Starting phenix.real_space_refine on Wed Jun 26 14:27:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/06_2024/8omo_16973_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/06_2024/8omo_16973.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/06_2024/8omo_16973.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/06_2024/8omo_16973.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/06_2024/8omo_16973_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omo_16973/06_2024/8omo_16973_updated.pdb" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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 P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6520 2.51 5 N 1761 2.21 5 O 1953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 159": "NH1" <-> "NH2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A GLU 278": "OE1" <-> "OE2" Residue "A GLU 357": "OE1" <-> "OE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A GLU 569": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 647": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A TYR 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 852": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B ARG 623": "NH1" <-> "NH2" Residue "B GLU 637": "OE1" <-> "OE2" Residue "B GLU 674": "OE1" <-> "OE2" Residue "B GLU 677": "OE1" <-> "OE2" Residue "B GLU 683": "OE1" <-> "OE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B GLU 718": "OE1" <-> "OE2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B GLU 755": "OE1" <-> "OE2" Residue "B GLU 787": "OE1" <-> "OE2" Residue "B GLU 797": "OE1" <-> "OE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B GLU 853": "OE1" <-> "OE2" Residue "B GLU 854": "OE1" <-> "OE2" Residue "B ASP 943": "OD1" <-> "OD2" Residue "B GLU 955": "OE1" <-> "OE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B ARG 964": "NH1" <-> "NH2" Residue "B GLU 976": "OE1" <-> "OE2" Residue "B GLU 995": "OE1" <-> "OE2" Residue "B ARG 1066": "NH1" <-> "NH2" Residue "B GLU 1124": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 10290 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 715, 5626 Classifications: {'peptide': 715} Link IDs: {'PTRANS': 20, 'TRANS': 694} Chain breaks: 5 Chain: "B" Number of atoms: 4600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 573, 4600 Classifications: {'peptide': 573} Link IDs: {'PTRANS': 17, 'TRANS': 555} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.71, per 1000 atoms: 0.55 Number of scatterers: 10290 At special positions: 0 Unit cell: (92.3342, 106.961, 161.813, 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) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1953 8.00 N 1761 7.00 C 6520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.78 Conformation dependent library (CDL) restraints added in 1.8 seconds 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 9 sheets defined 51.1% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.48 Creating SS restraints... Processing helix chain 'A' and resid 185 through 194 Processing helix chain 'A' and resid 208 through 219 removed outlier: 4.073A pdb=" N LYS A 212 " --> pdb=" O GLY A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'A' and resid 265 through 276 Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 326 through 330 Processing helix chain 'A' and resid 336 through 347 Processing helix chain 'A' and resid 353 through 368 removed outlier: 3.637A pdb=" N GLU A 358 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 401 through 422 Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 430 through 457 Proline residue: A 439 - end of helix removed outlier: 4.566A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N PHE A 450 " --> pdb=" O ASP A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 476 through 502 Processing helix chain 'A' and resid 554 through 612 removed outlier: 4.848A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASN A 583 " --> pdb=" O LYS A 579 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N TYR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Proline residue: A 591 - end of helix Processing helix chain 'A' and resid 675 through 691 Processing helix chain 'A' and resid 724 through 738 removed outlier: 3.633A pdb=" N THR A 732 " --> pdb=" O GLU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 771 Processing helix chain 'A' and resid 787 through 793 Processing helix chain 'A' and resid 827 through 833 Processing helix chain 'A' and resid 838 through 850 Processing helix chain 'A' and resid 874 through 889 removed outlier: 3.798A pdb=" N GLN A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 929 Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'B' and resid 587 through 601 Processing helix chain 'B' and resid 607 through 615 Processing helix chain 'B' and resid 621 through 630 removed outlier: 3.685A pdb=" N HIS B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 662 Proline residue: B 657 - end of helix Processing helix chain 'B' and resid 667 through 680 removed outlier: 4.031A pdb=" N ILE B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Proline residue: B 676 - end of helix removed outlier: 3.583A pdb=" N SER B 680 " --> pdb=" O PRO B 676 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 687 No H-bonds generated for 'chain 'B' and resid 684 through 687' Processing helix chain 'B' and resid 691 through 696 Processing helix chain 'B' and resid 706 through 708 No H-bonds generated for 'chain 'B' and resid 706 through 708' Processing helix chain 'B' and resid 710 through 737 removed outlier: 3.835A pdb=" N ARG B 715 " --> pdb=" O LEU B 711 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 Processing helix chain 'B' and resid 772 through 774 No H-bonds generated for 'chain 'B' and resid 772 through 774' Processing helix chain 'B' and resid 783 through 843 removed outlier: 4.088A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N HIS