Starting phenix.real_space_refine on Mon Dec 11 15:41:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/12_2023/6r1u_4705_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/12_2023/6r1u_4705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/12_2023/6r1u_4705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/12_2023/6r1u_4705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/12_2023/6r1u_4705_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r1u_4705/12_2023/6r1u_4705_updated.pdb" } resolution = 4.36 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 296 5.49 5 S 54 5.16 5 C 10684 2.51 5 N 3372 2.21 5 O 3985 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 129": "NH1" <-> "NH2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "D ARG 26": "NH1" <-> "NH2" Residue "D ARG 27": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "K GLU 54": "OE1" <-> "OE2" Residue "K ARG 72": "NH1" <-> "NH2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K GLU 146": "OE1" <-> "OE2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K ARG 151": "NH1" <-> "NH2" Residue "K GLU 156": "OE1" <-> "OE2" Residue "K GLU 189": "OE1" <-> "OE2" Residue "K GLU 195": "OE1" <-> "OE2" Residue "K GLU 290": "OE1" <-> "OE2" Residue "K GLU 296": "OE1" <-> "OE2" Residue "K GLU 324": "OE1" <-> "OE2" Residue "K ARG 338": "NH1" <-> "NH2" Residue "K GLU 348": "OE1" <-> "OE2" Residue "K GLU 452": "OE1" <-> "OE2" Residue "K ARG 464": "NH1" <-> "NH2" Residue "K GLU 470": "OE1" <-> "OE2" Residue "K GLU 496": "OE1" <-> "OE2" Residue "K ARG 498": "NH1" <-> "NH2" Residue "K GLU 511": "OE1" <-> "OE2" Residue "K GLU 515": "OE1" <-> "OE2" Residue "K GLU 523": "OE1" <-> "OE2" Residue "K GLU 530": "OE1" <-> "OE2" Residue "K GLU 532": "OE1" <-> "OE2" Residue "K GLU 563": "OE1" <-> "OE2" Residue "K GLU 584": "OE1" <-> "OE2" Residue "K GLU 588": "OE1" <-> "OE2" Residue "K GLU 645": "OE1" <-> "OE2" Residue "K GLU 660": "OE1" <-> "OE2" Residue "K GLU 716": "OE1" <-> "OE2" Residue "K GLU 743": "OE1" <-> "OE2" Residue "K GLU 795": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 18394 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 689 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "E" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 820 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 870 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 775 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 5837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5837 Classifications: {'peptide': 737} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 36, 'TRANS': 698} Chain breaks: 2 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 105 Classifications: {'peptide': 12} Link IDs: {'PTRANS': 1, 'TRANS': 10} Chain: "M" Number of atoms: 193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 193 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "K" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {' ZN': 3, 'FAD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12239 SG CYS K 53 75.441 111.267 70.128 1.00 48.02 S ATOM 12272 SG CYS K 58 73.966 113.629 73.201 1.00 47.27 S ATOM 12317 SG CYS K 65 85.145 104.914 75.500 1.00 37.13 S ATOM 12376 SG CYS K 73 88.895 105.346 75.202 1.00 40.55 S ATOM 12534 SG CYS K 92 86.794 104.861 71.584 1.00 37.37 S ATOM 12557 SG CYS K 95 87.344 102.062 74.063 1.00 36.80 S ATOM 12964 SG CYS K 142 77.571 111.293 100.726 1.00 35.45 S ATOM 13002 SG CYS K 147 77.414 114.859 99.519 1.00 37.39 S ATOM 13195 SG CYS K 169 80.000 112.370 98.082 1.00 34.97 S ATOM 13246 SG CYS K 185 80.326 113.849 101.839 1.00 38.56 S Time building chain proxies: 10.00, per 1000 atoms: 0.54 Number of scatterers: 18394 At special positions: 0 Unit cell: (134.62, 132.5, 137.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 54 16.00 P 296 15.00 O 3985 8.00 N 3372 7.00 C 10684 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 9765 O5' DC J -46 .