Starting phenix.real_space_refine on Mon Jul 6 15:47:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jl2_22370/07_2026/7jl2_22370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jl2_22370/07_2026/7jl2_22370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jl2_22370/07_2026/7jl2_22370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jl2_22370/07_2026/7jl2_22370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jl2_22370/07_2026/7jl2_22370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jl2_22370/07_2026/7jl2_22370.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7jl2_22370/07_2026/7jl2_22370.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jl2_22370/07_2026/7jl2_22370.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 17661 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 3 6.06 5 Al 3 5.89 5 P 94 5.49 5 Mg 3 5.21 5 S 126 5.16 5 C 13691 2.51 5 N 3854 2.21 5 O 4342 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22128 Number of models: 1 Model: "" Number of chains: 11 Chain: "X" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 944 Classifications: {'RNA': 44} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 25, 'rna3p_pyr': 18} Link IDs: {'rna2p': 1, 'rna3p': 42} Chain: "Y" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 925 Classifications: {'RNA': 44} Modifications used: {'rna3p_pur': 18, 'rna3p_pyr': 26} Link IDs: {'rna3p': 43} Chain: "A" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 1408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 1432 Chain: "C" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 1408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 1432 Chain: "E" Number of atoms: 5311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 662, 5311 Classifications: {'peptide': 662} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 640} Chain breaks: 8 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "F" Number of atoms: 1408 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 Conformer: "B" Number of residues, atoms: 180, 1398 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 167} Chain breaks: 1 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'GLN:plan1': 3, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 bond proxies already assigned to first conformer: 1432 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6372 SG CYS A 907 84.451 54.137 76.421 1.00181.77 S ATOM 6395 SG CYS A 910 86.208 51.144 75.913 1.00194.53 S ATOM 6728 SG CYS A 962 84.298 52.526 72.877 1.00190.33 S ATOM 6743 SG CYS A 964 82.507 50.685 75.575 1.00196.45 S ATOM 13091 SG CYS C 907 109.597 83.124 123.362 1.00191.35 S ATOM 13114 SG CYS C 910 112.674 84.733 122.867 1.00198.31 S ATOM 13447 SG CYS C 962 111.206 82.904 119.821 1.00189.02 S ATOM 13462 SG CYS C 964 112.950 81.014 122.515 1.00195.39 S ATOM 19810 SG CYS E 907 54.307 77.760 29.630 1.00180.73 S ATOM 19833 SG CYS E 910 51.411 75.846 29.129 1.00197.41 S ATOM 20166 SG CYS E 962 52.686 77.823 26.089 1.00201.33 S ATOM 20181 SG CYS E 964 50.757 79.518 28.787 1.00210.14 S Time building chain proxies: 5.39, per 1000 atoms: 0.24 Number of scatterers: 22128 At special positions: 0 Unit cell: (134.672, 165.75, 163.679, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 3 29.99 S 126 16.00 P 94 15.00 Al 3 13.00 Mg 3 11.99 F 12 9.00 O 4342 8.00 N 3854 7.00 C 13691 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.05 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 910 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 962 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 907 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 910 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 962 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 964 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 907 " pdb=" ZN E1101 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 910 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 962 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 964 " pdb="ZN ZN E1101 " - pdb=" SG CYS E 907 " Number of angles added : 18 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4806 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 21 sheets defined 44.6% alpha, 15.0% beta 28 base pairs and 53 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 309 through 317 Processing helix chain 'A' and resid 318 through 321 removed outlier: 3.587A pdb=" N GLU A 321 " --> pdb=" O PRO A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 318 through 321' Processing helix chain 'A' and resid 334 through 354 removed outlier: 3.736A pdb=" N VAL A 338 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 377 removed outlier: 3.639A pdb=" N VAL A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 399 through 407 Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 433 through 437 Processing helix chain 'A' and resid 445 through 448 Processing helix chain 'A' and resid 452 through 473 removed outlier: 3.721A pdb=" N ILE A 457 " --> pdb=" O VAL A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 524 through 532 Processing helix chain 'A' and resid 548 through 565 removed outlier: 4.303A pdb=" N GLU A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS A 565 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 575 through 593 Processing helix chain 'A' and resid 597 through 617 Processing helix chain 'A' and resid 618 through 640 removed outlier: 4.002A pdb=" N ALA A 622 " --> pdb=" O ARG A 618 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 639 " --> pdb=" O ASP A 635 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A 640 " --> pdb=" O LYS A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 692 removed outlier: 3.762A pdb=" N MET A 677 " --> pdb=" O ASP A 673 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU A 679 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU A 682 " --> pdb=" O THR A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 716 Processing helix chain 'A' and resid 727 through 741 removed outlier: 3.844A pdb=" N ASN A 741 " --> pdb=" O TRP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 747 removed outlier: 4.325A pdb=" N ALA A 745 " --> pdb=" O ASN A 741 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 747 " --> pdb=" O LYS A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 781 Processing helix chain 'A' and resid 790 through 793 Processing helix chain 'A' and resid 813 through 823 removed outlier: 4.151A pdb=" N ALA A 819 " --> pdb=" O ALA A 815 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA A 823 " --> pdb=" O ALA A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 862 Processing helix chain 'A' and resid 865 through 895 removed outlier: 3.532A pdb=" N ILE A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 939 removed outlier: 3.794A pdb=" N TYR A 939 " --> pdb=" O PHE A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 987 Processing helix chain 'B' and resid 322 through 328 removed outlier: 4.149A pdb=" N GLN B 328 " --> pdb=" O ARG B 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 317 Processing helix chain 'C' and resid 318 through 321 removed outlier: 3.587A pdb=" N GLU C 321 " --> pdb=" O PRO C 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 318 through 321' Processing helix chain 'C' and resid 334 through 354 removed outlier: 3.737A pdb=" N VAL C 338 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 377 removed outlier: 3.639A pdb=" N VAL C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU C 376 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE C 377 " --> pdb=" O PHE C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 399 through 407 Processing helix chain 'C' and resid 414 through 422 Processing helix chain 'C' and resid 433 through 437 Processing helix chain 'C' and resid 445 through 448 Processing helix chain 'C' and resid 452 through 473 removed outlier: 3.722A pdb=" N ILE C 457 " --> pdb=" O VAL C 453 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 514 Processing helix chain 'C' and resid 524 through 532 