B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N SER B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 902 through 918 Processing helix chain 'B' and resid 945 through 947 No H-bonds generated for 'chain 'B' and resid 945 through 947' Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 983 through 999 Processing helix chain 'B' and resid 1012 through 1020 removed outlier: 3.629A pdb=" N GLU B1016 " --> pdb=" O PRO B1012 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLU B1018 " --> pdb=" O VAL B1014 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS B1019 " --> pdb=" O CYS B1015 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASN B1020 " --> pdb=" O GLU B1016 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1012 through 1020' Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1080 through 1110 Processing helix chain 'B' and resid 1118 through 1122 Processing sheet with id= A, first strand: chain 'A' and resid 172 through 178 removed outlier: 4.162A pdb=" N VAL A 166 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N VAL A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU A 198 " --> pdb=" O VAL A 148 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N VAL A 150 " --> pdb=" O GLU A 198 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL A 200 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N MET A 152 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU A 223 " --> pdb=" O CYS A 199 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU A 201 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 225 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 512 through 516 removed outlier: 6.226A pdb=" N THR A 552 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N THR A 541 " --> pdb=" O THR A 552 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 632 through 635 removed outlier: 3.610A pdb=" N SER A 699 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 797 through 802 removed outlier: 6.298A pdb=" N PHE A 664 " --> pdb=" O ASN A 798 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 800 " --> pdb=" O PHE A 664 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE A 666 " --> pdb=" O LEU A 800 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL A 802 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N THR A 668 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N CYS A 778 " --> pdb=" O HIS A 665 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 667 " --> pdb=" O CYS A 778 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N PHE A 780 " --> pdb=" O ILE A 667 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N GLY A 669 " --> pdb=" O PHE A 780 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 804 through 807 Processing sheet with id= F, first strand: chain 'B' and resid 754 through 756 Processing sheet with id= G, first strand: chain 'B' and resid 857 through 860 removed outlier: 3.600A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 1059 through 1061 removed outlier: 6.855A pdb=" N THR B1005 " --> pdb=" O MET B 892 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ILE B 894 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE B1007 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLY B 896 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL B 972 " --> pdb=" O LEU B1006 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N VAL B1008 " --> pdb=" O VAL B 972 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU B 974 " --> pdb=" O VAL B1008 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 1032 through 1034 removed outlier: 3.734A pdb=" N THR B1054 " --> pdb=" O LEU B1033 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1413 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: 3.12 Time building geometry restraints manager: 4.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2755 1.34 - 1.46: 2845 1.46 - 1.58: 4775 1.58 - 1.71: 10 1.71 - 1.83: 75 Bond restraints: 10460 Sorted by residual: bond pdb=" CA SER B 904 " pdb=" CB SER B 904 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.55e-02 4.16e+03 1.03e+01 bond pdb=" C LEU A 414 " pdb=" O LEU A 414 " ideal model delta sigma weight residual 1.244 1.214 0.029 9.80e-03 1.04e+04 9.00e+00 bond pdb=" C LEU B 618 " pdb=" O LEU B 618 " ideal model delta sigma weight residual 1.249 1.224 0.025 8.50e-03 1.38e+04 8.84e+00 bond pdb=" O5' ATP A2000 " pdb=" PA ATP A2000 " ideal model delta sigma weight residual 1.579 1.611 -0.032 1.10e-02 8.26e+03 8.60e+00 bond pdb=" CA SER B 836 " pdb=" CB SER B 836 " ideal model delta sigma weight residual 1.529 1.485 0.044 1.55e-02 4.16e+03 7.89e+00 ... (remaining 10455 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.95: 194 105.95 - 113.10: 5378 113.10 - 120.25: 4656 120.25 - 127.40: 3834 127.40 - 134.55: 60 Bond angle restraints: 14122 Sorted by residual: angle pdb=" PA ATP B2000 " pdb=" O3A ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 136.83 115.74 21.09 1.00e+00 1.00e+00 4.45e+02 angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 118.82 21.05 1.00e+00 1.00e+00 4.43e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 124.96 14.91 1.00e+00 1.00e+00 2.22e+02 angle pdb=" C5' ATP B2000 " pdb=" O5' ATP B2000 " pdb=" PA ATP B2000 " ideal model delta sigma weight residual 121.27 112.00 9.27 1.00e+00 1.00e+00 8.60e+01 angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 128.43 8.40 1.00e+00 1.00e+00 7.06e+01 ... (remaining 14117 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5480 17.91 - 35.82: 716 35.82 - 53.74: 156 53.74 - 71.65: 33 71.65 - 89.56: 27 Dihedral angle restraints: 6412 sinusoidal: 2666 harmonic: 3746 Sorted by residual: dihedral pdb=" CA ASP B1077 " pdb=" C ASP B1077 " pdb=" N VAL B1078 " pdb=" CA VAL B1078 " ideal model delta harmonic sigma weight residual 180.00 153.72 26.28 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA GLY A 504 " pdb=" C GLY A 504 " pdb=" N LEU A 505 " pdb=" CA LEU A 505 " ideal