*. O " rejected from bonding due to valence issues. Atom "ATOM 9765 O5' DC J -46 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.39 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 902 " pdb="ZN ZN K 902 " - pdb=" NE2 HIS K 90 " pdb="ZN ZN K 902 " - pdb=" SG CYS K 58 " pdb="ZN ZN K 902 " - pdb=" ND1 HIS K 84 " pdb="ZN ZN K 902 " - pdb=" SG CYS K 53 " pdb=" ZN K 903 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 95 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 65 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 73 " pdb="ZN ZN K 903 " - pdb=" SG CYS K 92 " pdb=" ZN K 904 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 147 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 142 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 185 " pdb="ZN ZN K 904 " - pdb=" SG CYS K 169 " Number of angles added : 13 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 67 helices and 7 sheets defined 48.4% alpha, 4.6% beta 142 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 10.62 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 78 removed outlier: 4.087A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 31 through 40 Processing helix chain 'B' and resid 50 through 75 removed outlier: 3.677A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 73 removed outlier: 4.332A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 78 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 86 through 114 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 74 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 47 through 72 Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'G' and resid 91 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 102 through 119 removed outlier: 3.603A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 93 through 100 Processing helix chain 'K' and resid 107 through 116 Processing helix chain 'K' and resid 127 through 134 Processing helix chain 'K' and resid 161 through 166 Processing helix chain 'K' and resid 184 through 186 No H-bonds generated for 'chain 'K' and resid 184 through 186' Processing helix chain 'K' and resid 192 through 197 removed outlier: 3.673A pdb=" N VAL K 196 " --> pdb=" O ARG K 192 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER K 197 " --> pdb=" O VAL K 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 192 through 197' Processing helix chain 'K' and resid 199 through 204 removed outlier: 3.984A pdb=" N SER K 203 " --> pdb=" O HIS K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 219 No H-bonds generated for 'chain 'K' and resid 217 through 219' Processing helix chain 'K' and resid 225 through 227 No H-bonds generated for 'chain 'K' and resid 225 through 227' Processing helix chain 'K' and resid 291 through 296 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 305 through 320 Processing helix chain 'K' and resid 328 through 334 Proline residue: K 333 - end of helix Processing helix chain 'K' and resid 340 through 359 removed outlier: 3.628A pdb=" N VAL K 349 " --> pdb=" O VAL K 346 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU K 350 " --> pdb=" O GLN K 347 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS K 359 " --> pdb=" O MET K 356 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 380 No H-bonds generated for 'chain 'K' and resid 378 through 380' Processing helix chain 'K' and resid 392 through 404 Processing helix chain 'K' and resid 446 through 454 Processing helix chain 'K' and resid 477 through 500 removed outlier: 3.963A pdb=" N LYS K 499 " --> pdb=" O SER K 495 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASP K 500 " --> pdb=" O GLU K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 503 through 505 No H-bonds generated for 'chain 'K' and resid 503 through 505' Processing helix chain 'K' and resid 509 through 523 Processing helix chain 'K' and resid 530 through 547 Processing helix chain 'K' and resid 561 through 564 Processing helix chain 'K' and resid 579 through 587 removed outlier: 3.615A pdb=" N GLU K 584 " --> pdb=" O VAL K 581 " (cutoff:3.500A) Processing helix chain 'K' and resid 629 through 634 Processing helix chain 'K' and resid 645 through 653 Processing helix chain 'K' and resid 672 through 675 No H-bonds generated for 'chain 'K' and resid 672 through 675' Processing helix chain 'K' and resid 688 through 690 No H-bonds generated for 'chain 'K' and resid 688 through 690' Processing