Processing helix chain 'C' and resid 548 through 565 removed outlier: 4.301A pdb=" N GLU C 552 " --> pdb=" O ASP C 548 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS C 565 " --> pdb=" O ILE C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 593 Processing helix chain 'C' and resid 597 through 617 Processing helix chain 'C' and resid 618 through 640 removed outlier: 4.002A pdb=" N ALA C 622 " --> pdb=" O ARG C 618 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 639 " --> pdb=" O ASP C 635 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL C 640 " --> pdb=" O LYS C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 673 through 692 removed outlier: 3.762A pdb=" N MET C 677 " --> pdb=" O ASP C 673 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 679 " --> pdb=" O PHE C 675 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU C 682 " --> pdb=" O THR C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 698 through 716 Processing helix chain 'C' and resid 727 through 741 removed outlier: 3.844A pdb=" N ASN C 741 " --> pdb=" O TRP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 747 removed outlier: 4.325A pdb=" N ALA C 745 " --> pdb=" O ASN C 741 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL C 747 " --> pdb=" O LYS C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 767 through 781 Processing helix chain 'C' and resid 790 through 793 Processing helix chain 'C' and resid 813 through 823 removed outlier: 4.151A pdb=" N ALA C 819 " --> pdb=" O ALA C 815 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA C 823 " --> pdb=" O ALA C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 840 through 862 Processing helix chain 'C' and resid 865 through 895 removed outlier: 3.533A pdb=" N ILE C 881 " --> pdb=" O GLN C 877 " (cutoff:3.500A) Processing helix chain 'C' and resid 932 through 939 removed outlier: 3.795A pdb=" N TYR C 939 " --> pdb=" O PHE C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 987 Processing helix chain 'D' and resid 322 through 327 Processing helix chain 'D' and resid 328 through 330 No H-bonds generated for 'chain 'D' and resid 328 through 330' Processing helix chain 'E' and resid 309 through 317 Processing helix chain 'E' and resid 318 through 321 removed outlier: 3.587A pdb=" N GLU E 321 " --> pdb=" O PRO E 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 318 through 321' Processing helix chain 'E' and resid 334 through 354 removed outlier: 3.737A pdb=" N VAL E 338 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 377 removed outlier: 3.638A pdb=" N VAL E 369 " --> pdb=" O LYS E 365 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLU E 370 " --> pdb=" O VAL E 366 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU E 376 " --> pdb=" O LEU E 372 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE E 377 " --> pdb=" O PHE E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 382 Processing helix chain 'E' and resid 399 through 407 Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 433 through 437 Processing helix chain 'E' and resid 445 through 448 Processing helix chain 'E' and resid 452 through 473 removed outlier: 3.721A pdb=" N ILE E 457 " --> pdb=" O VAL E 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 514 Processing helix chain 'E' and resid 524 through 532 Processing helix chain 'E' and resid 548 through 565 removed outlier: 4.302A pdb=" N GLU E 552 " --> pdb=" O ASP E 548 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N CYS E 565 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 575 through 593 Processing helix chain 'E' and resid 597 through 617 Processing helix chain 'E' and resid 618 through 640 removed outlier: 4.003A pdb=" N ALA E 622 " --> pdb=" O ARG E 618 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 639 " --> pdb=" O ASP E 635 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL E 640 " --> pdb=" O LYS E 636 " (cutoff:3.500A) Processing helix chain 'E' and resid 673 through 692 removed outlier: 3.762A pdb=" N MET E 677 " --> pdb=" O ASP E 673 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU E 679 " --> pdb=" O PHE E 675 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU E 682 " --> pdb=" O THR E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 716 Processing helix chain 'E' and resid 727 through 741 removed outlier: 3.844A pdb=" N ASN E 741 " --> pdb=" O TRP E 737 " (cutoff:3.500A) Processing helix chain 'E' and resid 741 through 747 removed outlier: 4.325A pdb=" N ALA E 745 " --> pdb=" O ASN E 741 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL E 747 " --> pdb=" O LYS E 743 " (cutoff:3.500A) Processing helix chain 'E' and resid 767 through 781 Processing helix chain 'E' and resid 790 through 793 Processing helix chain 'E' and resid 813 through 823 removed outlier: 4.151A pdb=" N ALA E 819 " --> pdb=" O ALA E 815 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA E 823 " --> pdb=" O ALA E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 840 through 862 Processing helix chain 'E' and resid 865 through 895 removed outlier: 3.532A pdb=" N ILE E 881 " --> pdb=" O GLN E 877 " (cutoff:3.500A) Processing helix chain 'E' and resid 932 through 939 removed outlier: 3.794A pdb=" N TYR E 939 " --> pdb=" O PHE E 935 " (cutoff:3.500A) Processing helix chain 'E' and resid 983 through 987 Processing helix chain 'F' and resid 322 through 327 Processing helix chain 'F' and resid 328 through 330 No H-bonds generated for 'chain 'F' and resid 328 through 330' Processing sheet with id=AA1, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.755A pdb=" N GLY A 486 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE A 440 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU A 487 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE A 442 " --> pdb=" O LEU A 487 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL A 359 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N SER A 412 " --> pdb=" O VAL A 359 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL A 361 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 536 through 542 removed outlier: 6.544A pdb=" N VAL A 804 " --> pdb=" O VAL A 831 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL A 833 " --> pdb=" O VAL A 804 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG A 806 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N HIS A 835 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE A 722 " --> pdb=" O ILE A 805 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR A 807 " --> pdb=" O ILE A 722 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE A 724 " --> pdb=" O TYR A 807 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY A 721 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA A 788 " --> pdb=" O GLY A 721 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE A 723 " --> pdb=" O ALA A 788 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 913 through 916 removed outlier: 6.669A pdb=" N PHE A 905 " --> pdb=" O ALA A 914 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 998 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 920 through 923 Processing sheet with id=AA5, first strand: chain 'A' and resid 940 through 942 removed outlier: 4.382A pdb=" N GLY A 969 " --> pdb=" O ILE A 960 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 344 through 347 removed outlier: 3.556A pdb=" N TYR B 475 " --> pdb=" O PHE B 464 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N SER B 466 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 372 through 374 Processing sheet with id=AA8, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.754A pdb=" N GLY C 486 " --> pdb=" O ILE C 325 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ILE C 440 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU C 487 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE C 442 " --> pdb=" O LEU C 487 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL C 359 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N SER C 412 " --> pdb=" O VAL C 359 