Starting phenix.real_space_refine on Sat Mar 7 02:09:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jl2_22370/03_2026/7jl2_22370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jl2_22370/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7jl2_22370/03_2026/7jl2_22370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jl2_22370/03_2026/7jl2_22370.map" model { file = "/net/cci-nas-00/data/ceres_data/7jl2_22370/03_2026/7jl2_22370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jl2_22370/03_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-5986/lib/python3.9/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: 5.25, 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: 2.00 Conformation dependent library (CDL) restraints added in 1.1 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: 2.93 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: 4.23 Time building geometry restraints manager: 2.61 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: 13472 34.56 - 69.13: 398 69.13 - 103.69: 51 103.69 - 138.25: 3 138.25 - 172.82: 4 Dihedral angle restraints: 13928 sinusoidal: 6539 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 13925 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 25.260 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 16.275 172.817 9122 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 covalent geometry : bond 0.00614 (22736) covalent geometry : angle 1.34828 (31125) hydrogen bonds : bond 0.16850 ( 1035) hydrogen bonds : angle 7.01083 ( 2857) metal coordination : bond 0.00789 ( 12) metal coordination : angle 6.93425 ( 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 : 0.850 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: 0.1436 time to fit residues: 48.3142 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 : 0.738 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.060095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.046962 restraints weight = 331429.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.048883 restraints weight = 129755.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.049636 restraints weight = 65346.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.049684 restraints weight = 50710.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050055 restraints weight = 48066.313| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1732 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= 0.119 Angle : 0.611 8.463 31143 Z= 0.306 Chirality : 0.041 0.141 3551 Planarity : 0.004 0.028 3631 Dihedral : 14.540 161.103 4076 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % 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: 1.58 (0.17), residues: 948 sheet: 0.27 (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 D 348 TYR 0.014 0.001 TYR E 311 PHE 0.014 0.001 PHE C 680 TRP 0.021 0.001 TRP F 386 HIS 0.006 0.001 HIS B 383 Details of bonding type rmsd covalent geometry : bond 0.00245 (22736) covalent geometry : angle 0.59349 (31125) hydrogen bonds : bond 0.04399 ( 1035) hydrogen bonds : angle 4.85674 ( 2857) metal coordination : bond 0.00690 ( 12) metal coordination : angle 6.10826 ( 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 : 0.667 Fit side-chains revert: symmetry clash REVERT: A 313 MET cc_start: 0.7416 (tpp) cc_final: 0.6974 (tpt) REVERT: A 526 ASP cc_start: 0.8301 (t0) cc_final: 0.8036 (p0) REVERT: A 567 MET cc_start: 0.5517 (mmp) cc_final: 0.5234 (mmm) REVERT: A 854 MET cc_start: 0.9017 (tmm) cc_final: 0.8243 (tmm) REVERT: A 968 TRP cc_start: 0.6668 (m-10) cc_final: 0.6270 (m-10) REVERT: B 343 HIS cc_start: 