helix chain 'K' and resid 715 through 721 Processing helix chain 'K' and resid 726 through 740 Processing helix chain 'K' and resid 757 through 759 No H-bonds generated for 'chain 'K' and resid 757 through 759' Processing helix chain 'K' and resid 776 through 783 removed outlier: 3.544A pdb=" N ILE K 782 " --> pdb=" O TYR K 779 " (cutoff:3.500A) Processing helix chain 'K' and resid 795 through 797 No H-bonds generated for 'chain 'K' and resid 795 through 797' Processing helix chain 'K' and resid 805 through 821 Processing helix chain 'L' and resid 220 through 222 No H-bonds generated for 'chain 'L' and resid 220 through 222' Processing helix chain 'M' and resid 2 through 4 No H-bonds generated for 'chain 'M' and resid 2 through 4' Processing sheet with id= A, first strand: chain 'K' and resid 139 through 141 Processing sheet with id= B, first strand: chain 'K' and resid 407 through 411 removed outlier: 6.869A pdb=" N LYS K 622 " --> pdb=" O ILE K 386 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ILE K 388 " --> pdb=" O LYS K 622 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU K 624 " --> pdb=" O ILE K 388 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 438 through 440 Processing sheet with id= D, first strand: chain 'K' and resid 467 through 469 removed outlier: 8.552A pdb=" N ILE K 468 " --> pdb=" O PHE K 680 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLY K 682 " --> pdb=" O ILE K 468 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL K 696 " --> pdb=" O VAL K 712 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL K 712 " --> pdb=" O VAL K 696 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS K 751 " --> pdb=" O GLN K 665 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'K' and resid 638 through 640 removed outlier: 6.756A pdb=" N THR K 611 " --> pdb=" O GLN K 599 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE K 601 " --> pdb=" O GLN K 609 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLN K 609 " --> pdb=" O ILE K 601 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'K' and resid 654 through 657 Processing sheet with id= G, first strand: chain 'K' and resid 82 through 86 removed outlier: 6.486A pdb=" N GLU K 89 " --> pdb=" O LEU K 85 " (cutoff:3.500A) 517 hydrogen bonds defined for protein. 1455 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 10.90 Time building geometry restraints manager: 10.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2389 1.31 - 1.44: 6635 1.44 - 1.57: 9668 1.57 - 1.70: 586 1.70 - 1.82: 81 Bond restraints: 19359 Sorted by residual: bond pdb=" O5B FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.634 1.386 0.248 2.00e-02 2.50e+03 1.54e+02 bond pdb=" O3P FAD K 901 " pdb=" P FAD K 901 " ideal model delta sigma weight residual 1.660 1.470 0.190 2.00e-02 2.50e+03 9.07e+01 bond pdb=" O3P FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.633 1.454 0.179 2.00e-02 2.50e+03 8.05e+01 bond pdb=" O5' FAD K 901 " pdb=" P FAD K 901 " ideal model delta sigma weight residual 1.637 1.464 0.173 2.00e-02 2.50e+03 7.48e+01 bond pdb=" O1A FAD K 901 " pdb=" PA FAD K 901 " ideal model delta sigma weight residual 1.509 1.365 0.144 2.00e-02 2.50e+03 5.22e+01 ... (remaining 19354 not shown) Histogram of bond angle deviations from ideal: 95.39 - 103.14: 708 103.14 - 110.90: 8207 110.90 - 118.66: 7874 118.66 - 126.41: 9670 126.41 - 134.17: 964 Bond angle restraints: 27423 Sorted by residual: angle pdb=" C LYS K 75 " pdb=" CA LYS K 75 " pdb=" CB LYS K 75 " ideal model delta sigma weight residual 117.23 108.32 8.91 1.36e+00 5.41e-01 4.29e+01 angle pdb=" O1P FAD K 901 " pdb=" P FAD K 901 " pdb=" O2P FAD K 901 " ideal model delta sigma weight residual 122.50 105.35 17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C ASP L 214 " pdb=" N PRO L 215 " pdb=" CA PRO L 215 " ideal model delta sigma weight residual 119.47 125.97 -6.50 1.16e+00 7.43e-01 3.14e+01 angle pdb=" CA LYS K 75 " pdb=" C LYS K 75 " pdb=" N ASN K 76 " ideal model delta sigma weight residual 119.98 115.33 4.65 8.50e-01 1.38e+00 3.00e+01 angle pdb=" C ASP K 760 " pdb=" N PRO K 761 " pdb=" CA PRO K 761 " ideal model delta sigma weight