 " --> pdb=" O CYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 325 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 334 through 348 Processing helix chain 'A' and resid 349 through 380 removed outlier: 3.535A pdb=" N CYS A 380 " --> pdb=" O LEU A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.966A pdb=" N ILE A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 3.766A pdb=" N LEU A 400 " --> pdb=" O ARG A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 422 Processing helix chain 'A' and resid 424 through 429 removed outlier: 3.935A pdb=" N PHE A 429 " --> pdb=" O LEU A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 448 Processing helix chain 'A' and resid 455 through 478 Processing helix chain 'A' and resid 490 through 499 Processing helix chain 'A' and resid 509 through 518 removed outlier: 4.449A pdb=" N GLY A 518 " --> pdb=" O ILE A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 545 through 553 removed outlier: 3.583A pdb=" N ILE A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N TRP A 550 " --> pdb=" O ASN A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 4.399A pdb=" N LEU A 571 " --> pdb=" O GLU A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 595 through 604 removed outlier: 3.776A pdb=" N ASN A 599 " --> pdb=" O CYS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 651 Processing helix chain 'A' and resid 652 through 659 Proline residue: A 656 - end of helix removed outlier: 3.777A pdb=" N LEU A 659 " --> pdb=" O PRO A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 703 through 708 removed outlier: 3.959A pdb=" N PHE A 708 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 724 removed outlier: 4.718A pdb=" N ILE A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N CYS A 716 " --> pdb=" O THR A 712 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL A 719 " --> pdb=" O ILE A 715 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 737 Processing helix chain 'A' and resid 781 through 801 Processing helix chain 'A' and resid 832 through 852 Processing helix chain 'A' and resid 882 through 887 Processing helix chain 'A' and resid 900 through 919 removed outlier: 3.743A pdb=" N GLU A 914 " --> pdb=" O SER A 910 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LEU A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 939 Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 949 through 966 Processing helix chain 'A' and resid 970 through 981 Processing helix chain 'A' and resid 982 through 986 removed outlier: 3.538A pdb=" N PHE A 985 " --> pdb=" O PRO A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 997 Processing helix chain 'A' and resid 1003 through 1020 removed outlier: 4.300A pdb=" N GLU A1007 " --> pdb=" O ASP A1003 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TYR A1018 " --> pdb=" O PHE A1014 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR A1019 " --> pdb=" O ILE A1015 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1052 through 1060 Processing helix chain 'A' and resid 1072 through 1087 removed outlier: 3.719A pdb=" N ILE A1076 " --> pdb=" O ILE A1072 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A1079 " --> pdb=" O GLU A1075 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA A1080 " --> pdb=" O ILE A1076 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR A1087 " --> pdb=" O GLU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1099 Processing helix chain 'A' and resid 1099 through 1110 Processing helix chain 'A' and resid 1118 through 1129 Processing helix chain 'A' and resid 1130 through 1143 removed outlier: 3.861A pdb=" N ALA A1134 " --> pdb=" O PRO A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1174 Processing helix chain 'A' and resid 1175 through 1180 Processing helix chain 'A' and resid 1198 through 1212 Processing helix chain 'A' and resid 1223 through 1228 Processing helix chain 'A' and resid 1282 through 1299 Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1320 through 1326 removed outlier: 4.256A pdb=" N LYS A1326 " --> pdb=" O GLU A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1356 through 1359 Processing helix chain 'A' and resid 1365 through 1375 Processing helix chain 'A' and resid 1384 through 1404 removed outlier: 3.514A pdb=" N CYS A1388 " --> pdb=" O VAL A1384 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1419 Processing helix chain 'A' and resid 1432 through 1443 