model delta harmonic sigma weight residual -180.00 -155.45 -24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA PRO B 619 " pdb=" C PRO B 619 " pdb=" N ASP B 620 " pdb=" CA ASP B 620 " ideal model delta harmonic sigma weight residual 180.00 155.81 24.19 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 6409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 907 0.071 - 0.141: 521 0.141 - 0.212: 159 0.212 - 0.282: 27 0.282 - 0.353: 3 Chirality restraints: 1617 Sorted by residual: chirality pdb=" CA ARG A 171 " pdb=" N ARG A 171 " pdb=" C ARG A 171 " pdb=" CB ARG A 171 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" CA GLU A 808 " pdb=" N GLU A 808 " pdb=" C GLU A 808 " pdb=" CB GLU A 808 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA GLU A 278 " pdb=" N GLU A 278 " pdb=" C GLU A 278 " pdb=" CB GLU A 278 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 1614 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP A2000 " -0.053 2.00e-02 2.50e+03 2.45e-02 1.65e+01 pdb=" C2 ATP A2000 " -0.010 2.00e-02 2.50e+03 pdb=" C4 ATP A2000 " 0.020 2.00e-02 2.50e+03 pdb=" C5 ATP A2000 " 0.012 2.00e-02 2.50e+03 pdb=" C6 ATP A2000 " 0.010 2.00e-02 2.50e+03 pdb=" C8 ATP A2000 " -0.010 2.00e-02 2.50e+03 pdb=" N1 ATP A2000 " -0.017 2.00e-02 2.50e+03 pdb=" N3 ATP A2000 " 0.028 2.00e-02 2.50e+03 pdb=" N6 ATP A2000 " -0.025 2.00e-02 2.50e+03 pdb=" N7 ATP A2000 " 0.011 2.00e-02 2.50e+03 pdb=" N9 ATP A2000 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 953 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C MET B 953 " -0.036 2.00e-02 2.50e+03 pdb=" O MET B 953 " 0.014 2.00e-02 2.50e+03 pdb=" N GLU B 954 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 807 " -0.022 2.00e-02 2.50e+03 1.01e-02 2.56e+00 pdb=" CG TRP B 807 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TRP B 807 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 807 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP B 807 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 807 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 807 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 807 " -0.009 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 807 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 807 " -0.009 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 6 2.17 - 2.85: 3702 2.85 - 3.54: 16609 3.54 - 4.22: 25707 4.22 - 4.90: 41849 Nonbonded interactions: 87873 Sorted by model distance: nonbonded pdb=" OE2 GLU B 889 " pdb=" OH TYR B1028 " model vdw 1.488 2.440 nonbonded pdb=" O2G ATP A2000 " pdb="MG MG A2001 " model vdw 1.783 2.170 nonbonded pdb=" O2B ATP B2000 " pdb="MG MG B2001 " model vdw 1.973 2.170 nonbonded pdb=" OG SER A 676 " pdb="MG MG A2001 " model vdw 1.983 2.170 nonbonded pdb=" O2B ATP A2000 " pdb="MG MG A2001 " model vdw 1.992 2.170 ... (remaining 87868 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.890 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: 6.910 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 30.270 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.007 0.050 10460 Z= 0.481 Angle : 1.363 21.092 14122 Z= 0.941 Chirality : 0.090 0.353 1617 Planarity : 0.004 0.030 1796 Dihedral : 17.683 89.561 3982 Min Nonbonded Distance : 1.488 Molprobity Statistics. All-atom Clashscore : 21.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.68 % Allowed : 14.92 % Favored : 80.41 % Cbeta Deviations : 0.16 % 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: -3.82 (0.19), residues: 1270 helix: -1.72 (0.16), residues: 695 sheet: -2.97 (0.38), residues: 143 loop : -3.53 (0.24), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.005 TRP B 807 HIS 0.010 0.003 HIS A 428 PHE 0.019 0.004 PHE B 810 TYR 0.021 0.004 TYR A 815 ARG 0.012 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 307 time to evaluate : 1.117 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: A 210 MET cc_start: 0.7145 (ttt) cc_final: 0.6879 (ttt) REVERT: A 299 TYR cc_start: 0.8732 (m-80) cc_final: 0.8346 (m-80) REVERT: A 313 PHE cc_start: 0.8165 (m-80) cc_final: 0.7941 (m-10) REVERT: A 331 ASN cc_start: 0.8317 (t0) cc_final: 0.7939 (t0) REVERT: A 340 ARG cc_start: 0.8542 (mtm110) cc_final: 0.7909 (mtp180) REVERT: A 344 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8668 (tm-30) REVERT: A 347 LYS cc_start: 0.9009 (tptp) cc_final: 0.8689 (tptp) REVERT: A 369 ASP cc_start: 0.8116 (t0) cc_final: 0.7674 (t0) REVERT: A 382 ARG cc_start: 0.8279 (ttt180) cc_final: 0.7795 (ttp-110) REVERT: A 397 GLN cc_start: 0.8988 (mt0) cc_final: 0.8751 (mm-40) REVERT: A 409 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8380 (mm-40) REVERT: A 418 ILE cc_start: 0.8788 (tp) cc_final: 0.8389 (tt) REVERT: A 422 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8737 (mt-10) REVERT: A 423 LYS cc_start: 0.8880 (tttt) cc_final: 0.8651 (ttmt) REVERT: A 459 ASP cc_start: 0.7659 (p0) cc_final: 0.7177 (m-30) REVERT: A 460 MET cc_start: 0.8461 (mtp) cc_final: 0.8201 (mtp) REVERT: A 464 GLU cc_start: 0.9368 (mp0) cc_final: 0.9162 (mp0) REVERT: A 466 HIS cc_start: 0.8791 (m90) cc_final: 0.8444 (m90) REVERT: A 485 MET cc_start: 0.8431 (mtm) cc_final: 0.8091 (mtm) REVERT: A 646 ASP cc_start: 0.8717 (p0) cc_final: 0.8506 (p0) REVERT: A 672 MET cc_start: 0.8368 (tpt) cc_final: 0.7877 (tpt) REVERT: A 682 THR cc_start: 0.8412 (m) cc_final: 0.8159 (t) REVERT: A 685 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.7600 (tt) REVERT: A 691 ILE cc_start: 0.8114 (mt) cc_final: 0.7823 (mm) REVERT: A 695 VAL cc_start: 0.8603 (t) cc_final: 0.8391 (t) REVERT: A 704 ILE cc_start: 0.8432 (mt) cc_final: 0.8196 (mt) REVERT: A 719 LEU cc_start: 0.8893 (mm) cc_final: 0.8457 (mt) REVERT: A 726 MET cc_start: 0.8314 (ttm) cc_final: 0.7305 (ttm) REVERT: A 741 LYS cc_start: 0.8478 (tptp) cc_final: 0.8144 (tptp) REVERT: A 742 ASP cc_start: 0.8140 (p0) cc_final: 0.7842 (p0) REVERT: A 757 TYR cc_start: 0.8959 (m-80) cc_final: 0.8688 (m-10) REVERT: A 762 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8224 (tt) REVERT: A 802 VAL cc_start: 0.8648 (t) cc_final: 0.8347 (m) REVERT: A 813 MET cc_start: 0.7972 (mmt) cc_final: 0.7388 (mmt) REVERT: A 847 LYS cc_start: 0.8921 (tptt) cc_final: 0.8636 (tptp) REVERT: B 546 GLU cc_start: 0.8361 (mp0) cc_final: 0.8017 (pm20) REVERT: B 553 ASP cc_start: 0.8496 (t0) cc_final: 0.7996 (t0) REVERT: B 554 MET cc_start: 0.8539 (mmm) cc_final: 0.8211 (mmm) REVERT: B 586 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8383 (mmmm) REVERT: B 591 ASN cc_start: 0.8356 (m-40) cc_final: 0.8079 (m-40) REVERT: B 593 ARG cc_start: 0.7953 (mtt180) cc_final: 0.7332 (mtt180) REVERT: B 617 LYS cc_start: 0.8739 (mmmt) cc_final: 0.8536 (mmmm) REVERT: B 637 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7562 (pt0) REVERT: B 653 GLN cc_start: 0.8570 (tp40) cc_final: 0.8224 (tp40) REVERT: B 660 ASN cc_start: 0.8946 (m-40) cc_final: 0.8738 (m-40) REVERT: B 672 ILE cc_start: 0.8472 (tt) cc_final: 0.8137 (mt) REVERT: B 674 GLU cc_start: 0.8493 (tt0) cc_final: 0.8140 (tt0) REVERT: B 683 GLU cc_start: 0.8155 (tt0) cc_final: 0.7954 (tt0) REVERT: B 684 HIS cc_start: 0.8791 (t70) cc_final: 0.8570 (t-170) REVERT: B 699 LYS cc_start: 0.9212 (mttt) cc_final: 0.8977 (mtmm) REVERT: B 712 ILE cc_start: 0.8532 (mm) cc_final: 0.8236 (tp) REVERT: B 714 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7847 (mmtm) REVERT: B 739 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.8134 (t0) REVERT: B 791 HIS cc_start: 0.9119 (t-90) cc_final: 0.8891 (t70) REVERT: B 794 GLN cc_start: 0.8653 (tm-30) cc_final: 0.8439 (tm-30) REVERT: B 796 ARG cc_start: 0.8777 (mtp-110) cc_final: 0.8515 (mtp180) REVERT: B 798 GLN cc_start: 0.8332 (tp-100) cc_final: 0.7933 (tp40) REVERT: B 860 LYS cc_start: 0.8695 (tttm) cc_final: 0.8383 (ttmt) REVERT: B 884 LEU cc_start: 0.8611 (mt) cc_final: 0.8339 (mm) REVERT: B 892 MET cc_start: 0.8250 (ttm) cc_final: 0.8036 (ttm) REVERT: B 899 MET cc_start: 0.7922 (tpt) cc_final: 0.7262 (tpt) REVERT: B 917 GLN cc_start: 0.8552 (mt0) cc_final: 0.7664 (mt0) REVERT: B 926 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8348 (tp30) REVERT: B 956 LEU cc_start: 0.8213 (mt) cc_final: 0.7992 (mt) REVERT: B 995 GLU cc_start: 0.8507 (tt0) cc_final: 0.8219 (tt0) REVERT: B 1000 ASP cc_start: 0.8336 (t0) cc_final: 0.8049 (t0) REVERT: B 1027 ASN cc_start: 0.8595 (m-40) cc_final: 0.8159 (m-40) REVERT: B 1057 TYR cc_start: 0.8567 (m-80) cc_final: 0.8353 (m-80) REVERT: B 1088 HIS cc_start: 0.7203 (t70) cc_final: 0.6945 (t-90) outliers start: 53 outliers final: 25 residues processed: 353 average time/residue: 0.2716 time to fit residues: 126.7396 Evaluate side-chains 304 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 274 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 436 PHE Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 559 SER Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 714 LYS Chi-restraints excluded: chain B residue 739 ASN Chi-restraints excluded: chain B residue 770 LYS Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 921 TYR Chi-restraints excluded: chain B residue 963 ILE Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.6980 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.1980 chunk 33 optimal weight: 30.0000 chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 100 optimal weight: 0.5980 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 285 ASN A 413 GLN A 535 ASN A 560 ASN A 613 ASN A 653 ASN A 681 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 GLN A 879 GLN B 544 ASN B 582 GLN B 739 ASN B 750 GLN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 817 HIS B 852 GLN B 880 ASN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN B1098 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10460 Z= 0.236 Angle : 0.648 7.597 14122 Z= 0.342 Chirality : 0.043 0.148 1617 Planarity : 0.004 0.039 1796 Dihedral : 10.001 86.452 1495 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.03 % Allowed : 19.68 % Favored : 75.29 % 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: -2.37 (0.22), residues: 1270 helix: -0.40 (0.18), residues: 693 sheet: -2.80 (0.38), residues: 138 loop : -2.97 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 764 HIS 0.012 0.001 HIS B 614 PHE 0.021 0.002 PHE A 178 TYR 0.017 0.002 TYR A 656 ARG 0.009 0.001 ARG B1066 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 287 time to evaluate : 1.092 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: A 210 MET cc_start: 0.7125 (ttt) cc_final: 0.6801 (ttt) REVERT: A 299 TYR cc_start: 0.8673 (m-80) cc_final: 0.8323 (m-80) REVERT: A 308 ARG cc_start: 0.8751 (mtt180) cc_final: 0.8539 (mtt180) REVERT: A 326 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7797 (tt) REVERT: A 331 ASN cc_start: 0.8176 (t0) cc_final: 0.7911 (t0) REVERT: A 340 ARG cc_start: 0.8488 (mtm110) cc_final: 0.7670 (mtp180) REVERT: A 344 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8529 (tm-30) REVERT: A 347 LYS cc_start: 0.8978 (tptp) cc_final: 0.8678 (tptp) REVERT: A 364 GLU cc_start: 0.8072 (tt0) cc_final: 0.7296 (mt-10) REVERT: A 369 ASP cc_start: 0.7999 (t0) cc_final: 0.7638 (t0) REVERT: A 396 ARG cc_start: 0.8977 (mtm110) cc_final: 0.8644 (mtm110) REVERT: A 397 GLN cc_start: 0.9012 (mt0) cc_final: 0.8571 (mp10) REVERT: A 409 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.8209 (mm-40) REVERT: A 418 ILE cc_start: 0.8713 (tp) cc_final: 0.8301 (tt) REVERT: A 419 GLN cc_start: 0.8667 (tm-30) cc_final: 0.8362 (tm-30) REVERT: A 422 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8508 (mt-10) REVERT: A 423 LYS cc_start: 0.8705 (tttt) cc_final: 0.8449 (ttmt) REVERT: A 459 ASP cc_start: 0.7691 (p0) cc_final: 0.7133 (m-30) REVERT: A 460 MET cc_start: 0.8473 (mtp) cc_final: 0.8227 (mtp) REVERT: A 464 GLU cc_start: 0.9302 (OUTLIER) cc_final: 0.9022 (mp0) REVERT: A 466 HIS cc_start: 0.8766 (m90) cc_final: 0.8420 (m90) REVERT: A 485 