residual 119.05 125.04 -5.99 1.11e+00 8.12e-01 2.92e+01 ... (remaining 27418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 9220 35.91 - 71.82: 1648 71.82 - 107.73: 32 107.73 - 143.64: 1 143.64 - 179.56: 1 Dihedral angle restraints: 10902 sinusoidal: 6408 harmonic: 4494 Sorted by residual: dihedral pdb=" CD ARG A 40 " pdb=" NE ARG A 40 " pdb=" CZ ARG A 40 " pdb=" NH1 ARG A 40 " ideal model delta sinusoidal sigma weight residual 0.00 -85.61 85.61 1 1.00e+01 1.00e-02 8.87e+01 dihedral pdb=" CD ARG G 11 " pdb=" NE ARG G 11 " pdb=" CZ ARG G 11 " pdb=" NH1 ARG G 11 " ideal model delta sinusoidal sigma weight residual 0.00 -66.88 66.88 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CD ARG H 30 " pdb=" NE ARG H 30 " pdb=" CZ ARG H 30 " pdb=" NH1 ARG H 30 " ideal model delta sinusoidal sigma weight residual 0.00 -57.45 57.45 1 1.00e+01 1.00e-02 4.43e+01 ... (remaining 10899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2312 0.062 - 0.124: 630 0.124 - 0.186: 107 0.186 - 0.247: 16 0.247 - 0.309: 3 Chirality restraints: 3068 Sorted by residual: chirality pdb=" C3' FAD K 901 " pdb=" C2' FAD K 901 " pdb=" C4' FAD K 901 " pdb=" O3' FAD K 901 " both_signs ideal model delta sigma weight residual False -2.55 -2.24 -0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA THR K 143 " pdb=" N THR K 143 " pdb=" C THR K 143 " pdb=" CB THR K 143 " both_signs ideal model delta sigma weight residual False 2.53 2.25 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CG LEU G 34 " pdb=" CB LEU G 34 " pdb=" CD1 LEU G 34 " pdb=" CD2 LEU G 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 3065 not shown) Planarity restraints: 2456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FAD K 901 " -0.396 2.00e-02 2.50e+03 2.24e-01 2.38e+03 pdb=" C10 FAD K 901 " -0.140 2.00e-02 2.50e+03 pdb=" C2 FAD K 901 " 0.214 2.00e-02 2.50e+03 pdb=" C4 FAD K 901 " 0.037 2.00e-02 2.50e+03 pdb=" C4X FAD K 901 " -0.149 2.00e-02 2.50e+03 pdb=" C5X FAD K 901 " -0.219 2.00e-02 2.50e+03 pdb=" C6 FAD K 901 " -0.124 2.00e-02 2.50e+03 pdb=" C7 FAD K 901 " 0.076 2.00e-02 2.50e+03 pdb=" C7M FAD K 901 " 0.199 2.00e-02 2.50e+03 pdb=" C8 FAD K 901 " 0.173 2.00e-02 2.50e+03 pdb=" C8M FAD K 901 " 0.382 2.00e-02 2.50e+03 pdb=" C9 FAD K 901 " 0.055 2.00e-02 2.50e+03 pdb=" C9A FAD K 901 " -0.148 2.00e-02 2.50e+03 pdb=" N1 FAD K 901 " 0.045 2.00e-02 2.50e+03 pdb=" N10 FAD K 901 " -0.262 2.00e-02 2.50e+03 pdb=" N3 FAD K 901 " 0.222 2.00e-02 2.50e+03 pdb=" N5 FAD K 901 " -0.369 2.00e-02 2.50e+03 pdb=" O2 FAD K 901 " 0.371 2.00e-02 2.50e+03 pdb=" O4 FAD K 901 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 40 " 1.099 9.50e-02 1.11e+02 4.92e-01 1.46e+02 pdb=" NE ARG A 40 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG A 40 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 40 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 40 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 11 " 1.007 9.50e-02 1.11e+02 4.51e-01 1.23e+02 pdb=" NE ARG G 11 " -0.061 2.00e-02 2.50e+03 pdb=" CZ ARG G 11 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG G 11 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 11 " 0.023 2.00e-02 2.50e+03 ... (remaining 2453 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.42: 11 1.42 - 2.29: 64 2.29 - 3.16: 14617 3.16 - 4.03: 54964 4.03 - 4.90: 89350 Warning: very small nonbonded interaction distances. Nonbonded interactions: 159006 Sorted by model distance: nonbonded pdb=" NH1 ARG H 30 " pdb=" O5' DC J -46 " model vdw 0.544 2.520 nonbonded pdb=" NH2 ARG H 30 " pdb=" O3' DT J -47 " model vdw 0.796 2.520 nonbonded pdb=" CB ARG A 128 " pdb=" OE1 GLU A 133 " model vdw 0.821 3.440 nonbonded pdb=" NE ARG A 128 " pdb=" OE2 GLU A 133 " model vdw 0.827 2.520 nonbonded pdb=" NZ LYS D 28 " pdb=" O3' DA J 50 " model vdw 0.922 2.520 ... (remaining 159001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 134) selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 101) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 120) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 26 through 121) } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.460 Check model and map are aligned: 0.310 Set