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL C 361 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 536 through 542 removed outlier: 6.544A pdb=" N VAL C 804 " --> pdb=" O VAL C 831 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL C 833 " --> pdb=" O VAL C 804 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG C 806 " --> pdb=" O VAL C 833 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N HIS C 835 " --> pdb=" O ARG C 806 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE C 722 " --> pdb=" O ILE C 805 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N TYR C 807 " --> pdb=" O ILE C 722 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE C 724 " --> pdb=" O TYR C 807 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY C 721 " --> pdb=" O LEU C 786 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA C 788 " --> pdb=" O GLY C 721 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ILE C 723 " --> pdb=" O ALA C 788 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 913 through 916 removed outlier: 6.669A pdb=" N PHE C 905 " --> pdb=" O ALA C 914 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS C 998 " --> pdb=" O VAL C 989 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 920 through 923 Processing sheet with id=AB3, first strand: chain 'C' and resid 940 through 942 removed outlier: 4.382A pdb=" N GLY C 969 " --> pdb=" O ILE C 960 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 344 through 347 removed outlier: 3.730A pdb=" N TRP D 386 " --> pdb=" O MET D 453 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET D 453 " --> pdb=" O TRP D 386 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TYR D 475 " --> pdb=" O PHE D 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER D 466 " --> pdb=" O PRO D 473 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 372 through 374 Processing sheet with id=AB6, first strand: chain 'E' and resid 325 through 328 removed outlier: 3.754A pdb=" N GLY E 486 " --> pdb=" O ILE E 325 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE E 440 " --> pdb=" O LEU E 485 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU E 487 " --> pdb=" O ILE E 440 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE E 442 " --> pdb=" O LEU E 487 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N VAL E 359 " --> pdb=" O ILE E 410 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N SER E 412 " --> pdb=" O VAL E 359 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL E 361 " --> pdb=" O SER E 412 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 536 through 542 removed outlier: 6.544A pdb=" N VAL E 804 " --> pdb=" O VAL E 831 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N VAL E 833 " --> pdb=" O VAL E 804 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ARG E 806 " --> pdb=" O VAL E 833 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N HIS E 835 " --> pdb=" O ARG E 806 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE E 722 " --> pdb=" O ILE E 805 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N TYR E 807 " --> pdb=" O ILE E 722 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N PHE E 724 " --> pdb=" O TYR E 807 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY E 721 " --> pdb=" O LEU E 786 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ALA E 788 " --> pdb=" O GLY E 721 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ILE E 723 " --> pdb=" O ALA E 788 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 913 through 916 removed outlier: 6.669A pdb=" N PHE E 905 " --> pdb=" O ALA E 914 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS E 998 " --> pdb=" O VAL E 989 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 920 through 923 Processing sheet with id=AC1, first strand: chain 'E' and resid 940 through 942 removed outlier: 4.382A pdb=" N GLY E 969 " --> pdb=" O ILE E 960 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 344 through 347 removed outlier: 3.680A pdb=" N TRP F 386 " --> pdb=" O MET F 453 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET F 453 " --> pdb=" O TRP F 386 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR F 475 " --> pdb=" O PHE F 464 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER F 466 " --> pdb=" O PRO F 473 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 372 through 374 964 hydrogen bonds defined for protein. 2715 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 142 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 53 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 2.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6190 1.33 - 1.46: 4853 1.46 - 1.58: 11300 1.58 - 1.70: 186 1.70 - 1.82: 207 Bond restraints: 22736 Sorted by residual: bond pdb=" CA LYS A 782 " pdb=" C LYS A 782 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.48e-02 4.57e+03 2.64e+01 bond pdb=" CA LYS E 782 " pdb=" C LYS E 782 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.48e-02 4.57e+03 2.62e+01 bond pdb=" CA LYS C 782 " pdb=" C LYS C 782 " ideal model delta sigma weight residual 1.523 1.599 -0.076 1.48e-02 4.57e+03 2.62e+01 bond pdb=" F1 ALF E1103 " pdb="AL ALF E1103 " ideal model delta sigma weight residual 1.684 1.781 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" F1 ALF C1103 " pdb="AL ALF C1103 " ideal model delta sigma weight residual 1.684 1.781 -0.097 2.00e-02 2.50e+03 2.34e+01 ... (remaining 22731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.16: 31104 14.16 - 28.31: 15 28.31 - 42.47: 0 42.47 - 56.63: 0 56.63 - 70.78: 6 Bond angle restraints: 31125 Sorted by residual: angle pdb=" F1 ALF E1103 " pdb="AL ALF E1103 " pdb=" F2 ALF E1103 " ideal model delta sigma weight residual 108.68 179.46 -70.78 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F1 ALF A1103 " pdb="AL ALF A1103 " pdb=" F2 ALF A1103 " ideal model delta sigma weight residual 108.68 179.44 -70.76 3.00e+00 1.11e-01 5.56e+02 angle pdb=" F1 ALF C1103 " pdb="AL ALF C1103 " pdb=" F2 ALF C1103 " ideal model delta sigma weight residual 108.68 179.42 -70.74 3.00e+00 1.11e-01 5.56e+02 angle pdb=" F3 ALF C1103 " pdb="AL ALF C1103 " pdb=" F4 ALF C1103 " ideal model delta sigma weight residual 109.63 179.53 -69.90 3.00e+00 1.11e-01 5.43e+02 angle pdb=" F3 ALF A1103 " pdb="AL ALF A1103 " pdb=" F4 ALF A1103 " ideal model delta sigma weight residual 109.63 179.52 -69.89 3.00e+00 1.11e-01 5.43e+02 ... (remaining 31120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 13345 34.56 - 69.13: 244 69.13 - 103.69: 30 103.69 - 138.25: 3 138.25 - 172.82: 4 Dihedral angle restraints: 13626 sinusoidal: 6237 harmonic: 7389 Sorted by residual: dihedral pdb=" C5' ADP A1102 " pdb=" O5' ADP A1102 " pdb=" PA ADP A1102 " pdb=" O2A ADP A1102 " ideal model delta sinusoidal sigma weight residual -60.00 83.47 -143.47 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP E1102 " pdb=" O5' ADP E1102 " pdb=" PA ADP E1102 " pdb=" O2A ADP E1102 " ideal model delta sinusoidal sigma weight residual -60.00 83.43 -143.43 1 2.00e+01 2.50e-03 4.33e+01 dihedral pdb=" C5' ADP C1102 " pdb=" O5' ADP C1102 " pdb=" PA ADP C1102 " pdb=" O2A ADP C1102 " ideal model delta sinusoidal sigma weight residual -60.00 83.40 -143.40 1 2.00e+01 2.50e-03 4.33e+01 ... (remaining 13623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3110 0.066 - 0.132: 416 0.132 - 0.198: 19 0.198 - 0.265: 3 0.265 - 0.331: 3 Chirality restraints: 3551 Sorted by residual: chirality pdb=" CA LYS A 782 " pdb=" N LYS A 782 " pdb=" C LYS A 782 " pdb=" CB LYS A 782 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" CA LYS E 782 " pdb=" N LYS E 782 " pdb=" C LYS E 782 " pdb=" CB LYS E 782 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA LYS C 782 " pdb=" N LYS C 782 " pdb=" C LYS C 782 " pdb=" CB LYS C 782 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.70e+00 ... (remaining 3548 not shown) Planarity restraints: 3631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A X 15 " 0.042 2.00e-02 2.50e+03 1.88e-02 9.73e+00 pdb=" N9 A X 15 " -0.043 2.00e-02 2.50e+03 pdb=" C8 A X 15 