MET cc_start: 0.8381 (mtm) cc_final: 0.8052 (mtm) REVERT: A 660 ASP cc_start: 0.8477 (t0) cc_final: 0.8221 (t0) REVERT: A 672 MET cc_start: 0.8044 (tpt) cc_final: 0.7536 (tpt) REVERT: A 691 ILE cc_start: 0.7943 (mt) cc_final: 0.7533 (mm) REVERT: A 705 VAL cc_start: 0.7977 (t) cc_final: 0.7747 (m) REVERT: A 726 MET cc_start: 0.8172 (ttm) cc_final: 0.7412 (tpp) REVERT: A 737 ARG cc_start: 0.8623 (mtt-85) cc_final: 0.8372 (mtt180) REVERT: A 741 LYS cc_start: 0.8312 (tptp) cc_final: 0.7970 (tptp) REVERT: A 742 ASP cc_start: 0.7938 (p0) cc_final: 0.7668 (p0) REVERT: A 758 ASP cc_start: 0.8514 (t0) cc_final: 0.8311 (t0) REVERT: A 802 VAL cc_start: 0.8656 (t) cc_final: 0.8352 (m) REVERT: A 813 MET cc_start: 0.7860 (mmt) cc_final: 0.7358 (mmt) REVERT: A 847 LYS cc_start: 0.8807 (tptt) cc_final: 0.8499 (tptp) REVERT: B 532 MET cc_start: 0.8416 (mpp) cc_final: 0.7894 (mpp) REVERT: B 535 MET cc_start: 0.7410 (ttm) cc_final: 0.7004 (ttm) REVERT: B 553 ASP cc_start: 0.8428 (t0) cc_final: 0.7888 (t0) REVERT: B 554 MET cc_start: 0.8537 (mmm) cc_final: 0.8257 (mmm) REVERT: B 573 ARG cc_start: 0.7830 (ttt180) cc_final: 0.7628 (ttm110) REVERT: B 582 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7725 (pt0) REVERT: B 586 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8264 (mmmm) REVERT: B 653 GLN cc_start: 0.8461 (tp40) cc_final: 0.8150 (tp40) REVERT: B 672 ILE cc_start: 0.8356 (tt) cc_final: 0.8104 (mt) REVERT: B 674 GLU cc_start: 0.8382 (tt0) cc_final: 0.8007 (tt0) REVERT: B 699 LYS cc_start: 0.9127 (mttt) cc_final: 0.8857 (mtmm) REVERT: B 718 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8138 (mm-30) REVERT: B 784 PHE cc_start: 0.8650 (t80) cc_final: 0.8438 (t80) REVERT: B 791 HIS cc_start: 0.9077 (t-90) cc_final: 0.8843 (t70) REVERT: B 794 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8210 (tm-30) REVERT: B 796 ARG cc_start: 0.8691 (mtp-110) cc_final: 0.8222 (mtt180) REVERT: B 798 GLN cc_start: 0.8085 (tp-100) cc_final: 0.7669 (tp40) REVERT: B 853 GLU cc_start: 0.8246 (tp30) cc_final: 0.8016 (tp30) REVERT: B 860 LYS cc_start: 0.8655 (tttm) cc_final: 0.8316 (ttmt) REVERT: B 884 LEU cc_start: 0.8568 (mt) cc_final: 0.8311 (mm) REVERT: B 899 MET cc_start: 0.7759 (tpt) cc_final: 0.7382 (tpt) REVERT: B 917 GLN cc_start: 0.8340 (mt0) cc_final: 0.7651 (mt0) REVERT: B 925 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7701 (mm-30) REVERT: B 926 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8242 (tm-30) REVERT: B 938 ARG cc_start: 0.8653 (tpm170) cc_final: 0.8362 (tpm170) REVERT: B 949 ARG cc_start: 0.8045 (mtm110) cc_final: 0.7756 (mtm110) REVERT: B 956 LEU cc_start: 0.8275 (mt) cc_final: 0.8059 (mt) REVERT: B 1000 ASP cc_start: 0.8206 (t0) cc_final: 0.7892 (t0) REVERT: B 1027 ASN cc_start: 0.8375 (m-40) cc_final: 0.8109 (m110) REVERT: B 1057 TYR cc_start: 0.8352 (m-80) cc_final: 0.8074 (m-80) REVERT: B 1077 ASP cc_start: 0.8427 (t0) cc_final: 0.7551 (t70) REVERT: B 1081 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8367 (mm-30) REVERT: B 1092 GLU cc_start: 0.8584 (mm-30) cc_final: 0.7982 (mm-30) outliers start: 57 outliers final: 32 residues processed: 326 average time/residue: 0.2715 time to fit residues: 117.4476 Evaluate side-chains 317 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 281 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 560 ASN Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 777 PHE Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 841 ILE Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 628 ILE Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 30.0000 chunk 96 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 116 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 GLN A 409 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 ASN A 653 ASN ** A 665 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 718 GLN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10460 Z= 0.254 Angle : 0.618 7.627 14122 Z= 0.325 Chirality : 0.043 0.177 1617 Planarity : 0.004 0.046 1796 Dihedral : 9.194 89.666 1462 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.12 % Allowed : 22.68 % Favored : 72.20 % 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: -1.74 (0.23), residues: 1270 helix: 0.13 (0.19), residues: 688 sheet: -2.57 (0.40), residues: 138 loop : -2.70 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 764 HIS 0.011 0.001 HIS B 614 PHE 0.021 0.002 PHE A 436 TYR 0.016 0.002 TYR A 656 ARG 0.005 0.000 ARG B 734 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 280 time to evaluate : 1.116 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: A 210 MET cc_start: 0.7090 (ttt) cc_final: 0.6742 (ttt) REVERT: A 299 TYR cc_start: 0.8653 (m-80) cc_final: 0.8244 (m-80) REVERT: A 308 ARG cc_start: 0.8750 (mtt180) cc_final: 0.8537 (mtt180) REVERT: A 326 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7874 (tt) REVERT: A 331 ASN cc_start: 0.8177 (t0) cc_final: 0.7765 (t0) REVERT: A 347 LYS cc_start: 0.8964 (tptp) cc_final: 0.8667 (tptp) REVERT: A 349 PRO cc_start: 0.8905 (Cg_endo) cc_final: 0.8701 (Cg_exo) REVERT: A 369 ASP cc_start: 0.7935 (t0) cc_final: 0.7548 (t0) REVERT: A 382 ARG cc_start: 0.8129 (ttt180) cc_final: 0.7719 (ttp-110) REVERT: A 396 ARG cc_start: 0.8982 (mtm110) cc_final: 0.8600 (mtm110) REVERT: A 397 GLN cc_start: 0.9009 (mt0) cc_final: 0.8802 (mm-40) REVERT: A 418 ILE cc_start: 0.8739 (tp) cc_final: 0.8334 (tt) REVERT: A 419 GLN cc_start: 0.8673 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 422 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8501 (mt-10) REVERT: A 423 LYS cc_start: 0.8706 (tttt) cc_final: 0.8453 (ttmt) REVERT: A 459 ASP cc_start: 0.7698 (p0) cc_final: 0.7092 (m-30) REVERT: A 464 GLU cc_start: 0.9293 (OUTLIER) cc_final: 0.9045 (mt-10) REVERT: A 466 HIS cc_start: 0.8761 (m90) cc_final: 0.8422 (m90) REVERT: A 485 MET cc_start: 0.8415 (mtm) cc_final: 0.8068 (mtm) REVERT: A 569 GLU cc_start: 0.8265 (mt-10) cc_final: 0.8062 (pt0) REVERT: A 589 VAL cc_start: 0.8494 (p) cc_final: 0.8245 (t) REVERT: A 626 GLU cc_start: 0.8393 (pm20) cc_final: 0.8147 (pm20) REVERT: A 672 MET cc_start: 0.7983 (tpt) cc_final: 0.7461 (tpt) REVERT: A 705 VAL cc_start: 0.7936 (t) cc_final: 0.7680 (m) REVERT: A 726 MET cc_start: 0.8174 (ttm) cc_final: 0.7363 (tpp) REVERT: A 737 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8394 (mtt180) REVERT: A 741 LYS cc_start: 0.8324 (tptp) cc_final: 0.7989 (tptp) REVERT: A 742 ASP cc_start: 0.7979 (p0) cc_final: 0.7705 (p0) REVERT: A 802 VAL cc_start: 0.8645 (t) cc_final: 0.8376 (m) REVERT: A 813 MET cc_start: 0.7822 (mmt) cc_final: 0.7338 (mmt) REVERT: A 847 LYS cc_start: 0.8789 (tptt) cc_final: 0.8517 (tptp) REVERT: B 532 MET cc_start: 0.8386 (mpp) cc_final: 0.7890 (mpp) REVERT: B 534 PHE cc_start: 0.8079 (m-80) cc_final: 0.7835 (m-10) REVERT: B 535 MET cc_start: 0.7391 (ttm) cc_final: 0.6985 (ttm) REVERT: B 554 MET cc_start: 0.8502 (mmm) cc_final: 0.8208 (mmm) REVERT: B 573 ARG cc_start: 0.7831 (ttt180) cc_final: 0.7591 (ttm170) REVERT: B 586 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8235 (mmmm) REVERT: B 620 ASP cc_start: 0.8621 (t0) cc_final: 0.8214 (t0) REVERT: B 649 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7519 (tmtt) REVERT: B 672 ILE cc_start: 0.8317 (tt) cc_final: 0.8087 (mt) REVERT: B 674 GLU cc_start: 0.8321 (tt0) cc_final: 0.7925 (tt0) REVERT: B 695 LYS cc_start: 0.8857 (tptp) cc_final: 0.8437 (pttt) REVERT: B 699 LYS cc_start: 0.9131 (mttt) cc_final: 0.8842 (mtmm) REVERT: B 718 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8172 (mm-30) REVERT: B 791 HIS cc_start: 0.9034 (t-90) cc_final: 0.8763 (t70) REVERT: B 794 GLN cc_start: 0.8449 (tm-30) cc_final: 0.8189 (tm-30) REVERT: B 796 ARG cc_start: 0.8692 (mtp-110) cc_final: 0.8388 (mtp180) REVERT: B 798 GLN cc_start: 0.8063 (tp-100) cc_final: 0.7627 (tp40) REVERT: B 853 GLU cc_start: 0.8315 (tp30) cc_final: 0.8014 (tp30) REVERT: B 863 ARG cc_start: 0.7954 (ptp-170) cc_final: 0.7729 (mtm180) REVERT: B 899 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7308 (tpt) REVERT: B 917 GLN cc_start: 0.8295 (mt0) cc_final: 0.7671 (mt0) REVERT: B 925 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 926 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 938 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8441 (tpm170) REVERT: B 949 ARG cc_start: 0.8061 (mtm110) cc_final: 0.7783 (ttm-80) REVERT: B 1000 ASP cc_start: 0.8187 (t0) cc_final: 0.7852 (t0) REVERT: B 1016 GLU cc_start: 0.8287 (tp30) cc_final: 0.7798 (tp30) REVERT: B 1027 ASN cc_start: 0.8390 (m-40) cc_final: 0.8094 (m110) REVERT: B 1057 TYR cc_start: 0.8415 (m-80) cc_final: 0.8046 (m-80) REVERT: B 1077 ASP cc_start: 0.8371 (t0) cc_final: 0.7306 (t0) REVERT: B 1081 GLU cc_start: 0.8587 (mm-30) cc_final: 0.8350 (mm-30) REVERT: B 1092 GLU cc_start: 0.8608 (mm-30) cc_final: 0.8006 (mm-30) outliers start: 58 outliers final: 37 residues processed: 319 average time/residue: 0.2640 time to fit residues: 113.4738 Evaluate side-chains 315 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 273 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 552 THR Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 692 GLN Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 878 VAL Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1072 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 0.2980 chunk 33 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 ASN B 582 GLN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10460 Z= 0.330 Angle : 0.621 7.752 14122 Z= 0.329 Chirality : 0.045 0.182 1617 Planarity : 0.004 0.042 1796 Dihedral : 8.689 88.772 1457 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 20.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 6.62 % Allowed : 22.68 % Favored : 70.70 % 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: -1.47 (0.23), residues: 1270 helix: 0.32 (0.19), residues: 689 sheet: -2.46 (0.40), residues: 138 loop : -2.52 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 807 HIS 0.012 0.001 HIS B 614 PHE 0.036 0.002 PHE B 709 TYR 0.015 0.002 TYR A 656 ARG 0.004 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 273 time to evaluate : 1.227 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: A 210 MET cc_start: 0.7027 (ttt) cc_final: 0.6685 (ttt) REVERT: A 299 TYR cc_start: 0.8682 (m-80) cc_final: 0.8259 (m-80) REVERT: A 326 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7952 (tt) REVERT: A 331 ASN cc_start: 0.8152 (t0) cc_final: 0.7772 (t0) REVERT: A 344 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 347 LYS cc_start: 0.8933 (tptp) cc_final: 0.8606 (tptp) REVERT: A 382 ARG cc_start: 0.8132 (ttt180) cc_final: 0.7726 (ttp-110) REVERT: A 396 ARG cc_start: 0.8986 (mtm110) cc_final: 0.8609 (mtm110) REVERT: A 397 GLN cc_start: 0.9010 (mt0) cc_final: 0.8809 (mm-40) REVERT: A 418 ILE cc_start: 0.8751 (tp) cc_final: 0.8325 (tt) REVERT: A 419 GLN cc_start: 0.8675 (tm-30) cc_final: 0.8354 (tm-30) REVERT: A 422 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8528 (mt-10) REVERT: A 423 LYS cc_start: 0.8764 (tttt) cc_final: 0.8509 (ttmt) REVERT: A 459 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7036 (m-30) REVERT: A 464 GLU cc_start: 0.9280 (OUTLIER) cc_final: 0.9009 (mt-10) REVERT: A 466 HIS cc_start: 0.8771 (m90) cc_final: 0.8415 (m90) REVERT: A 485 MET cc_start: 0.8463 (mtm) cc_final: 0.8144 (mtm) REVERT: A 523 PHE cc_start: 0.5835 (OUTLIER) cc_final: 0.5381 (t80) REVERT: A 589 VAL cc_start: 0.8285 (p) cc_final: 0.8077 (t) REVERT: A 626 GLU cc_start: 0.8400 (pm20) cc_final: 0.8118 (pm20) REVERT: A 672 MET cc_start: 0.7933 (tpt) cc_final: 0.7473 (tpt) REVERT: A 691 ILE cc_start: 0.7785 (mt) cc_final: 0.7499 (pt) REVERT: A 705 VAL cc_start: 0.7997 (t) cc_final: 0.7745 (m) REVERT: A 726 MET cc_start: 0.8139 (ttm) cc_final: 0.7582 (ttm) REVERT: A 737 ARG cc_start: 0.8591 (mtt-85) cc_final: 