scattering table: 0.180 Process input model: 66.350 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4616 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 : 0.009 0.248 19359 Z= 0.521 Angle : 1.043 17.149 27423 Z= 0.634 Chirality : 0.058 0.309 3068 Planarity : 0.023 0.492 2456 Dihedral : 25.719 179.556 8006 Min Nonbonded Distance : 0.544 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 1.25 % Allowed : 4.66 % Favored : 94.09 % Rotamer: Outliers : 6.26 % Allowed : 4.58 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: -2.99 (0.18), residues: 1524 helix: -2.27 (0.14), residues: 787 sheet: 0.51 (0.69), residues: 61 loop : -1.71 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 117 HIS 0.014 0.002 HIS B 75 PHE 0.033 0.003 PHE C 25 TYR 0.019 0.003 TYR K 767 ARG 0.016 0.001 ARG K 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 276 time to evaluate : 1.858 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 outliers start: 82 outliers final: 26 residues processed: 347 average time/residue: 0.4354 time to fit residues: 206.2855 Evaluate side-chains 147 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 121 time to evaluate : 1.655 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 3 residues processed: 26 average time/residue: 0.4459 time to fit residues: 17.7411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 71 optimal weight: 0.0570 chunk 138 optimal weight: 20.0000 chunk 53 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 0.1980 chunk 160 optimal weight: 50.0000 overall best weight: 2.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 81 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN G 110 ASN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 ASN K 276 ASN K 400 GLN ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 218 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4781 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19359 Z= 0.250 Angle : 0.677 7.899 27423 Z= 0.383 Chirality : 0.041 0.182 3068 Planarity : 0.007 0.123 2456 Dihedral : 29.442 176.948 4968 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.15 % Favored : 96.59 % Rotamer: Outliers : 0.31 % Allowed : 3.44 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: -0.54 (0.20), residues: 1524 helix: -0.05 (0.17), residues: 802 sheet: 1.13 (0.64), residues: 61 loop : -0.78 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 762 HIS 0.009 0.001 HIS A 113 PHE 0.021 0.002 PHE C 25 TYR 0.028 0.002 TYR B 88 ARG 0.022 0.001 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 1.736 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 outliers start: 4 outliers final: 0 residues processed: 178 average time/residue: 0.3947 time to fit residues: 99.9363 Evaluate side-chains 109 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 1.766 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 173 optimal weight: 10.0000 chunk 143 optimal weight: 50.0000 chunk 159 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 HIS K 98 HIS K 469 GLN ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4917 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 19359 Z= 0.270 Angle : 0.636 9.005 27423 Z= 0.364 Chirality : 0.039 0.225 3068 Planarity : 0.005 0.089 2456 Dihedral : 29.484 178.327 4968 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.28 % Favored : 96.46 % Rotamer: Outliers : 0.08 % Allowed : 3.21 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.10 (0.21), residues: 1524 helix: 0.55 (0.18), residues: 805 sheet: 1.22 (0.60), residues: 72 loop : -0.59 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 762 HIS 0.013 0.001 HIS E 39 PHE 0.013 0.001 PHE K 91 TYR 0.035 0.002 TYR E 54 ARG 0.010 0.001 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.620 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 outliers start: 1 outliers final: 0 residues processed: 150 average time/residue: 0.3591 time to fit residues: 78.3165 Evaluate side-chains 108 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 108 optimal weight: 50.0000 chunk 161 optimal weight: 30.0000 chunk 171 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 chunk 153 optimal weight: 30.0000 chunk 46 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 135 GLN ** K 732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 19359 Z= 0.400 Angle : 0.709 12.285 27423 Z= 0.401 Chirality : 0.042 0.195 3068 Planarity : 0.006 0.082 2456 Dihedral : 29.748 177.176 4968 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.61 % Favored : 96.19 % Rotamer: Outliers : 0.23 % Allowed : 4.12 % Favored : 95.