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A X 15 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A X 15 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A X 15 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A X 15 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A X 15 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A X 15 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A X 15 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A X 15 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 790 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C THR A 790 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A 790 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 791 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 790 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C THR C 790 " 0.034 2.00e-02 2.50e+03 pdb=" O THR C 790 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL C 791 " -0.011 2.00e-02 2.50e+03 ... (remaining 3628 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 209 2.49 - 3.09: 16866 3.09 - 3.70: 35180 3.70 - 4.30: 48551 4.30 - 4.90: 75054 Nonbonded interactions: 175860 Sorted by model distance: nonbonded pdb=" F4 ALF C1103 " pdb="MG MG C1104 " model vdw 1.889 2.120 nonbonded pdb=" F4 ALF E1103 " pdb="MG MG E1104 " model vdw 1.889 2.120 nonbonded pdb=" F4 ALF A1103 " pdb="MG MG A1104 " model vdw 1.889 2.120 nonbonded pdb=" F1 ALF E1103 " pdb="MG MG E1104 " model vdw 1.891 2.120 nonbonded pdb=" F1 ALF A1103 " pdb="MG MG A1104 " model vdw 1.892 2.120 ... (remaining 175855 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) selection = (chain 'D' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) selection = (chain 'F' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) } 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=0.00 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.030 Process input model: 25.240 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.006 0.097 22748 Z= 0.300 Angle : 1.358 70.785 31143 Z= 0.577 Chirality : 0.045 0.331 3551 Planarity : 0.004 0.034 3631 Dihedral : 14.410 172.817 8820 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.55 % Allowed : 0.87 % Favored : 98.59 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2466 helix: 0.45 (0.16), residues: 927 sheet: 0.18 (0.23), residues: 501 loop : -1.38 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 323 TYR 0.030 0.002 TYR E 732 PHE 0.020 0.002 PHE A 724 TRP 0.030 0.002 TRP F 386 HIS 0.013 0.002 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00614 / 0.30 (22736) covalent geometry : angle 1.34828 / 0.58 (31125) hydrogen bonds : bond 0.16850 / 9.97 ( 1035) hydrogen bonds : angle 7.01083 / 4.01 ( 2857) metal coordination : bond 0.00789 / 0.49 ( 12) metal coordination : angle 6.93425 / 2.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7620 (tpp) cc_final: 0.7337 (tpp) REVERT: A 854 MET cc_start: 0.9086 (tmm) cc_final: 0.8605 (tmm) REVERT: A 968 TRP cc_start: 0.6673 (m-10) cc_final: 0.6388 (m-10) REVERT: A 972 MET cc_start: 0.6772 (ptp) cc_final: 0.6359 (ptm) REVERT: B 368 PHE cc_start: 0.8094 (m-10) cc_final: 0.7869 (m-10) REVERT: C 313 MET cc_start: 0.7721 (tpp) cc_final: 0.7276 (tpp) REVERT: C 567 MET cc_start: 0.5579 (mmp) cc_final: 0.5299 (mmp) REVERT: C 683 ASN cc_start: 0.8047 (m110) cc_final: 0.7779 (m-40) REVERT: C 878 MET cc_start: 0.9219 (mtp) cc_final: 0.8976 (mtp) REVERT: C 968 TRP cc_start: 0.6761 (m-10) cc_final: 0.6286 (m-10) REVERT: D 368 PHE cc_start: 0.8003 (m-10) cc_final: 0.7802 (m-10) REVERT: D 415 ASN cc_start: 0.7213 (m-40) cc_final: 0.6875 (m-40) REVERT: D 478 HIS cc_start: 0.8080 (m-70) cc_final: 0.7667 (m90) REVERT: E 313 MET cc_start: 0.7451 (tpp) cc_final: 0.6993 (tpp) REVERT: E 683 ASN cc_start: 0.7768 (m110) cc_final: 0.7388 (m-40) REVERT: F 368 PHE cc_start: 0.7941 (m-10) cc_final: 0.7690 (m-80) outliers start: 12 outliers final: 6 residues processed: 208 average time/residue: 0.1409 time to fit residues: 47.5255 Evaluate side-chains 156 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 7.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 ASN ** A 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN C 524 ASN ** C 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 GLN ** D 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 ASN E 835 HIS E 966 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.060079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.046933 restraints weight = 331466.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.048763 restraints weight = 129803.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049611 restraints weight = 66124.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.049659 restraints weight = 51138.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050061 restraints weight = 47877.358| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22748 Z= 0.120 Angle : 0.610 8.290 31143 Z= 0.305 Chirality : 0.041 0.138 3551 Planarity : 0.003 0.028 3631 Dihedral : 8.621 162.979 3774 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2466 helix: 1.59 (0.17), residues: 948 sheet: 0.26 (0.24), residues: 522 loop : -1.16 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 331 TYR 0.014 0.001 TYR A 732 PHE 0.013 0.001 PHE C 680 TRP 0.020 0.001 TRP B 386 HIS 0.006 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 (22736) covalent geometry : angle 0.59233 / 0.30 (31125) hydrogen bonds : bond 0.04430 / 2.60 ( 1035) hydrogen bonds : angle 4.85931 / 2.76 ( 2857) metal coordination : bond 0.00662 / 0.42 ( 12) metal coordination : angle 6.07560 / 2.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.673 Fit side-chains revert: symmetry clash REVERT: A 313 MET cc_start: 0.7410 (tpp) cc_final: 0.6983 (tpt) REVERT: A 526 ASP cc_start: 0.8300 (t0) cc_final: 0.8031 (p0) REVERT: A 567 MET cc_start: 0.5530 (mmp) cc_final: 0.5246 (mmm) REVERT: A 854 MET cc_start: 0.9015 (tmm) cc_final: 0.8243 (tmm) REVERT: A 968 TRP cc_start: 0.6676 (m-10) cc_final: 0.6273 (m-10) REVERT: B 343 HIS cc_start: 0.7958 (m170) cc_final: 0.7628 (m170) REVERT: B 345 TYR cc_start: 0.7100 (m-80) cc_final: 0.6867 (m-80) REVERT: B 415 ASN cc_start: 0.7268 (m-40) cc_final: 0.7027 (m-40) REVERT: B 453 MET cc_start: 0.7445 (ppp) cc_final: 0.6726 (ppp) REVERT: C 306 LEU cc_start: 0.7954 (mp) cc_final: 0.7288 (tp) REVERT: C 313 MET cc_start: 0.7643 (tpp) cc_final: 0.7394 (tpt) REVERT: C 567 MET cc_start: 0.5153 (mmp) cc_final: 0.4905 (mmp) REVERT: C 854 MET cc_start: 0.9061 (tmm) cc_final: 0.8777 (tmm) REVERT: C 864 MET cc_start: 0.7619 (mtp) cc_final: 0.6965 (ttm) REVERT: C 878 MET cc_start: 0.8934 (mtp) cc_final: 0.8605 (mtp) REVERT: C 879 GLN cc_start: 0.8818 (tt0) cc_final: 0.8607 (mm-40) REVERT: C 926 MET cc_start: 0.8488 (mmt) cc_final: 0.8151 (tpp) REVERT: C 968 TRP cc_start: 0.6982 (m-10) cc_final: 0.6486 (m-10) REVERT: C 971 MET cc_start: 0.7093 (tpp) cc_final: 0.6639 (tpp) REVERT: D 415 ASN cc_start: 0.7313 (m-40) cc_final: 0.6871 (m-40) REVERT: D 461 CYS cc_start: 0.6439 (m) cc_final: 0.6152 (m) REVERT: D 478 HIS cc_start: 0.8093 (m-70) cc_final: 0.7500 (m-70) REVERT: D 497 LEU cc_start: 0.9116 (tp) cc_final: 0.8915 (tp) REVERT: E 313 MET cc_start: 0.7443 (tpp) cc_final: 0.7115 (tpp) REVERT: E 854 MET cc_start: 0.8937 (tmm) cc_final: 0.8241 (tmm) REVERT: E 878 MET cc_start: 0.8729 (mtp) cc_final: 0.8413 (mtp) REVERT: E 968 TRP cc_start: 0.6702 (m-10) cc_final: 0.5932 (m-10) REVERT: F 343 HIS cc_start: 0.8140 (m170) cc_final: 0.7756 (m170) REVERT: F 354 LYS cc_start: 0.7503 (pttt) cc_final: 0.7228 (pttm) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1423 time to fit residues: 52.1671 Evaluate side-chains 169 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 68 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 135 optimal weight: 0.8980 chunk 180 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 8.9990 chunk 228 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 464 GLN A 835 HIS A 966 GLN B 428 GLN B 478 HIS ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 464 GLN C 835 HIS D 383 HIS ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 464 GLN ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.057362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.043989 restraints weight = 322918.