Processing helix chain 'A' and resid 1452 through 1457 Processing helix chain 'A' and resid 1458 through 1461 removed outlier: 3.952A pdb=" N LEU A1461 " --> pdb=" O GLU A1458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1458 through 1461' Processing helix chain 'B' and resid 131 through 156 Processing helix chain 'B' and resid 157 through 165 removed outlier: 3.570A pdb=" N ALA B 162 " --> pdb=" O GLY B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 172 Processing helix chain 'B' and resid 174 through 187 Processing helix chain 'C' and resid 129 through 157 removed outlier: 4.798A pdb=" N GLU C 140 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 183 Processing helix chain 'D' and resid 129 through 158 Processing helix chain 'D' and resid 171 through 200 removed outlier: 3.570A pdb=" N MET D 195 " --> pdb=" O ARG D 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 removed outlier: 4.050A pdb=" N ARG E 137 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ILE E 138 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 183 Processing helix chain 'E' and resid 191 through 200 Processing helix chain 'E' and resid 203 through 210 Processing helix chain 'E' and resid 217 through 229 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.319A pdb=" N LYS A 80 " --> pdb=" O ILE A 261 " (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 629 through 631 removed outlier: 6.543A pdb=" N VAL A 614 " --> pdb=" O ILE A 743 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 691 through 694 Processing sheet with id=AA6, first strand: chain 'A' and resid 812 through 815 Processing sheet with id=AA7, first strand: chain 'A' and resid 873 through 875 removed outlier: 3.845A pdb=" N ILE A 873 " --> pdb=" O TYR A 880 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1361 through 1364 750 hydrogen bonds defined for protein. 2178 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: 4.49 Time building geometry restraints manager: 3.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2265 1.31 - 1.44: 3591 1.44 - 1.56: 8000 1.56 - 1.69: 15 1.69 - 1.81: 127 Bond restraints: 13998 Sorted by residual: bond pdb=" CA PHE A 704 " pdb=" C PHE A 704 " ideal model delta sigma weight residual 1.523 1.458 0.065 1.30e-02 5.92e+03 2.50e+01 bond pdb=" CA MET A 631 " pdb=" C MET A 631 " ideal model delta sigma weight residual 1.524 1.462 0.062 1.24e-02 6.50e+03 2.50e+01 bond pdb=" CA LYS A1145 " pdb=" C LYS A1145 " ideal model delta sigma weight residual 1.524 1.471 0.052 1.26e-02 6.30e+03 1.73e+01 bond pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 1.522 1.463 0.058 1.40e-02 5.10e+03 1.73e+01 bond pdb=" CA GLN A 913 " pdb=" C GLN A 913 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.29e-02 6.01e+03 1.66e+01 ... (remaining 13993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 18717 2.43 - 4.85: 197 4.85 - 7.28: 22 7.28 - 9.71: 7 9.71 - 12.14: 3 Bond angle restraints: 18946 Sorted by residual: angle pdb=" N LEU A 667 " pdb=" CA LEU A 667 " pdb=" C LEU A 667 " ideal model delta sigma weight residual 111.02 98.88 12.14 1.22e+00 6.72e-01 9.90e+01 angle pdb=" N ALA A 675 " pdb=" CA ALA A 675 " pdb=" C ALA A 675 " ideal model delta sigma weight residual 111.07 102.61 8.46 1.07e+00 8.73e-01 6.25e+01 angle pdb=" N LEU A 673 " pdb=" CA LEU A 673 " pdb=" C LEU A 673 " ideal model delta sigma weight residual 112.90 103.68 9.22 1.31e+00 5.83e-01 4.95e+01 angle pdb=" N LYS A1025 " pdb=" CA LYS A1025 " pdb=" C LYS A1025 " ideal model delta sigma weight residual 114.04 105.99 8.05 1.24e+00 6.50e-01 4.21e+01 angle pdb=" C PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta sigma weight residual 110.79 100.65 10.14 1.66e+00 3.63e-01 3.73e+01 ... (remaining 18941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 7570 17.83 - 35.66: 811 35.66 - 53.49: 153 53.49 - 71.32: 36 71.32 - 89.15: 14 Dihedral angle restraints: 8584 sinusoidal: 3627 harmonic: 4957 Sorted by residual: dihedral pdb=" C PHE A 704 " pdb=" N PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta harmonic sigma weight residual -122.60 -108.68 -13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N PHE A 704 " pdb=" C PHE A 704 " pdb=" CA PHE A 704 " pdb=" CB PHE A 704 " ideal model delta harmonic sigma weight residual 122.80 112.96 9.84 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" CA GLN A 874 " pdb=" C GLN A 874 " pdb=" N HIS A 875 " pdb=" CA HIS A 875 " ideal model delta harmonic sigma weight residual 180.00 161.75 18.25 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 8581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1847 0.055 - 0.110: 310 0.110 - 0.166: 35 0.166 - 0.221: 7 0.221 - 0.276: 2 Chirality restraints: 2201 Sorted by residual: chirality pdb=" CG LEU A 671 " pdb=" CB LEU A 671 " pdb=" CD1 LEU A 671 " pdb=" CD2 LEU A 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.31 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" CA LEU A 422 " pdb=" N LEU A 422 " pdb=" C LEU A 422 " pdb=" CB LEU A 422 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB THR A 93 " pdb=" CA THR A 93 " pdb=" OG1 THR A 93 " pdb=" CG2 THR A 93 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.54e-01 ... (remaining 2198 not shown) Planarity restraints: 2361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 707 " 0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C ALA A 707 " -0.038 2.00e-02 2.50e+03 pdb=" O ALA A 707 " 0.014 2.00e-02 2.50e+03 pdb=" N PHE A 708 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 53 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 54 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 83 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO A 84 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 84 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 84 " -0.027 5.00e-02 4.00e+02 ... (remaining 2358 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 116 2.53 - 3.12: 10875 3.12 - 3.71: 22625 3.71 - 4.31: 31221 4.31 - 4.90: 52711 Nonbonded interactions: 117548 Sorted by model distance: nonbonded pdb=" O ASN A 991 " pdb=" ND2 ASN A 991 " model vdw 1.932 3.120 nonbonded pdb=" O CYS A 251 " pdb=" OG1 THR A 264 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP D 136 " pdb=" NH1 ARG E 134 " model vdw 2.242 3.120 nonbonded pdb=" NH2 ARG A 588 " pdb=" O LEU A1151 " model vdw 2.256 3.120 nonbonded pdb=" O VAL A1399 " pdb=" OG1 THR A1403 " model vdw 2.271 3.040 ... (remaining 117543 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 Found NCS groups: ncs_group { reference = (chain 'B' and resid 130 through 184) selection = (chain 'C' and resid 130 through 184) } 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=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 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: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 31.770 Find NCS groups from input model: 0.150 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.004 0.065 13998 Z= 0.231 Angle : 0.625 12.136 18946 Z= 0.350 Chirality : 0.042 0.276 2201 Planarity : 0.004 0.049 2361 Dihedral : 15.353 89.155 5366 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.33 % Allowed : 0.85 % Favored : 98.83 % Cbeta Deviations : 0.06 % 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: 0.92 (0.21), residues: 1662 helix: 1.75 (0.17), residues: 955 sheet: -1.69 (0.55), residues: 72 loop : -0.86 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 480 HIS 0.019 0.001 HIS C 150 PHE 0.024 0.001 PHE A 704 TYR 0.021 0.001 TYR A1356 ARG 0.009 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 309 time to evaluate : 1.505 Fit side-chains REVERT: A 669 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7588 (pttp) REVERT: A 824 MET cc_start: 0.6091 (tmm) cc_final: 0.5831 (tmm) REVERT: A 1023 ASP cc_start: 0.6407 (m-30) cc_final: 0.6169 (t0) REVERT: B 152 LEU cc_start: 0.9017 (tp) cc_final: 0.8600 (tt) REVERT: C 140 GLU cc_start: 0.7632 (mp0) cc_final: 0.6963 (mp0) REVERT: C 177 MET cc_start: 0.8371 (tpp) cc_final: 0.8031 (tpp) REVERT: D 177 MET cc_start: 0.7450 (ppp) cc_final: 0.6904 (ppp) REVERT: D 178 ILE cc_start: 0.7151 (mm) cc_final: 0.6830 (mm) REVERT: E 145 ILE cc_start: 0.7918 (mt) cc_final: 0.7545 (mt) outliers start: 5 outliers final: 2 residues processed: 313 average time/residue: 0.2455 time to fit residues: 114.7911 Evaluate side-chains 241 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 238 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LYS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 674 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1149 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13998 Z= 0.295 Angle : 0.577 8.067 18946 Z= 0.300 Chirality : 0.043 0.170 2201 Planarity : 0.004 0.045 2361 Dihedral : 7.740 73.527 1966 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.76 % Allowed : 