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.35 (0.21), residues: 1524 helix: 0.71 (0.18), residues: 806 sheet: 1.52 (0.61), residues: 72 loop : -0.42 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 200 HIS 0.016 0.002 HIS F 75 PHE 0.022 0.001 PHE K 91 TYR 0.021 0.002 TYR A 54 ARG 0.016 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.871 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 outliers start: 3 outliers final: 1 residues processed: 128 average time/residue: 0.3452 time to fit residues: 66.6354 Evaluate side-chains 86 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.709 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1648 time to fit residues: 2.4632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 50.0000 chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 127 optimal weight: 40.0000 chunk 70 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 118 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 7.9990 chunk 153 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 31 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5062 moved from start: 0.5959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19359 Z= 0.242 Angle : 0.602 8.274 27423 Z= 0.342 Chirality : 0.038 0.153 3068 Planarity : 0.004 0.062 2456 Dihedral : 29.768 177.444 4968 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.82 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.74 (0.21), residues: 1524 helix: 1.15 (0.18), residues: 808 sheet: 1.66 (0.61), residues: 72 loop : -0.42 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.011 0.001 HIS D 106 PHE 0.013 0.001 PHE K 753 TYR 0.016 0.001 TYR A 54 ARG 0.012 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.722 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 outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.3655 time to fit residues: 68.2431 Evaluate side-chains 90 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 2.9990 chunk 154 optimal weight: 40.0000 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 42 optimal weight: 0.7980 chunk 171 optimal weight: 30.0000 chunk 142 optimal weight: 50.0000 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 89 optimal weight: 6.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5115 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19359 Z= 0.283 Angle : 0.610 8.261 27423 Z= 0.349 Chirality : 0.038 0.158 3068 Planarity : 0.004 0.062 2456 Dihedral : 29.713 177.429 4968 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.41 % Favored : 96.46 % Rotamer: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.87 (0.21), residues: 1524 helix: 1.25 (0.18), residues: 803 sheet: 1.66 (0.61), residues: 72 loop : -0.32 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 762 HIS 0.010 0.001 HIS D 106 PHE 0.014 0.001 PHE E 104 TYR 0.019 0.001 TYR A 54 ARG 0.006 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 1.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.3396 time to fit residues: 59.6893 Evaluate side-chains 79 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 1.705 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.0628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 125 optimal weight: 0.9980 chunk 96 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 104 optimal weight: 50.0000 chunk 78 optimal weight: 5.