0.7961 (m170) cc_final: 0.7629 (m170) REVERT: B 345 TYR cc_start: 0.7240 (m-80) cc_final: 0.6949 (m-80) REVERT: B 415 ASN cc_start: 0.7271 (m-40) cc_final: 0.7022 (m-40) REVERT: B 453 MET cc_start: 0.7449 (ppp) cc_final: 0.6730 (ppp) REVERT: C 306 LEU cc_start: 0.7953 (mp) cc_final: 0.7288 (tp) REVERT: C 313 MET cc_start: 0.7647 (tpp) cc_final: 0.7400 (tpt) REVERT: C 567 MET cc_start: 0.5147 (mmp) cc_final: 0.4898 (mmp) REVERT: C 854 MET cc_start: 0.9061 (tmm) cc_final: 0.8777 (tmm) REVERT: C 864 MET cc_start: 0.7592 (mtp) cc_final: 0.6920 (ttm) REVERT: C 878 MET cc_start: 0.8936 (mtp) cc_final: 0.8607 (mtp) REVERT: C 879 GLN cc_start: 0.8821 (tt0) cc_final: 0.8613 (mm-40) REVERT: C 926 MET cc_start: 0.8484 (mmt) cc_final: 0.8147 (tpp) REVERT: C 968 TRP cc_start: 0.7028 (m-10) cc_final: 0.6512 (m-10) REVERT: D 415 ASN cc_start: 0.7320 (m-40) cc_final: 0.6991 (m-40) REVERT: D 461 CYS cc_start: 0.6443 (m) cc_final: 0.6153 (m) REVERT: D 478 HIS cc_start: 0.8095 (m-70) cc_final: 0.7501 (m-70) REVERT: E 313 MET cc_start: 0.7466 (tpp) cc_final: 0.7133 (tpp) REVERT: E 854 MET cc_start: 0.8939 (tmm) cc_final: 0.8240 (tmm) REVERT: E 878 MET cc_start: 0.8730 (mtp) cc_final: 0.8410 (mtp) REVERT: E 968 TRP cc_start: 0.6694 (m-10) cc_final: 0.5918 (m-10) REVERT: F 343 HIS cc_start: 0.8139 (m170) cc_final: 0.7756 (m170) REVERT: F 354 LYS cc_start: 0.7509 (pttt) cc_final: 0.7231 (pttm) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1438 time to fit residues: 52.8205 Evaluate side-chains 171 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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: 20.0000 chunk 110 optimal weight: 10.0000 chunk 145 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 228 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 446 HIS A 464 GLN A 835 HIS A 966 GLN C 446 HIS C 464 GLN C 835 HIS D 383 HIS ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN E 446 HIS E 464 GLN ** 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 = 0.3324 r_free = 0.3324 target = 0.058400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.045134 restraints weight = 322657.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.046941 restraints weight = 131228.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047679 restraints weight = 67452.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047755 restraints weight = 53749.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048098 restraints weight = 49953.437| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 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 = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22748 Z= 0.161 Angle : 0.632 10.153 31143 Z= 0.322 Chirality : 0.042 0.157 3551 Planarity : 0.004 0.032 3631 Dihedral : 14.370 161.576 4076 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % 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: 0.24 (0.17), residues: 2466 helix: 1.60 (0.17), residues: 951 sheet: 0.04 (0.24), residues: 528 loop : -1.21 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 822 TYR 0.015 0.002 TYR A 461 PHE 0.015 0.002 PHE A 681 TRP 0.020 0.001 TRP B 386 HIS 0.005 0.001 HIS D 383 Details of bonding type rmsd covalent geometry : bond 0.00340 (22736) covalent geometry : angle 0.61464 (31125) hydrogen bonds : bond 0.04458 ( 1035) hydrogen bonds : angle 4.91079 ( 2857) metal coordination : bond 0.01258 ( 12) metal coordination : angle 6.21931 ( 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 214 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7503 (tpp) cc_final: 0.7089 (tpt) REVERT: A 567 MET cc_start: 0.5946 (mmp) cc_final: 0.5571 (mmm) REVERT: A 854 MET cc_start: 0.9087 (tmm) cc_final: 0.8315 (tmm) REVERT: A 968 TRP cc_start: 0.6826 (m-10) cc_final: 0.6408 (m-10) REVERT: B 343 HIS cc_start: 0.8073 (m170) cc_final: 0.7666 (m170) REVERT: B 415 ASN cc_start: 0.7196 (m-40) cc_final: 0.6962 (m-40) REVERT: B 453 MET cc_start: 0.7311 (ppp) cc_final: 0.6356 (ppp) REVERT: C 306 LEU cc_start: 0.7965 (mp) cc_final: 0.7435 (tp) REVERT: C 313 MET cc_start: 0.7773 (tpp) cc_final: 0.7539 (tpt) REVERT: C 632 GLU cc_start: 0.8790 (pt0) cc_final: 0.8576 (pt0) REVERT: C 854 MET cc_start: 0.9097 (tmm) cc_final: 0.8427 (tmm) REVERT: C 864 MET cc_start: 0.7697 (mtp) cc_final: 0.6977 (ttm) REVERT: C 878 MET cc_start: 0.9048 (mtp) cc_final: 0.8762 (mtp) REVERT: C 968 TRP cc_start: 0.6914 (m-10) cc_final: 0.6401 (m-10) REVERT: D 415 ASN cc_start: 0.7302 (m110) cc_final: 0.6875 (m-40) REVERT: D 461 CYS cc_start: 0.6280 (m) cc_final: 0.5920 (m) REVERT: D 478 HIS cc_start: 0.7958 (m-70) cc_final: 0.7272 (m-70) REVERT: E 313 MET cc_start: 0.7435 (tpp) cc_final: 0.7148 (tpp) REVERT: E 445 CYS cc_start: 0.7800 (p) cc_final: 0.7524 (p) REVERT: E 854 MET cc_start: 0.8973 (tmm) cc_final: 0.8443 (tmm) REVERT: E 878 MET cc_start: 0.8921 (mtp) cc_final: 0.8531 (mtp) REVERT: E 968 TRP cc_start: 0.6842 (m-10) cc_final: 0.5935 (m-10) REVERT: F 343 HIS cc_start: 0.8205 (m170) cc_final: 0.7836 (m170) REVERT: F 354 LYS cc_start: 0.7519 (pttt) cc_final: 0.7122 (pttm) REVERT: F 368 PHE cc_start: 0.7741 (m-80) cc_final: 0.7499 (m-80) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1516 time to fit residues: 52.4696 Evaluate side-chains 179 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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: 20.0000 chunk 69 optimal weight: 5.9990 chunk 210 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 101 optimal weight: 0.0070 chunk 164 optimal weight: 20.0000 chunk 144 optimal weight: 0.9980 chunk 152 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 131 optimal weight: 0.7980 overall best weight: 2.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN B 393 HIS C 531 GLN C 862 GLN ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 531 GLN E 966 GLN E 974 HIS F 393 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.058784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045272 restraints weight = 351559.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.047646 restraints weight = 141210.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.048198 restraints weight = 67011.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048154 restraints weight = 53213.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.048362 restraints weight = 53251.508| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 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 = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2621 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 10.431 31143 Z= 0.302 Chirality : 0.041 0.164 3551 Planarity : 0.003 0.031 3631 Dihedral : 14.244 161.089 4076 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.05 % Allowed : 3.28 % Favored : 96.67 % 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: 0.39 (0.17), residues: 2466 helix: 1.81 (0.17), residues: 948 sheet: 0.04 (0.24), residues: 507 loop : -1.15 (0.20), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 822 TYR 0.012 0.001 TYR A 461 PHE 0.012 0.001 PHE A 681 TRP 0.033 0.001 TRP B 386 HIS 0.006 0.001 HIS F 393 Details of bonding type rmsd covalent geometry : bond 0.00291 (22736) covalent geometry : angle 0.58526 (31125) hydrogen