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045978 restraints weight = 132171.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046642 restraints weight = 66114.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046625 restraints weight = 54729.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.046991 restraints weight = 51852.835| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22748 Z= 0.208 Angle : 0.695 11.462 31143 Z= 0.356 Chirality : 0.044 0.168 3551 Planarity : 0.004 0.035 3631 Dihedral : 9.129 162.723 3774 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.17), residues: 2466 helix: 1.37 (0.17), residues: 942 sheet: -0.13 (0.23), residues: 531 loop : -1.24 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 822 TYR 0.019 0.002 TYR A 461 PHE 0.019 0.002 PHE A 681 TRP 0.019 0.002 TRP B 386 HIS 0.008 0.002 HIS D 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 (22736) covalent geometry : angle 0.67580 / 0.35 (31125) hydrogen bonds : bond 0.04911 / 2.88 ( 1035) hydrogen bonds : angle 5.18461 / 2.90 ( 2857) metal coordination : bond 0.01248 / 0.79 ( 12) metal coordination : angle 6.82384 / 2.27 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7489 (tpp) cc_final: 0.7102 (tpt) REVERT: A 854 MET cc_start: 0.9068 (tmm) cc_final: 0.8324 (tmm) REVERT: A 878 MET cc_start: 0.9158 (mtm) cc_final: 0.8716 (mtm) REVERT: A 968 TRP cc_start: 0.6917 (m-10) cc_final: 0.6525 (m-10) REVERT: B 415 ASN cc_start: 0.7274 (m-40) cc_final: 0.7043 (m-40) REVERT: B 453 MET cc_start: 0.7393 (ppp) cc_final: 0.6444 (ppp) REVERT: C 306 LEU cc_start: 0.7950 (mp) cc_final: 0.7429 (tp) REVERT: C 313 MET cc_start: 0.7792 (tpp) cc_final: 0.7569 (tpt) REVERT: C 854 MET cc_start: 0.9073 (tmm) cc_final: 0.8524 (tmm) REVERT: C 864 MET cc_start: 0.7713 (mtp) cc_final: 0.7050 (ttm) REVERT: C 878 MET cc_start: 0.9075 (mtp) cc_final: 0.8830 (mtp) REVERT: C 968 TRP cc_start: 0.6854 (m-10) cc_final: 0.6289 (m-10) REVERT: C 971 MET cc_start: 0.7199 (tpp) cc_final: 0.6855 (tpp) REVERT: D 343 HIS cc_start: 0.8280 (m-70) cc_final: 0.7935 (m90) REVERT: D 368 PHE cc_start: 0.7822 (m-80) cc_final: 0.7298 (m-80) REVERT: D 386 TRP cc_start: 0.6393 (p90) cc_final: 0.5970 (p90) REVERT: D 415 ASN cc_start: 0.7341 (m-40) cc_final: 0.6896 (m-40) REVERT: D 461 CYS cc_start: 0.6383 (m) cc_final: 0.6138 (m) REVERT: E 313 MET cc_start: 0.7460 (tpp) cc_final: 0.7207 (tpp) REVERT: E 445 CYS cc_start: 0.7843 (p) cc_final: 0.7627 (p) REVERT: E 854 MET cc_start: 0.8989 (tmm) cc_final: 0.8423 (tmm) REVERT: E 878 MET cc_start: 0.8962 (mtp) cc_final: 0.8599 (mtp) REVERT: E 968 TRP cc_start: 0.6847 (m-10) cc_final: 0.6173 (m-10) REVERT: E 972 MET cc_start: 0.6111 (ptp) cc_final: 0.5741 (ptp) REVERT: F 343 HIS cc_start: 0.8209 (m170) cc_final: 0.7769 (m170) REVERT: F 345 TYR cc_start: 0.7451 (m-80) cc_final: 0.7212 (m-80) REVERT: F 368 PHE cc_start: 0.7826 (m-80) cc_final: 0.7599 (m-80) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1490 time to fit residues: 50.6881 Evaluate side-chains 175 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 249 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 144 optimal weight: 4.9990 chunk 152 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 131 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN A 562 GLN A 862 GLN ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN C 371 GLN ** C 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 531 GLN C 562 GLN C 862 GLN ** C 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 562 GLN E 862 GLN ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.056880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.043805 restraints weight = 353529.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.045237 restraints weight = 146197.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.045979 restraints weight = 75533.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.046499 restraints weight = 58488.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.046578 restraints weight = 56141.493| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 22748 Z= 0.243 Angle : 0.728 14.051 31143 Z= 0.365 Chirality : 0.045 0.190 3551 Planarity : 0.004 0.034 3631 Dihedral : 9.240 164.606 3774 Min Nonbonded Distance : 1.734 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.18 % Allowed : 4.01 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.17), residues: 2466 helix: 1.16 (0.16), residues: 954 sheet: -0.38 (0.23), residues: 534 loop : -1.44 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 822 TYR 0.027 0.002 TYR B 475 PHE 0.018 0.002 PHE A 681 TRP 0.036 0.002 TRP B 386 HIS 0.005 0.002 HIS A 974 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.24 (22736) covalent geometry : angle 0.69564 / 0.36 (31125) hydrogen bonds : bond 0.04920 / 2.89 ( 1035) hydrogen bonds : angle 5.26131 / 2.96 ( 2857) metal coordination : bond 0.01097 / 0.68 ( 12) metal coordination : angle 8.91695 / 2.97 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7573 (tpp) cc_final: 0.7207 (tpt) REVERT: A 854 MET cc_start: 0.9080 (tmm) cc_final: 0.8402 (tmm) REVERT: A 968 TRP cc_start: 0.6743 (m-10) cc_final: 0.6439 (m-10) REVERT: B 345 TYR cc_start: 0.7950 (m-10) cc_final: 0.7186 (m-80) REVERT: B 368 PHE cc_start: 0.8093 (m-80) cc_final: 0.7375 (m-80) REVERT: B 415 ASN cc_start: 0.7278 (m-40) cc_final: 0.7040 (m-40) REVERT: C 306 LEU cc_start: 0.8014 (mp) cc_final: 0.7299 (tp) REVERT: C 854 MET cc_start: 0.9036 (tmm) cc_final: 0.8384 (tmm) REVERT: C 878 MET cc_start: 0.9036 (mtp) cc_final: 0.8768 (mtp) REVERT: C 968 TRP cc_start: 0.6890 (m-10) cc_final: 0.6270 (m-10) REVERT: C 971 MET cc_start: 0.7422 (tpp) cc_final: 0.7068 (tpp) REVERT: D 343 HIS cc_start: 0.8140 (m-70) cc_final: 0.7821 (m-70) REVERT: D 368 PHE cc_start: 0.7664 (m-80) cc_final: 0.7120 (m-80) REVERT: D 386 TRP cc_start: 0.6541 (p90) cc_final: 0.5432 (p90) REVERT: D 415 ASN cc_start: 0.7271 (m-40) cc_final: 0.6870 (m-40) REVERT: D 453 MET cc_start: 0.7188 (ppp) cc_final: 0.6255 (ppp) REVERT: D 461 CYS cc_start: 0.6270 (m) cc_final: 0.6019 (m) REVERT: D 492 LEU cc_start: 0.8047 (tp) cc_final: 0.7828 (tp) REVERT: D 497 LEU cc_start: 0.9176 (tp) cc_final: 0.8939 (tp) REVERT: E 313 MET cc_start: 0.7482 (tpp) cc_final: 0.7273 (tpp) REVERT: E 854 MET cc_start: 0.8936 (tmm) cc_final: 0.8283 (tmm) REVERT: E 878 MET cc_start: 0.8960 (mtp) cc_final: 0.8614 (mtp) REVERT: E 968 TRP cc_start: 0.6890 (m-10) cc_final: 0.6055 (m100) REVERT: F 408 ARG cc_start: 0.7941 (ptm160) cc_final: 0.7685 (ptm-80) REVERT: F 475 TYR cc_start: 0.6932 (t80) cc_final: 0.6694 (t80) outliers start: 4 outliers final: 1 residues processed: 209 average time/residue: 0.1542 time to fit residues: 51.2866 Evaluate side-chains 169 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 168 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 181 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 254 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 238 optimal weight: 0.1980 chunk 117 optimal weight: 20.0000 chunk 125 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 233 optimal weight: 0.7980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN A 446 HIS A 468 ASN C 862 GLN D 393 HIS E 371 GLN E 974 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.058971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.045570 restraints weight = 351673.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.047813 restraints weight = 139289.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048599 restraints weight = 67762.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048523 restraints weight = 53203.