11.18 % Favored : 87.06 % 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: 0.80 (0.21), residues: 1662 helix: 1.58 (0.17), residues: 971 sheet: -1.64 (0.59), residues: 61 loop : -0.88 (0.26), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.017 0.001 HIS C 150 PHE 0.023 0.002 PHE A 629 TYR 0.020 0.002 TYR A1356 ARG 0.005 0.001 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 251 time to evaluate : 1.594 Fit side-chains REVERT: A 565 TYR cc_start: 0.8629 (t80) cc_final: 0.8262 (t80) REVERT: A 669 LYS cc_start: 0.7842 (mtmt) cc_final: 0.7477 (pttm) REVERT: A 1308 PHE cc_start: 0.7659 (t80) cc_final: 0.7443 (t80) REVERT: B 152 LEU cc_start: 0.9119 (tp) cc_final: 0.8720 (tt) REVERT: C 140 GLU cc_start: 0.7607 (mp0) cc_final: 0.7039 (mp0) REVERT: D 131 ILE cc_start: 0.6190 (mp) cc_final: 0.5903 (mp) REVERT: D 177 MET cc_start: 0.7582 (ppp) cc_final: 0.7228 (ppp) REVERT: E 195 MET cc_start: 0.7545 (mtp) cc_final: 0.7210 (mtt) outliers start: 27 outliers final: 12 residues processed: 263 average time/residue: 0.2402 time to fit residues: 95.0163 Evaluate side-chains 238 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 226 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 175 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 150 optimal weight: 0.6980 chunk 162 optimal weight: 20.0000 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 120 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13998 Z= 0.276 Angle : 0.550 7.972 18946 Z= 0.288 Chirality : 0.042 0.141 2201 Planarity : 0.004 0.047 2361 Dihedral : 7.674 73.428 1960 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.15 % Allowed : 15.15 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.21), residues: 1662 helix: 1.60 (0.16), residues: 959 sheet: -1.86 (0.55), residues: 69 loop : -0.85 (0.26), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.030 0.002 PHE A 87 TYR 0.014 0.001 TYR A 221 ARG 0.006 0.000 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 1.593 Fit side-chains REVERT: A 565 TYR cc_start: 0.8651 (t80) cc_final: 0.8240 (t80) REVERT: A 669 LYS cc_start: 0.7872 (mtmt) cc_final: 0.7461 (pttm) REVERT: A 1135 GLU cc_start: 0.8068 (tt0) cc_final: 0.7819 (tt0) REVERT: A 1372 LEU cc_start: 0.8235 (mm) cc_final: 0.8021 (mp) REVERT: B 152 LEU cc_start: 0.9133 (tp) cc_final: 0.8757 (tt) REVERT: C 140 GLU cc_start: 0.7683 (mp0) cc_final: 0.7166 (mp0) REVERT: D 131 ILE cc_start: 0.6244 (mp) cc_final: 0.5898 (mp) outliers start: 33 outliers final: 24 residues processed: 267 average time/residue: 0.2411 time to fit residues: 97.2415 Evaluate side-chains 249 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 225 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 840 SER Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 831 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13998 Z= 0.198 Angle : 0.514 7.357 18946 Z= 0.270 Chirality : 0.040 0.151 2201 Planarity : 0.004 0.050 2361 Dihedral : 7.600 73.354 1960 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.34 % Allowed : 17.36 % Favored : 80.30 % 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: 0.93 (0.21), residues: 1662 helix: 1.72 (0.16), residues: 952 sheet: -1.82 (0.54), residues: 69 loop : -0.77 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.020 0.001 PHE A 87 TYR 0.014 0.001 TYR A 221 ARG 0.005 0.000 ARG C 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 252 time to evaluate : 1.640 Fit side-chains revert: symmetry clash REVERT: A 483 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7685 (pp) REVERT: A 565 TYR cc_start: 0.8705 (t80) cc_final: 0.8249 (t80) REVERT: A 669 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7495 (pttm) REVERT: A 1135 GLU cc_start: 0.8071 (tt0) cc_final: 0.7806 (tt0) REVERT: B 152 LEU cc_start: 0.9109 (tp) cc_final: 0.8728 (tt) REVERT: C 140 GLU cc_start: 0.7549 (mp0) cc_final: 0.7224 (mp0) REVERT: D 131 ILE cc_start: 0.6225 (mp) cc_final: 0.5875 (mp) outliers start: 36 outliers final: 30 residues processed: 271 average time/residue: 0.2366 time to fit residues: 97.1240 Evaluate side-chains 259 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 228 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 763 VAL Chi-restraints excluded: chain A residue 815 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 2 optimal weight: 7.9990 chunk 118 optimal weight: 0.0770 chunk 65 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 