bonds : bond 0.04004 ( 1035) hydrogen bonds : angle 4.64785 ( 2857) metal coordination : bond 0.00733 ( 12) metal coordination : angle 5.93363 ( 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 225 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 224 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7532 (tpp) cc_final: 0.7147 (tpt) REVERT: A 526 ASP cc_start: 0.8394 (t0) cc_final: 0.8071 (p0) REVERT: A 766 MET cc_start: 0.8440 (tmm) cc_final: 0.8124 (tmm) REVERT: A 854 MET cc_start: 0.9032 (tmm) cc_final: 0.8797 (tmm) REVERT: A 878 MET cc_start: 0.8862 (mtm) cc_final: 0.8467 (mtp) REVERT: A 968 TRP cc_start: 0.6713 (m-10) cc_final: 0.6355 (m-10) REVERT: B 344 PHE cc_start: 0.8273 (m-10) cc_final: 0.8063 (m-10) REVERT: B 345 TYR cc_start: 0.7822 (m-10) cc_final: 0.7245 (m-80) REVERT: B 368 PHE cc_start: 0.8185 (m-80) cc_final: 0.7423 (m-80) REVERT: B 369 GLU cc_start: 0.7542 (tm-30) cc_final: 0.7314 (tm-30) REVERT: B 386 TRP cc_start: 0.6946 (p90) cc_final: 0.6596 (p90) REVERT: B 415 ASN cc_start: 0.7234 (m-40) cc_final: 0.6963 (m-40) REVERT: C 306 LEU cc_start: 0.8011 (mp) cc_final: 0.7407 (tp) REVERT: C 313 MET cc_start: 0.7848 (tpp) cc_final: 0.7618 (tpt) REVERT: C 558 MET cc_start: 0.9196 (ppp) cc_final: 0.8976 (ppp) REVERT: C 632 GLU cc_start: 0.8719 (pt0) cc_final: 0.8510 (pt0) REVERT: C 766 MET cc_start: 0.8702 (tmm) cc_final: 0.8444 (tmm) REVERT: C 864 MET cc_start: 0.7636 (mtp) cc_final: 0.7005 (ttm) REVERT: C 878 MET cc_start: 0.8928 (mtp) cc_final: 0.8619 (mtp) REVERT: C 882 MET cc_start: 0.5073 (mpp) cc_final: 0.4814 (mpp) REVERT: C 968 TRP cc_start: 0.6763 (m-10) cc_final: 0.6071 (m100) REVERT: D 343 HIS cc_start: 0.8257 (m90) cc_final: 0.7878 (m90) REVERT: D 368 PHE cc_start: 0.8032 (m-80) cc_final: 0.7827 (m-80) REVERT: D 415 ASN cc_start: 0.7272 (m110) cc_final: 0.6855 (m-40) REVERT: D 461 CYS cc_start: 0.6353 (m) cc_final: 0.6007 (m) REVERT: D 478 HIS cc_start: 0.7972 (m-70) cc_final: 0.7314 (m-70) REVERT: D 497 LEU cc_start: 0.9192 (tp) cc_final: 0.8979 (tp) REVERT: E 313 MET cc_start: 0.7475 (tpp) cc_final: 0.7217 (tpp) REVERT: E 445 CYS cc_start: 0.7894 (p) cc_final: 0.7589 (p) REVERT: E 567 MET cc_start: 0.5665 (mmp) cc_final: 0.5386 (mmp) REVERT: E 683 ASN cc_start: 0.7445 (m110) cc_final: 0.7222 (m-40) REVERT: E 854 MET cc_start: 0.8956 (tmm) cc_final: 0.8678 (tmm) REVERT: E 878 MET cc_start: 0.8847 (mtp) cc_final: 0.8403 (mtp) REVERT: E 968 TRP cc_start: 0.6738 (m-10) cc_final: 0.6060 (m-10) REVERT: F 343 HIS cc_start: 0.8203 (m170) cc_final: 0.7831 (m170) REVERT: F 354 LYS cc_start: 0.7313 (pttt) cc_final: 0.6970 (pttm) REVERT: F 368 PHE cc_start: 0.8001 (m-80) cc_final: 0.7736 (m-80) REVERT: F 475 TYR cc_start: 0.6869 (t80) cc_final: 0.6523 (t80) outliers start: 1 outliers final: 0 residues processed: 225 average time/residue: 0.1459 time to fit residues: 53.1431 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 : 0.861 ------------------------------------------------------------------------------- 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: 4.9990 chunk 188 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 254 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 238 optimal weight: 0.0270 chunk 117 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 233 optimal weight: 6.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 GLN A 862 GLN A 966 GLN C 371 GLN C 862 GLN D 343 HIS D 393 HIS E 371 GLN E 862 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.058485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.045266 restraints weight = 354118.