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048680 restraints weight = 51076.833| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 22748 Z= 0.113 Angle : 0.594 10.874 31143 Z= 0.292 Chirality : 0.041 0.171 3551 Planarity : 0.003 0.033 3631 Dihedral : 8.365 163.475 3774 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.05 % Allowed : 2.01 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.18), residues: 2466 helix: 1.71 (0.17), residues: 948 sheet: -0.28 (0.24), residues: 531 loop : -1.15 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 689 TYR 0.011 0.001 TYR E 623 PHE 0.017 0.001 PHE D 379 TRP 0.025 0.001 TRP B 386 HIS 0.004 0.001 HIS A 835 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 (22736) covalent geometry : angle 0.57159 / 0.29 (31125) hydrogen bonds : bond 0.03795 / 2.22 ( 1035) hydrogen bonds : angle 4.63166 / 2.61 ( 2857) metal coordination : bond 0.00821 / 0.51 ( 12) metal coordination : angle 6.70856 / 2.24 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 228 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7487 (tpp) cc_final: 0.7128 (tpt) REVERT: A 632 GLU cc_start: 0.8747 (pt0) cc_final: 0.8542 (pt0) REVERT: A 766 MET cc_start: 0.8595 (tmm) cc_final: 0.8321 (tmm) REVERT: A 854 MET cc_start: 0.9045 (tmm) cc_final: 0.8281 (tmm) REVERT: A 968 TRP cc_start: 0.6420 (m-10) cc_final: 0.6116 (m-10) REVERT: B 345 TYR cc_start: 0.7722 (m-10) cc_final: 0.7498 (m-80) REVERT: B 368 PHE cc_start: 0.8160 (m-80) cc_final: 0.7369 (m-80) REVERT: B 369 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7508 (tm-30) REVERT: B 415 ASN cc_start: 0.7181 (m-40) cc_final: 0.6881 (m-40) REVERT: B 453 MET cc_start: 0.7056 (ppp) cc_final: 0.6350 (ppp) REVERT: B 475 TYR cc_start: 0.6504 (t80) cc_final: 0.6283 (t80) REVERT: C 458 MET cc_start: 0.9250 (mmp) cc_final: 0.9039 (mmp) REVERT: C 632 GLU cc_start: 0.8671 (pt0) cc_final: 0.8446 (pt0) REVERT: C 766 MET cc_start: 0.8631 (tmm) cc_final: 0.8407 (tmm) REVERT: C 854 MET cc_start: 0.9060 (tmm) cc_final: 0.8542 (tmm) REVERT: C 864 MET cc_start: 0.7603 (mtp) cc_final: 0.6956 (ttm) REVERT: C 878 MET cc_start: 0.8963 (mtp) cc_final: 0.8732 (mtp) REVERT: C 968 TRP cc_start: 0.6599 (m-10) cc_final: 0.5960 (m100) REVERT: C 971 MET cc_start: 0.6970 (tpp) cc_final: 0.6628 (tpp) REVERT: D 343 HIS cc_start: 0.8156 (m-70) cc_final: 0.7910 (m-70) REVERT: D 415 ASN cc_start: 0.7302 (m-40) cc_final: 0.6876 (m-40) REVERT: D 453 MET cc_start: 0.6802 (ppp) cc_final: 0.6536 (pmm) REVERT: D 461 CYS cc_start: 0.6458 (m) cc_final: 0.6162 (m) REVERT: D 497 LEU cc_start: 0.9222 (tp) cc_final: 0.9019 (tp) REVERT: E 313 MET cc_start: 0.7487 (tpp) cc_final: 0.7125 (tpp) REVERT: E 854 MET cc_start: 0.9003 (tmm) cc_final: 0.8352 (tmm) REVERT: E 869 TYR cc_start: 0.8905 (t80) cc_final: 0.8650 (t80) REVERT: E 908 LYS cc_start: 0.6648 (mtmt) cc_final: 0.6355 (mttt) REVERT: E 968 TRP cc_start: 0.6564 (m-10) cc_final: 0.5605 (m-10) REVERT: F 343 HIS cc_start: 0.8014 (m170) cc_final: 0.7765 (m170) REVERT: F 368 PHE cc_start: 0.7757 (m-80) cc_final: 0.7093 (m-80) REVERT: F 408 ARG cc_start: 0.7959 (ptm160) cc_final: 0.7666 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1452 time to fit residues: 53.7470 Evaluate side-chains 181 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 15 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 110 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 170 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 253 optimal weight: 0.9980 chunk 208 optimal weight: 0.0370 chunk 144 optimal weight: 5.9990 chunk 249 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 2.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 ASN B 343 HIS C 446 HIS ** C 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.058441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.045353 restraints weight = 261889.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.047004 restraints weight = 125773.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048098 restraints weight = 66421.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047973 restraints weight = 50824.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.048074 restraints weight = 48268.602| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22748 Z= 0.142 Angle : 0.610 10.235 31143 Z= 0.304 Chirality : 0.042 0.170 3551 Planarity : 0.004 0.035 3631 Dihedral : 8.410 164.662 3774 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2466 helix: 1.75 (0.17), residues: 954 sheet: -0.34 (0.24), residues: 510 loop : -1.29 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 323 TYR 0.014 0.002 TYR A 461 PHE 0.012 0.001 PHE A 681 TRP 0.029 0.001 TRP B 386 HIS 0.009 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (22736) covalent geometry : angle 0.59107 / 0.30 (31125) hydrogen bonds : bond 0.03970 / 2.32 ( 1035) hydrogen bonds : angle 4.60245 / 2.59 ( 2857) metal coordination : bond 0.00770 / 0.48 ( 12) metal coordination : angle 6.28663 / 2.10 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 221 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7528 (tpp) cc_final: 0.7181 (tpt) REVERT: A 526 ASP cc_start: 0.8255 (t0) cc_final: 0.7937 (p0) REVERT: A 632 GLU cc_start: 0.8777 (pt0) cc_final: 0.8570 (pt0) REVERT: A 766 MET cc_start: 0.8609 (tmm) cc_final: 0.8285 (tmm) REVERT: A 816 MET cc_start: 0.7930 (ttp) cc_final: 0.7710 (tmm) REVERT: A 854 MET cc_start: 0.9029 (tmm) cc_final: 0.8740 (tmm) REVERT: A 878 MET cc_start: 0.8888 (mtm) cc_final: 0.8504 (mtp) REVERT: A 968 TRP cc_start: 0.6421 (m-10) cc_final: 0.6084 (m-10) REVERT: B 415 ASN cc_start: 0.7277 (m-40) cc_final: 0.6995 (m-40) REVERT: B 453 MET cc_start: 0.7434 (ppp) cc_final: 0.6691 (ppp) REVERT: B 475 TYR cc_start: 0.6378 (t80) cc_final: 0.6151 (t80) REVERT: C 458 MET cc_start: 0.9287 (mmp) cc_final: 0.9042 (mmp) REVERT: C 632 GLU cc_start: 0.8679 (pt0) cc_final: 0.8463 (pt0) REVERT: C 729 GLN cc_start: 0.8711 (pm20) cc_final: 0.8496 (pm20) REVERT: C 864 MET cc_start: 0.7661 (mtp) cc_final: 0.7044 (ttm) REVERT: C 908 LYS cc_start: 0.6842 (mtpt) cc_final: 0.6487 (mttt) REVERT: C 926 MET cc_start: 0.8676 (mmt) cc_final: 0.8395 (tpp) REVERT: C 968 TRP cc_start: 0.6641 (m-10) cc_final: 0.6069 (m-10) REVERT: C 971 MET cc_start: 0.7066 (tpp) cc_final: 0.6561 (tpp) REVERT: D 368 PHE cc_start: 0.7926 (m-80) cc_final: 0.7717 (m-80) REVERT: D 415 ASN cc_start: 0.7266 (m-40) cc_final: 0.6851 (m-40) REVERT: D 461 CYS cc_start: 0.6478 (m) cc_final: 0.6158 (m) REVERT: E 313 MET cc_start: 0.7402 (tpp) cc_final: 0.7074 (tpp) REVERT: E 567 MET cc_start: 0.6241 (mmt) cc_final: 0.5893 (mmm) REVERT: E 854 MET cc_start: 0.8939 (tmm) cc_final: 0.8637 (tmm) REVERT: E 869 TYR cc_start: 0.8868 (t80) cc_final: 0.8614 (t80) REVERT: E 878 MET cc_start: 0.8897 (mtp) cc_final: 0.8482 (mtp) REVERT: E 968 TRP cc_start: 0.6575 (m-10) cc_final: 0.5547 (m-10) REVERT: F 354 LYS cc_start: 0.7357 (pttt) cc_final: 0.7091 (pttm) REVERT: F 408 ARG cc_start: 0.7929 (ptm160) cc_final: 0.6826 (ttm-80) REVERT: F 475 TYR cc_start: 0.6939 (t80) cc_final: 0.6668 (t80) outliers start: 0 outliers final: 0 residues processed: 221 average time/residue: 0.1492 time to fit residues: 53.2903 Evaluate side-chains 175 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 129 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 70 optimal weight: 0.0870 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 101 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 220 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 468 ASN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.059122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.045625 restraints weight = 336704.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047912 restraints weight = 134550.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.048764 restraints weight = 65181.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048665 restraints weight = 50935.