143 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 GLN A 547 ASN ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13998 Z= 0.198 Angle : 0.520 8.711 18946 Z= 0.270 Chirality : 0.040 0.165 2201 Planarity : 0.004 0.051 2361 Dihedral : 7.557 73.345 1960 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.12 % Allowed : 18.21 % Favored : 78.67 % 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: 0.97 (0.21), residues: 1662 helix: 1.73 (0.16), residues: 954 sheet: -1.80 (0.54), residues: 69 loop : -0.73 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.024 0.001 PHE A 87 TYR 0.014 0.001 TYR A 221 ARG 0.006 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 252 time to evaluate : 1.801 Fit side-chains revert: symmetry clash REVERT: A 34 TYR cc_start: 0.8105 (t80) cc_final: 0.7891 (t80) REVERT: A 92 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8048 (mmp) REVERT: A 131 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8436 (mp) REVERT: A 483 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.7700 (pp) REVERT: A 565 TYR cc_start: 0.8776 (t80) cc_final: 0.8253 (t80) REVERT: A 1135 GLU cc_start: 0.8064 (tt0) cc_final: 0.7788 (tt0) REVERT: B 152 LEU cc_start: 0.9113 (tp) cc_final: 0.8729 (tt) REVERT: C 140 GLU cc_start: 0.7570 (mp0) cc_final: 0.7359 (mp0) REVERT: D 131 ILE cc_start: 0.6300 (mp) cc_final: 0.5909 (mp) REVERT: E 177 MET cc_start: 0.7602 (mtm) cc_final: 0.7351 (mtm) outliers start: 48 outliers final: 32 residues processed: 279 average time/residue: 0.2486 time to fit residues: 107.3713 Evaluate side-chains 271 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 616 LEU Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 948 ASN Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1248 VAL Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 159 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13998 Z= 0.171 Angle : 0.514 8.398 18946 Z= 0.266 Chirality : 0.040 0.176 2201 Planarity : 0.003 0.053 2361 Dihedral : 7.484 73.339 1960 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.99 % Allowed : 19.77 % Favored : 77.24 % 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: 1.03 (0.21), residues: 1662 helix: 1.79 (0.16), residues: 955 sheet: -1.77 (0.52), residues: 69 loop : -0.71 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 932 HIS 0.015 0.001 HIS C 150 PHE 0.023 0.001 PHE A 629 TYR 0.014 0.001 TYR A 221 ARG 0.006 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 251 time to evaluate : 1.663 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7934 (mmp) REVERT: A 131 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8444 (mp) REVERT: A 321 LEU cc_start: 0.9310 (mt) cc_final: 0.9017 (mt) REVERT: A 340 MET cc_start: 0.8535 (tpt) cc_final: 0.8161 (tpt) REVERT: A 483 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.7680 (pp) REVERT: A 565 TYR cc_start: 0.8760 (t80) cc_final: 0.8418 (t80) REVERT: A 979 MET cc_start: 0.8717 (mmm) cc_final: 0.8474 (mmp) REVERT: A 1135 GLU cc_start: 0.8046 (tt0) cc_final: 0.7786 (tt0) REVERT: B 134 ARG cc_start: 0.7460 (ptm160) cc_final: 0.6670 (mtp-110) REVERT: B 152 LEU cc_start: 0.9084 (tp) cc_final: 0.8706 (tt) REVERT: D 131 ILE cc_start: 0.6265 (mp) cc_final: 0.5853 (mp) REVERT: E 220 SER cc_start: 0.8857 (OUTLIER) cc_final: 0.8623 (m) outliers start: 46 outliers final: 29 residues processed: 277 average time/residue: 0.2319 time to fit residues: 97.8221 Evaluate side-chains 267 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 234 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 895 ASN Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 116 optimal weight: 30.0000 chunk 134 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 73 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 813 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 ASN ** A 991 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13998 Z= 0.181 Angle : 0.521 7.757 18946 Z= 0.270 Chirality : 0.040 0.188 2201 Planarity : 0.003 0.053 2361 Dihedral : 7.469 73.330 1960 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.73 % Allowed : 20.74 % Favored : 76.53 % 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: 1.02 (0.21), residues: 1662 helix: 1.77 (0.16), residues: 952 sheet: -1.70 (0.53), residues: 69 loop : -0.71 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 932 HIS 0.016 0.001 HIS C 150 PHE 0.022 0.001 PHE A 629 TYR 0.014 0.001 TYR A 34 ARG 