0.8320 (mtt180) REVERT: A 741 LYS cc_start: 0.8366 (tptp) cc_final: 0.8014 (tptp) REVERT: A 742 ASP cc_start: 0.8014 (p0) cc_final: 0.7776 (p0) REVERT: A 802 VAL cc_start: 0.8639 (t) cc_final: 0.8365 (m) REVERT: A 813 MET cc_start: 0.7808 (mmt) cc_final: 0.7327 (mmt) REVERT: A 847 LYS cc_start: 0.8790 (tptt) cc_final: 0.8516 (tptp) REVERT: B 532 MET cc_start: 0.8406 (mpp) cc_final: 0.7920 (mpp) REVERT: B 547 ILE cc_start: 0.7947 (mm) cc_final: 0.7642 (mt) REVERT: B 586 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8227 (mmmm) REVERT: B 620 ASP cc_start: 0.8699 (t0) cc_final: 0.8299 (t0) REVERT: B 636 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7485 (tm-30) REVERT: B 649 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7504 (tmtt) REVERT: B 672 ILE cc_start: 0.8284 (tt) cc_final: 0.7973 (mt) REVERT: B 674 GLU cc_start: 0.8282 (tt0) cc_final: 0.7919 (tt0) REVERT: B 699 LYS cc_start: 0.9152 (mttt) cc_final: 0.8878 (mtmm) REVERT: B 704 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8518 (mmmm) REVERT: B 718 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8204 (mm-30) REVERT: B 794 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8230 (pt0) REVERT: B 796 ARG cc_start: 0.8713 (mtp-110) cc_final: 0.8376 (mtt180) REVERT: B 798 GLN cc_start: 0.8077 (tp-100) cc_final: 0.7526 (tp-100) REVERT: B 853 GLU cc_start: 0.8330 (tp30) cc_final: 0.8078 (tp30) REVERT: B 855 ARG cc_start: 0.7856 (ptm160) cc_final: 0.7550 (ptm160) REVERT: B 926 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 938 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8487 (tpm170) REVERT: B 949 ARG cc_start: 0.8069 (mtm110) cc_final: 0.7775 (ttm-80) REVERT: B 1000 ASP cc_start: 0.8186 (t0) cc_final: 0.7836 (t0) REVERT: B 1027 ASN cc_start: 0.8325 (m-40) cc_final: 0.8072 (m110) REVERT: B 1057 TYR cc_start: 0.8428 (m-80) cc_final: 0.8098 (m-80) REVERT: B 1077 ASP cc_start: 0.8311 (t0) cc_final: 0.7591 (t70) REVERT: B 1081 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8353 (mm-30) REVERT: B 1092 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8012 (mm-30) outliers start: 75 outliers final: 48 residues processed: 322 average time/residue: 0.2531 time to fit residues: 110.3079 Evaluate side-chains 318 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 264 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 339 GLN Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 699 SER Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 640 LEU Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 785 ILE Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1034 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1100 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 0.0070 chunk 51 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN B 582 GLN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10460 Z= 0.241 Angle : 0.595 10.827 14122 Z= 0.311 Chirality : 0.043 0.181 1617 Planarity : 0.004 0.042 1796 Dihedral : 8.302 85.873 1456 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 6.09 % Allowed : 24.62 % Favored : 69.29 % 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: -1.22 (0.23), residues: 1270 helix: 0.52 (0.20), residues: 686 sheet: -2.38 (0.40), residues: 137 loop : -2.37 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 764 HIS 0.005 0.001 HIS B 984 PHE 0.025 0.002 PHE B 709 TYR 0.015 0.001 TYR B1011 ARG 0.002 0.000 ARG A 444 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2540 Ramachandran restraints generated. 1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 272 time to evaluate : 1.168 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: A 210 MET cc_start: 0.6975 (ttt) cc_final: 0.6640 (ttt) REVERT: A 299 TYR cc_start: 0.8655 (m-80) cc_final: 0.8205 (m-80) REVERT: A 326 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7827 (tt) REVERT: A 331 ASN cc_start: 0.8137 (t0) cc_final: 0.7709 (t0) REVERT: A 347 LYS cc_start: 0.8927 (tptp) cc_final: 0.8628 (tptp) REVERT: A 382 ARG cc_start: 0.8092 (ttt180) cc_final: 0.7705 (ttp-110) REVERT: A 396 ARG cc_start: 0.8978 (mtm110) cc_final: 0.8600 (mtm110) REVERT: A 418 ILE cc_start: 0.8734 (tp) cc_final: 0.8276 (tt) REVERT: A 419 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8362 (tm-30) REVERT: A 422 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8492 (mt-10) REVERT: A 423 LYS cc_start: 0.8730 (tttt) cc_final: 0.8477 (ttmt) REVERT: A 458 LEU cc_start: 0.7935 (pp) cc_final: 0.7616 (pp) REVERT: A 459 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.6973 (m-30) REVERT: A 464 GLU cc_start: 0.9272 (OUTLIER) cc_final: 0.9026 (mt-10) REVERT: A 466 HIS cc_start: 0.8734 (m90) cc_final: 0.8376 (m90) REVERT: A 485 MET cc_start: 0.8468 (mtm) cc_final: 0.8144 (mtm) REVERT: A 523 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5355 (t80) REVERT: A 569 GLU cc_start: 0.8305 (mt-10) cc_final: 0.8100 (pt0) REVERT: A 589 VAL cc_start: 0.8235 (p) cc_final: 0.8004 (t) REVERT: A 626 GLU cc_start: 0.8383 (pm20) cc_final: 0.8087 (pm20) REVERT: A 672 MET cc_start: 0.7803 (tpt) cc_final: 0.7377 (tpt) REVERT: A 705 VAL cc_start: 0.7929 (t) cc_final: 0.7665 (m) REVERT: A 726 MET cc_start: 0.8151 (ttm) cc_final: 0.7827 (tpp) REVERT: A 728 GLU cc_start: 0.8065 (tt0) cc_final: 0.7537 (mm-30) REVERT: A 737 ARG cc_start: 0.8565 (mtt-85) cc_final: 0.8297 (mtt180) REVERT: A 741 LYS cc_start: 0.8329 (tptp) cc_final: 0.7986 (tptp) REVERT: A 742 ASP cc_start: 0.7988 (p0) cc_final: 0.7764 (p0) REVERT: A 802 VAL cc_start: 0.8651 (t) cc_final: 0.8407 (m) REVERT: A 813 MET cc_start: 0.7802 (mmt) cc_final: 0.7330 (mmt) REVERT: A 847 LYS cc_start: 0.8775 (tptt) cc_final: 0.8482 (tptp) REVERT: B 532 MET cc_start: 0.8253 (mpp) cc_final: 0.7758 (mpp) REVERT: B 586 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8219 (mmmm) REVERT: B 617 LYS cc_start: 0.8893 (mmmt) cc_final: 0.8669 (mmmt) REVERT: B 620 ASP cc_start: 0.8656 (t0) cc_final: 0.8257 (t0) REVERT: B 