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.048957 restraints weight = 49680.667| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22748 Z= 0.115 Angle : 0.587 8.961 31143 Z= 0.288 Chirality : 0.041 0.164 3551 Planarity : 0.003 0.035 3631 Dihedral : 8.031 163.852 3774 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.05 % Allowed : 1.19 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2466 helix: 1.90 (0.17), residues: 957 sheet: -0.25 (0.24), residues: 507 loop : -1.20 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 408 TYR 0.013 0.001 TYR E 623 PHE 0.010 0.001 PHE E 550 TRP 0.030 0.001 TRP B 386 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (22736) covalent geometry : angle 0.57246 / 0.29 (31125) hydrogen bonds : bond 0.03655 / 2.13 ( 1035) hydrogen bonds : angle 4.45382 / 2.51 ( 2857) metal coordination : bond 0.00722 / 0.46 ( 12) metal coordination : angle 5.40336 / 1.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7468 (tpp) cc_final: 0.7132 (tpt) REVERT: A 526 ASP cc_start: 0.8208 (t0) cc_final: 0.7957 (p0) REVERT: A 632 GLU cc_start: 0.8711 (pt0) cc_final: 0.8502 (pt0) REVERT: A 854 MET cc_start: 0.9045 (tmm) cc_final: 0.8787 (tmm) REVERT: A 878 MET cc_start: 0.8831 (mtm) cc_final: 0.8462 (mtp) REVERT: A 968 TRP cc_start: 0.6421 (m-10) cc_final: 0.6082 (m-10) REVERT: B 344 PHE cc_start: 0.8204 (m-10) cc_final: 0.7947 (m-10) REVERT: B 345 TYR cc_start: 0.7972 (m-10) cc_final: 0.7663 (m-80) REVERT: B 368 PHE cc_start: 0.8141 (m-80) cc_final: 0.7409 (m-80) REVERT: B 415 ASN cc_start: 0.7349 (m-40) cc_final: 0.7050 (m-40) REVERT: B 453 MET cc_start: 0.7414 (ppp) cc_final: 0.6629 (ppp) REVERT: B 475 TYR cc_start: 0.6368 (t80) cc_final: 0.6143 (t80) REVERT: B 489 PHE cc_start: 0.9480 (m-10) cc_final: 0.9254 (m-10) REVERT: C 306 LEU cc_start: 0.8001 (mp) cc_final: 0.7061 (tt) REVERT: C 567 MET cc_start: 0.5893 (mmp) cc_final: 0.5634 (mmp) REVERT: C 632 GLU cc_start: 0.8664 (pt0) cc_final: 0.8437 (pt0) REVERT: C 766 MET cc_start: 0.8575 (ttp) cc_final: 0.8214 (tmm) REVERT: C 864 MET cc_start: 0.7620 (mtp) cc_final: 0.6999 (ttm) REVERT: C 926 MET cc_start: 0.8621 (mmt) cc_final: 0.8362 (tpp) REVERT: C 968 TRP cc_start: 0.6622 (m-10) cc_final: 0.6011 (m-10) REVERT: C 971 MET cc_start: 0.7016 (tpp) cc_final: 0.6775 (tpp) REVERT: D 343 HIS cc_start: 0.8175 (m-70) cc_final: 0.7906 (m-70) REVERT: D 368 PHE cc_start: 0.7886 (m-80) cc_final: 0.7609 (m-80) REVERT: D 408 ARG cc_start: 0.8046 (ptm160) cc_final: 0.7665 (tmm-80) REVERT: D 415 ASN cc_start: 0.7376 (m-40) cc_final: 0.7152 (m-40) REVERT: D 461 CYS cc_start: 0.6526 (m) cc_final: 0.6213 (m) REVERT: D 475 TYR cc_start: 0.6978 (t80) cc_final: 0.6758 (t80) REVERT: E 313 MET cc_start: 0.7471 (tpp) cc_final: 0.7133 (tpp) REVERT: E 766 MET cc_start: 0.8376 (tmm) cc_final: 0.8148 (tmm) REVERT: E 854 MET cc_start: 0.8971 (tmm) cc_final: 0.8712 (tmm) REVERT: E 968 TRP cc_start: 0.6513 (m-10) cc_final: 0.5446 (m-10) REVERT: F 354 LYS cc_start: 0.7398 (pttt) cc_final: 0.7129 (pttm) REVERT: F 408 ARG cc_start: 0.7533 (ptm160) cc_final: 0.6792 (ttm-80) REVERT: F 475 TYR cc_start: 0.7165 (t80) cc_final: 0.6816 (t80) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1487 time to fit residues: 52.5930 Evaluate side-chains 176 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 247 optimal weight: 6.9990 chunk 174 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 219 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 250 optimal weight: 0.0770 chunk 173 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 966 GLN ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.058418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.044977 restraints weight = 283203.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.046899 restraints weight = 133006.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.047752 restraints weight = 68053.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047896 restraints weight = 50256.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.048004 restraints weight = 49364.740| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22748 Z= 0.137 Angle : 0.602 9.600 31143 Z= 0.299 Chirality : 0.042 0.164 3551 Planarity : 0.004 0.036 3631 Dihedral : 8.054 164.517 3774 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.05 % Allowed : 1.28 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.18), residues: 2466 helix: 1.84 (0.17), residues: 957 sheet: -0.29 (0.24), residues: 510 loop : -1.21 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 605 TYR 0.014 0.002 TYR A 461 PHE 0.011 0.001 PHE A 681 TRP 0.031 0.001 TRP B 386 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (22736) covalent geometry : angle 0.58778 / 0.30 (31125) hydrogen bonds : bond 0.03862 / 2.26 ( 1035) hydrogen bonds : angle 4.55918 / 2.57 ( 2857) metal coordination : bond 0.00722 / 0.45 ( 12) metal coordination : angle 5.35458 / 1.78 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7477 (tpp) cc_final: 0.7149 (tpt) REVERT: A 526 ASP cc_start: 0.8290 (t0) cc_final: 0.7946 (p0) REVERT: A 632 GLU cc_start: 0.8715 (pt0) cc_final: 0.8502 (pt0) REVERT: A 766 MET cc_start: 0.8527 (tmm) cc_final: 0.8286 (tmm) REVERT: A 854 MET cc_start: 0.9056 (tmm) cc_final: 0.8757 (tmm) REVERT: A 878 MET cc_start: 0.8931 (mtm) cc_final: 0.8528 (mtp) REVERT: A 968 TRP cc_start: 0.6510 (m-10) cc_final: 0.6147 (m-10) REVERT: B 415 ASN cc_start: 0.7247 (m-40) cc_final: 0.6974 (m-40) REVERT: B 453 MET cc_start: 0.7655 (ppp) cc_final: 0.6903 (ppp) REVERT: B 475 TYR cc_start: 0.6280 (t80) cc_final: 0.6073 (t80) REVERT: B 489 PHE cc_start: 0.9534 (m-10) cc_final: 0.9271 (m-10) REVERT: C 632 GLU cc_start: 0.8639 (pt0) cc_final: 0.8406 (pt0) REVERT: C 864 MET cc_start: 0.7683 (mtp) cc_final: 0.7067 (ttm) REVERT: C 968 TRP cc_start: 0.6624 (m-10) cc_final: 0.6024 (m-10) REVERT: C 971 MET cc_start: 0.6970 (tpp) cc_final: 0.6745 (tpp) REVERT: D 343 HIS cc_start: 0.8177 (m-70) cc_final: 0.7872 (m-70) REVERT: D 408 ARG cc_start: 0.7970 (ptm160) cc_final: 0.7732 (tmm-80) REVERT: D 461 CYS cc_start: 0.6603 (m) cc_final: 0.6303 (m) REVERT: E 313 MET cc_start: 0.7385 (tpp) cc_final: 0.7062 (tpp) REVERT: E 766 MET cc_start: 0.8431 (tmm) cc_final: 0.8182 (tmm) REVERT: E 854 MET cc_start: 0.8996 (tmm) cc_final: 0.8697 (tmm) REVERT: E 968 TRP cc_start: 0.6546 (m-10) cc_final: 0.5484 (m-10) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1476 time to fit residues: 51.8875 Evaluate side-chains 166 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 152 optimal weight: 6.9990 chunk 251 optimal weight: 0.1980 chunk 151 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 210 optimal weight: 7.9990 chunk 82 optimal weight: 0.6980 chunk 189 optimal weight: 0.9980 chunk 225 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 246 optimal weight: 0.0170 overall best weight: 0.9820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS C 966 GLN D 478 HIS E 468 ASN E 921 HIS F 352 GLN ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.047442 restraints weight = 190777.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.049067 restraints weight = 102403.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.049710 restraints weight = 60466.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.050027 restraints weight = 43962.