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5196 moved from start: 0.7206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 19359 Z= 0.368 Angle : 0.658 8.281 27423 Z= 0.374 Chirality : 0.040 0.185 3068 Planarity : 0.005 0.061 2456 Dihedral : 29.939 177.590 4968 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.39 % Rotamer: Outliers : 0.08 % Allowed : 1.76 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.65 (0.21), residues: 1524 helix: 1.00 (0.18), residues: 807 sheet: 1.49 (0.60), residues: 72 loop : -0.33 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 762 HIS 0.010 0.001 HIS F 75 PHE 0.014 0.001 PHE A 84 TYR 0.028 0.001 TYR K 99 ARG 0.011 0.001 ARG E 129 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.3738 time to fit residues: 57.6154 Evaluate side-chains 76 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 1.868 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.6733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 50.0000 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 9.9990 chunk 51 optimal weight: 0.4980 chunk 33 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 116 optimal weight: 30.0000 chunk 84 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 134 optimal weight: 30.0000 chunk 155 optimal weight: 50.0000 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 106 HIS ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5123 moved from start: 0.7366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19359 Z= 0.239 Angle : 0.607 9.400 27423 Z= 0.344 Chirality : 0.038 0.160 3068 Planarity : 0.004 0.060 2456 Dihedral : 29.847 178.458 4968 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.95 % Favored : 96.92 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.07 % 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: 0.91 (0.21), residues: 1524 helix: 1.28 (0.18), residues: 802 sheet: 1.52 (0.59), residues: 71 loop : -0.29 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 762 HIS 0.008 0.001 HIS D 106 PHE 0.013 0.001 PHE K 753 TYR 0.024 0.001 TYR K 99 ARG 0.004 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.3439 time to fit residues: 56.7429 Evaluate side-chains 77 residues out of total 1310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 1.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 59.1361 > 50: distance: 89 - 93: 12.073 distance: 93 - 94: 13.498 distance: 94 - 95: 5.589 distance: 94 - 97: 6.605 distance: 95 - 96: 5.115 distance: 95 - 101: 4.184 distance: 97 - 98: 14.662 distance: 98 - 99: 13.142 distance: 98 - 100: 14.226 distance: 101 - 102: 13.067 distance: 102 - 103: 3.812 distance: 102 - 105: 9.927 distance: 103 - 104: 27.985 distance: 103 - 108: 19.361 distance: 105 - 106: 5.667 distance: 105 - 107: 14.455 distance: 108 - 109: 4.383 distance: 108 - 114: 16.809 distance: 109 - 110: 34.239 distance: 109 - 112: 27.063 distance: 110 - 111: 8.460 distance: 110 - 115: 31.567 distance: 113 - 114: 16.615 distance: 115 - 116: 45.123 distance: 116 - 117: 13.628 distance: 117 - 118: 11.715 distance: 117 - 119: 8.366 distance: 119 - 120: 14.295 distance: 120 - 121: 6.411 distance: 120 - 123: 19.383 distance: 121 - 122: 35.483 distance: 121 - 131: 5.094 distance: 122 - 144: 29.818 distance: 123 - 124: 8.528 distance: 124 - 125: 19.890 distance: 124 - 126: 22.168 distance: 125 - 127: 11.841 distance: 126 - 128: 11.292 distance: 127 - 129: 12.176 distance: 128 - 129: 30.160 distance: 129 - 130: 15.633 distance: 131 - 132: 7.179 distance: 132 - 133: 10.787 distance: 132 - 135: 21.780 distance: 133 - 134: 27.556 distance: 133 - 137: 6.527 distance: 134 - 152: 27.807 distance: 135 - 136: 19.367 distance: 137 - 138: 9.769 distance: 138 - 139: 5.466 distance: 138 - 141: 8.871 distance: 139 - 140: 20.484 distance: 139 - 144: 19.694 distance: 141 - 142: 8.591 distance: 141 - 143: 8.884 distance: 144 - 145: 10.562 distance: 145 - 146: 6.250 distance: 145 - 148: 3.439 distance: 146 - 147: 9.676 distance: 146 - 152: 5.578 distance: 147 - 169: 7.648 distance: 148 - 149: 13.169 distance: 148 - 150: 6.357 distance: 149 - 151: 11.289 distance: 152 - 153: 4.006 distance: 153 - 154: 5.787 distance: 153 - 156: 6.627 distance: 154 - 155: 6.600 distance: 154 - 160: 7.286 distance: 155 - 175: 13.961 distance: 156 - 157: 14.616 distance: 156 - 158: 11.751 distance: 157 - 159: 6.401 distance: 160 - 161: 9.143 distance: 161 - 162: 6.549 distance: 161 - 164: 6.497 distance: 162 - 163: 5.058 distance: 162 - 169: 3.561 distance: 163 - 183: 10.157 distance: 165 - 166: 9.344 distance: 166 - 167: 5.121 distance: 166 - 168: 6.163