649 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7347 (tmtt) REVERT: B 672 ILE cc_start: 0.8245 (tt) cc_final: 0.7998 (mt) REVERT: B 674 GLU cc_start: 0.8243 (tt0) cc_final: 0.7900 (tt0) REVERT: B 699 LYS cc_start: 0.9114 (mttt) cc_final: 0.8851 (mtmm) REVERT: B 703 PHE cc_start: 0.7582 (m-10) cc_final: 0.7329 (m-80) REVERT: B 718 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8177 (mm-30) REVERT: B 796 ARG cc_start: 0.8692 (mtp-110) cc_final: 0.8355 (mtt180) REVERT: B 798 GLN cc_start: 0.8027 (tp-100) cc_final: 0.7671 (tp-100) REVERT: B 853 GLU cc_start: 0.8344 (tp30) cc_final: 0.8098 (tp30) REVERT: B 855 ARG cc_start: 0.7821 (ptm160) cc_final: 0.7543 (ptm160) REVERT: B 926 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8194 (tm-30) REVERT: B 938 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8365 (tpm170) REVERT: B 949 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7750 (ttm-80) REVERT: B 991 TYR cc_start: 0.8455 (t80) cc_final: 0.8061 (t80) REVERT: B 1000 ASP cc_start: 0.8154 (t0) cc_final: 0.7817 (t0) REVERT: B 1027 ASN cc_start: 0.8312 (m-40) cc_final: 0.8091 (m110) REVERT: B 1057 TYR cc_start: 0.8328 (m-80) cc_final: 0.8052 (m-80) REVERT: B 1077 ASP cc_start: 0.8231 (t0) cc_final: 0.7719 (t0) REVERT: B 1081 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8340 (mm-30) REVERT: B 1092 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8014 (mm-30) outliers start: 69 outliers final: 49 residues processed: 315 average time/residue: 0.2482 time to fit residues: 105.0997 Evaluate side-chains 328 residues out of total 1133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 273 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 421 LEU Chi-restraints excluded: chain A residue 428 HIS Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain A residue 464 GLU Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 641 CYS Chi-restraints excluded: chain A residue 644 VAL Chi-restraints excluded: chain A residue 681 GLN Chi-restraints excluded: chain A residue 684 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 752 ARG Chi-restraints excluded: chain A residue 772 THR Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 812 THR Chi-restraints excluded: chain A residue 926 ILE Chi-restraints excluded: chain B residue 538 ASN Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 582 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 649 LYS Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 659 VAL Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 707 SER Chi-restraints excluded: chain B residue 778 SER Chi-restraints excluded: chain B residue 782 SER Chi-restraints excluded: chain B residue 802 ASP Chi-restraints excluded: chain B residue 819 HIS Chi-restraints excluded: chain B residue 825 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 899 MET Chi-restraints excluded: chain B residue 938 ARG Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1023 HIS Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain B residue 1070 LEU Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain B residue 1100 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/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-5370/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-5370/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-5370/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-5370/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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-5370/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-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1477, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1379, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1260, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.4119 > 50: distance: 47 - 68: 29.473 distance: 52 - 79: 27.265 distance: 63 - 68: 27.806 distance: 68 - 69: 31.461 distance: 69 - 70: 13.347 distance: 69 - 72: 10.185 distance: 70 - 71: 15.960 distance: 70 - 79: 21.055 distance: 72 - 73: 29.932 distance: 73 - 74: 34.185 distance: 74 - 75: 23.599 distance: 75 - 76: 18.342 distance: 76 - 77: 25.288 distance: 76 - 78: 21.448 distance: 79 - 80: 23.764 distance: 80 - 81: 56.653 distance: 80 - 83: 42.387 distance: 81 - 82: 46.941 distance: 81 - 87: 49.030 distance: 83 - 84: 19.525 distance: 84 - 85: 56.486 distance: 84 - 86: 40.057 distance: 87 - 88: 30.031 distance: 88 - 89: 41.788 distance: 88 - 91: 33.160 distance: 89 - 90: 40.346 distance: 89 - 95: 30.054 distance: 91 - 92: 14.041 distance: 92 - 94: 40.138 distance: 95 - 96: 39.549 distance: 96 - 97: 38.131 distance: 96 - 99: 44.113 distance: 97 - 98: 37.680 distance: 97 - 104: 5.733 distance: 99 - 100: 24.933 distance: 100 - 101: 19.146 distance: 101 - 102: 30.711 distance: 102 - 103: 40.940 distance: 104 - 105: 48.560 distance: 105 - 106: 32.334 distance: 106 - 107: 22.086 distance: 108 - 109: 19.080 distance: 109 - 110: 17.457 distance: 109 - 112: 10.180 distance: 110 - 111: 15.165 distance: 110 - 117: 12.803 distance: 112 - 113: 4.751 distance: 113 - 114: 6.262 distance: 114 - 115: 5.523 distance: 114 - 116: 9.227 distance: 117 - 118: 15.866 distance: 118 - 119: 30.257 distance: 118 - 121: 19.010 distance: 119 - 120: 10.876 distance: 119 - 124: 25.585 distance: 120 - 142: 27.793 distance: 121 - 122: 34.784 distance: 121 - 123: 19.436 distance: 124 - 125: 20.402 distance: 125 - 126: 16.292 distance: 125 - 128: 3.555 distance: 126 - 127: 17.365 distance: 126 - 129: 17.330 distance: 127 - 148: 11.176 distance: 129 - 130: 14.652 distance: 130 - 131: 23.502 distance: 130 - 133: 35.390 distance: 131 - 132: 30.797 distance: 131 - 136: 37.405 distance: 132 - 154: 28.370 distance: 133 - 134: 7.503 distance: 133 - 135: 36.439 distance: 136 - 137: 32.317 distance: 137 - 138: 42.272 distance: 137 - 140: 12.671 distance: 138 - 139: 29.879 distance: 138 - 142: 21.320 distance: 139 - 160: 19.343 distance: 140 - 141: 34.410