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.050241 restraints weight = 40736.920| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 22748 Z= 0.100 Angle : 0.578 10.093 31143 Z= 0.280 Chirality : 0.041 0.168 3551 Planarity : 0.003 0.038 3631 Dihedral : 7.523 163.226 3774 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2466 helix: 2.01 (0.17), residues: 960 sheet: -0.05 (0.25), residues: 504 loop : -1.13 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 408 TYR 0.015 0.001 TYR E 939 PHE 0.012 0.001 PHE E 550 TRP 0.029 0.001 TRP F 386 HIS 0.012 0.001 HIS D 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (22736) covalent geometry : angle 0.56680 / 0.28 (31125) hydrogen bonds : bond 0.03345 / 1.95 ( 1035) hydrogen bonds : angle 4.32216 / 2.45 ( 2857) metal coordination : bond 0.00585 / 0.37 ( 12) metal coordination : angle 4.64000 / 1.55 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7586 (tpp) cc_final: 0.7221 (tpt) REVERT: A 632 GLU cc_start: 0.8648 (pt0) cc_final: 0.8424 (pt0) REVERT: A 766 MET cc_start: 0.8559 (tmm) cc_final: 0.8316 (tmm) REVERT: A 854 MET cc_start: 0.9059 (tmm) cc_final: 0.8843 (tmm) REVERT: A 878 MET cc_start: 0.8914 (mtm) cc_final: 0.8465 (mtp) REVERT: A 968 TRP cc_start: 0.6560 (m-10) cc_final: 0.6194 (m-10) REVERT: B 415 ASN cc_start: 0.7267 (m-40) cc_final: 0.6986 (m-40) REVERT: B 453 MET cc_start: 0.7438 (ppp) cc_final: 0.6680 (ppp) REVERT: B 461 CYS cc_start: 0.6193 (m) cc_final: 0.5896 (m) REVERT: B 475 TYR cc_start: 0.6307 (t80) cc_final: 0.6065 (t80) REVERT: B 489 PHE cc_start: 0.9433 (m-10) cc_final: 0.9169 (m-10) REVERT: C 567 MET cc_start: 0.6105 (mmp) cc_final: 0.5886 (mmm) REVERT: C 632 GLU cc_start: 0.8662 (pt0) cc_final: 0.8450 (pt0) REVERT: C 686 MET cc_start: 0.8947 (tpt) cc_final: 0.8620 (mtt) REVERT: C 766 MET cc_start: 0.8449 (ttp) cc_final: 0.8138 (tmm) REVERT: C 864 MET cc_start: 0.7362 (mtp) cc_final: 0.6934 (ttm) REVERT: C 882 MET cc_start: 0.5073 (mpp) cc_final: 0.4828 (mpp) REVERT: C 968 TRP cc_start: 0.6573 (m-10) cc_final: 0.5915 (m-10) REVERT: C 971 MET cc_start: 0.6902 (tpp) cc_final: 0.6672 (tpp) REVERT: D 343 HIS cc_start: 0.8091 (m-70) cc_final: 0.7870 (m90) REVERT: D 368 PHE cc_start: 0.7994 (m-80) cc_final: 0.7746 (m-80) REVERT: D 408 ARG cc_start: 0.8054 (ptm160) cc_final: 0.7841 (tmm-80) REVERT: D 461 CYS cc_start: 0.6539 (m) cc_final: 0.6267 (m) REVERT: D 475 TYR cc_start: 0.7025 (t80) cc_final: 0.6791 (t80) REVERT: D 489 PHE cc_start: 0.9352 (m-10) cc_final: 0.9076 (m-80) REVERT: E 313 MET cc_start: 0.7446 (tpp) cc_final: 0.7108 (tpp) REVERT: E 468 ASN cc_start: 0.8959 (m-40) cc_final: 0.8733 (m-40) REVERT: E 766 MET cc_start: 0.8359 (tmm) cc_final: 0.8091 (tmm) REVERT: E 854 MET cc_start: 0.9014 (tmm) cc_final: 0.8787 (tmm) REVERT: E 968 TRP cc_start: 0.6628 (m-10) cc_final: 0.5576 (m100) REVERT: F 354 LYS cc_start: 0.7400 (pttt) cc_final: 0.7045 (pttm) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1488 time to fit residues: 58.3074 Evaluate side-chains 176 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 244 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 228 optimal weight: 0.7980 chunk 239 optimal weight: 7.9990 chunk 216 optimal weight: 0.6980 chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 overall best weight: 3.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS C 693 ASN E 693 ASN F 352 GLN ** F 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.058436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.044740 restraints weight = 322008.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.047301 restraints weight = 131031.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047818 restraints weight = 62962.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.047886 restraints weight = 50143.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048058 restraints weight = 49451.608| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22748 Z= 0.154 Angle : 0.628 9.077 31143 Z= 0.312 Chirality : 0.043 0.177 3551 Planarity : 0.004 0.038 3631 Dihedral : 7.862 164.726 3774 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.09 % Allowed : 0.23 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.18), residues: 2466 helix: 1.86 (0.17), residues: 957 sheet: -0.18 (0.24), residues: 507 loop : -1.20 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 689 TYR 0.016 0.002 TYR A 461 PHE 0.014 0.001 PHE C 680 TRP 0.034 0.001 TRP B 386 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (22736) covalent geometry : angle 0.61611 / 0.31 (31125) hydrogen bonds : bond 0.03836 / 2.25 ( 1035) hydrogen bonds : angle 4.52748 / 2.55 ( 2857) metal coordination : bond 0.00686 / 0.42 ( 12) metal coordination : angle 5.08169 / 1.69 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 213 time to evaluate : 0.845 Fit side-chains REVERT: A 313 MET cc_start: 0.7569 (tpp) cc_final: 0.7233 (tpt) REVERT: A 567 MET cc_start: 0.6297 (mmm) cc_final: 0.5679 (mmm) REVERT: A 632 GLU cc_start: 0.8685 (pt0) cc_final: 0.8475 (pt0) REVERT: A 677 MET cc_start: 0.8890 (mpp) cc_final: 0.8684 (mpp) REVERT: A 766 MET cc_start: 0.8630 (tmm) cc_final: 0.8374 (tmm) REVERT: A 854 MET cc_start: 0.9080 (tmm) cc_final: 0.8773 (tmm) REVERT: A 878 MET cc_start: 0.8936 (mtm) cc_final: 0.8570 (mtp) REVERT: A 968 TRP cc_start: 0.6500 (m-10) cc_final: 0.6107 (m-10) REVERT: B 368 PHE cc_start: 0.8114 (m-80) cc_final: 0.7319 (m-80) REVERT: B 415 ASN cc_start: 0.7296 (m-40) cc_final: 0.6995 (m-40) REVERT: B 453 MET cc_start: 0.7686 (ppp) cc_final: 0.6826 (ppp) REVERT: B 489 PHE cc_start: 0.9431 (m-10) cc_final: 0.9171 (m-10) REVERT: C 632 GLU cc_start: 0.8640 (pt0) cc_final: 0.8406 (pt0) REVERT: C 766 MET cc_start: 0.8544 (ttp) cc_final: 0.8187 (tmm) REVERT: C 864 MET cc_start: 0.7647 (mtp) cc_final: 0.7154 (ttm) REVERT: C 878 MET cc_start: 0.8909 (mtp) cc_final: 0.8685 (mtp) REVERT: C 968 TRP cc_start: 0.6605 (m-10) cc_final: 0.5971 (m-10) REVERT: D 343 HIS cc_start: 0.8212 (m-70) cc_final: 0.7921 (m90) REVERT: D 368 PHE cc_start: 0.7984 (m-80) cc_final: 0.7760 (m-80) REVERT: D 408 ARG cc_start: 0.7903 (ptm160) cc_final: 0.7687 (tmm-80) REVERT: D 415 ASN cc_start: 0.7372 (m-40) cc_final: 0.7166 (m-40) REVERT: D 453 MET cc_start: 0.7059 (pmm) cc_final: 0.6828 (pmm) REVERT: D 461 CYS cc_start: 0.6642 (m) cc_final: 0.6351 (m) REVERT: E 313 MET cc_start: 0.7433 (tpp) cc_final: 0.7116 (tpp) REVERT: E 683 ASN cc_start: 0.7466 (m110) cc_final: 0.7182 (m110) REVERT: E 766 MET cc_start: 0.8427 (tmm) cc_final: 0.8163 (tmm) REVERT: E 854 MET cc_start: 0.9018 (tmm) cc_final: 0.8699 (tmm) REVERT: E 968 TRP cc_start: 0.6605 (m-10) cc_final: 0.5533 (m-10) outliers start: 2 outliers final: 0 residues processed: 215 average time/residue: 0.1439 time to fit residues: 50.6166 Evaluate side-chains 166 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.0482 > 50: distance: 89 - 94: 25.745 distance: 94 - 95: 30.448 distance: 95 - 96: 9.364 distance: 95 - 98: 22.845 distance: 96 - 97: 31.211 distance: 96 - 103: 22.317 distance: 98 - 99: 27.106 distance: 99 - 100: 14.218 distance: 100 - 101: 21.429 distance: 100 - 102: 24.108 distance: 103 - 104: 4.969 distance: 104 - 105: 11.552 distance: 104 - 107: 15.009 distance: 105 - 106: 26.318 distance: 105 - 111: 26.528 distance: 107 - 108: 9.442 distance: 108 - 109: 17.159 distance: 108 - 110: 14.840 distance: 111 - 112: 20.242 distance: 111 - 117: 13.446 distance: 112 - 113: 20.061 distance: 112 - 115: 28.271 distance: 113 - 114: 30.401 distance: 113 - 118: 15.128 distance: 115 - 116: 28.488 distance: 116 - 117: 18.988 distance: 118 - 119: 9.663 distance: 119 - 120: 29.932 distance: 119 - 122: 17.558 distance: 120 - 121: 40.986 distance: 120 - 126: 21.478 distance: 122 - 123: 8.032 distance: 122 - 124: 18.450 distance: 123 - 125: 11.176 distance: 126 - 127: 26.071 distance: 127 - 128: 12.207 distance: 127 - 130: 22.700 distance: 128 - 129: 39.105 distance: 128 - 133: 27.370 distance: 130 - 131: 35.284 distance: 130 - 132: 19.345 distance: 133 - 134: 23.931 distance: 134 - 135: 39.562 distance: 134 - 137: 19.108 distance: 135 - 136: 19.009 distance: 135 - 144: 28.188 distance: 137 - 138: 19.048 distance: 138 - 139: 33.427 distance: 138 - 140: 30.650 distance: 139 - 141: 9.907 distance: 140 - 142: 23.210 distance: 141 - 143: 12.492 distance: 142 - 143: 36.525 distance: 144 - 145: 17.913 distance: 144 - 150: 27.576 distance: 145 - 146: 10.474 distance: 145 - 148: 8.444 distance: 146 - 147: 21.558 distance: 146 - 151: 11.702 distance: 148 - 149: 34.950 distance: 149 - 150: 10.514 distance: 151 - 152: 6.745 distance: 152 - 153: 3.113 distance: 152 - 155: 9.201 distance: 153 - 154: 7.410 distance: 155 - 156: 5.583 distance: 156 - 157: 9.174 distance: 156 - 158: 10.454 distance: 160 - 161: 8.445 distance: 161 - 162: 6.803 distance: 163 - 164: 4.143 distance: 164 - 165: 5.709 distance: 164 - 166: 3.192 distance: 167 - 168: 17.245 distance: 168 - 169: 9.311 distance: 168 - 171: 5.689 distance: 169 - 170: 26.929 distance: 169 - 175: 14.720 distance: 171 - 172: 9.800 distance: 172 - 173: 7.016 distance: 172 - 174: 5.839