0.007 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 245 time to evaluate : 1.717 Fit side-chains revert: symmetry clash REVERT: A 92 MET cc_start: 0.8199 (OUTLIER) cc_final: 0.7956 (mmp) REVERT: A 131 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8429 (mp) REVERT: A 321 LEU cc_start: 0.9310 (mt) cc_final: 0.9013 (mt) REVERT: A 340 MET cc_start: 0.8489 (tpt) cc_final: 0.8062 (tpp) REVERT: A 483 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7706 (pp) REVERT: A 565 TYR cc_start: 0.8769 (t80) cc_final: 0.8225 (t80) REVERT: A 979 MET cc_start: 0.8707 (mmm) cc_final: 0.8480 (mmp) REVERT: A 1135 GLU cc_start: 0.8049 (tt0) cc_final: 0.7789 (tt0) REVERT: B 134 ARG cc_start: 0.7505 (ptm160) cc_final: 0.6536 (mtp-110) REVERT: B 152 LEU cc_start: 0.9088 (tp) cc_final: 0.8701 (tt) REVERT: D 131 ILE cc_start: 0.6298 (mp) cc_final: 0.5873 (mp) REVERT: E 136 ASP cc_start: 0.7356 (OUTLIER) cc_final: 0.6943 (t0) REVERT: E 220 SER cc_start: 0.8798 (m) cc_final: 0.8440 (m) outliers start: 42 outliers final: 32 residues processed: 269 average time/residue: 0.2549 time to fit residues: 104.8017 Evaluate side-chains 272 residues out of total 1538 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 92 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 393 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 487 ILE Chi-restraints excluded: chain A residue 583 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 617 THR Chi-restraints excluded: chain A residue 674 LYS Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 745 THR Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 836 LEU Chi-restraints excluded: chain A residue 851 ILE Chi-restraints excluded: chain A residue 921 SER Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 972 ASP Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1242 ILE Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1413 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain E residue 135 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 138 ILE Chi-restraints excluded: chain E residue 154 VAL Chi-restraints excluded: chain E residue 156 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 175 GLU Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 239 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-dev-5461/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-dev-5461/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: 54.2534 > 50: distance: 50 - 68: 5.453 distance: 54 - 75: 11.188 distance: 60 - 83: 9.268 distance: 64 - 68: 3.277 distance: 69 - 70: 8.302 distance: 69 - 72: 7.674 distance: 70 - 71: 5.993 distance: 70 - 75: 4.454 distance: 72 - 73: 5.000 distance: 75 - 76: 7.371 distance: 76 - 77: 6.017 distance: 76 - 79: 6.720 distance: 77 - 78: 10.575 distance: 77 - 83: 8.488 distance: 79 - 80: 5.337 distance: 80 - 81: 6.553 distance: 80 - 82: 3.026 distance: 83 - 84: 3.106 distance: 84 - 85: 6.825 distance: 84 - 87: 6.944 distance: 85 - 86: 20.345 distance: 85 - 89: 22.271 distance: 87 - 88: 4.292 distance: 89 - 90: 16.421 distance: 90 - 91: 17.310 distance: 90 - 93: 20.760 distance: 91 - 92: 16.139 distance: 91 - 96: 30.379 distance: 93 - 94: 12.872 distance: 93 - 95: 7.756 distance: 96 - 97: 40.268 distance: 97 - 98: 19.637 distance: 97 - 100: 27.956 distance: 98 - 99: 16.363 distance: 98 - 101: 11.052 distance: 101 - 107: 14.046 distance: 102 - 103: 4.589 distance: 102 - 105: 7.454 distance: 103 - 104: 6.434 distance: 106 - 107: 8.734 distance: 108 - 109: 5.073 distance: 109 - 110: 9.280 distance: 110 - 111: 20.960 distance: 110 - 116: 11.533 distance: 111 - 144: 20.645 distance: 112 - 113: 3.488 distance: 113 - 115: 3.794 distance: 116 - 117: 3.823 distance: 117 - 118: 13.489 distance: 117 - 120: 14.272 distance: 118 - 119: 9.486 distance: 118 - 125: 8.056 distance: 119 - 150: 16.005 distance: 120 - 121: 8.445 distance: 121 - 122: 10.880 distance: 122 - 123: 10.526 distance: 125 - 126: 15.291 distance: 126 - 127: 16.406 distance: 126 - 129: 16.859 distance: 127 - 128: 4.986 distance: 127 - 133: 6.244 distance: 128 - 157: 13.989 distance: 129 - 130: 6.268 distance: 129 - 131: 14.184 distance: 130 - 132: 4.514 distance: 133 - 134: 11.043 distance: 134 - 135: 4.307 distance: 134 - 137: 7.946 distance: 135 - 136: 6.706 distance: 136 - 163: 8.133 distance: 138 - 139: 5.566 distance: 138 - 140: 5.845 distance: 139 - 141: 4.625 distance: 140 - 142: 3.917 distance: 141 - 143: 3.401