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047076 restraints weight = 142905.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.048017 restraints weight = 71110.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.047924 restraints weight = 55888.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048182 restraints weight = 53387.657| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 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 = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22748 Z= 0.143 Angle : 0.614 11.193 31143 Z= 0.305 Chirality : 0.041 0.170 3551 Planarity : 0.004 0.035 3631 Dihedral : 14.199 162.476 4076 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 0.09 % Allowed : 2.10 % Favored : 97.81 % 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: 0.26 (0.17), residues: 2466 helix: 1.72 (0.17), residues: 954 sheet: -0.06 (0.24), residues: 510 loop : -1.24 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 689 TYR 0.014 0.001 TYR A 461 PHE 0.015 0.001 PHE F 379 TRP 0.029 0.001 TRP B 386 HIS 0.005 0.001 HIS F 393 Details of bonding type rmsd covalent geometry : bond 0.00304 (22736) covalent geometry : angle 0.59144 (31125) hydrogen bonds : bond 0.03984 ( 1035) hydrogen bonds : angle 4.66662 ( 2857) metal coordination : bond 0.00861 ( 12) metal coordination : angle 6.88808 ( 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 223 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7559 (tpp) cc_final: 0.7185 (tpt) REVERT: A 526 ASP cc_start: 0.8429 (t0) cc_final: 0.8112 (p0) REVERT: A 854 MET cc_start: 0.9075 (tmm) cc_final: 0.8823 (tmm) REVERT: A 878 MET cc_start: 0.8884 (mtm) cc_final: 0.8493 (mtp) REVERT: A 968 TRP cc_start: 0.6548 (m-10) cc_final: 0.6226 (m-10) REVERT: B 368 PHE cc_start: 0.8159 (m-80) cc_final: 0.7357 (m-80) REVERT: B 369 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7439 (tm-30) REVERT: B 415 ASN cc_start: 0.7189 (m-40) cc_final: 0.6919 (m-40) REVERT: B 453 MET cc_start: 0.7396 (ppp) cc_final: 0.6621 (ppp) REVERT: C 306 LEU cc_start: 0.7983 (mp) cc_final: 0.7314 (tp) REVERT: C 313 MET cc_start: 0.7983 (tpp) cc_final: 0.7723 (tpt) REVERT: C 632 GLU cc_start: 0.8703 (pt0) cc_final: 0.8502 (pt0) REVERT: C 854 MET cc_start: 0.9064 (tmm) cc_final: 0.8519 (tmm) REVERT: C 864 MET cc_start: 0.7685 (mtp) cc_final: 0.7017 (ttm) REVERT: C 926 MET cc_start: 0.8642 (mmt) cc_final: 0.8327 (tpp) REVERT: C 968 TRP cc_start: 0.6589 (m-10) cc_final: 0.5815 (m100) REVERT: C 971 MET cc_start: 0.7492 (tpt) cc_final: 0.7199 (tpt) REVERT: D 343 HIS cc_start: 0.8139 (m-70) cc_final: 0.7751 (m170) REVERT: D 368 PHE cc_start: 0.7986 (m-80) cc_final: 0.7711 (m-80) REVERT: D 415 ASN cc_start: 0.7295 (m110) cc_final: 0.6917 (m-40) REVERT: D 461 CYS cc_start: 0.6367 (m) cc_final: 0.6109 (m) REVERT: E 313 MET cc_start: 0.7586 (tpp) cc_final: 0.7211 (tpp) REVERT: E 445 CYS cc_start: 0.7809 (p) cc_final: 0.7497 (p) REVERT: E 854 MET cc_start: 0.8980 (tmm) cc_final: 0.8250 (tmm) REVERT: E 869 TYR cc_start: 0.8931 (t80) cc_final: 0.8602 (t80) REVERT: E 968 TRP cc_start: 0.6685 (m-10) cc_final: 0.5809 (m100) REVERT: F 343 HIS cc_start: 0.8264 (m170) cc_final: 0.7914 (m90) outliers start: 2 outliers final: 0 residues processed: 223 average time/residue: 0.1403 time to fit residues: 50.5051 Evaluate side-chains 168 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.716 ------------------------------------------------------------------------------- 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: 10.0000 chunk 122 optimal weight: 9.9990 chunk 110 optimal weight: 0.4980 chunk 87 optimal weight: 4.9990 chunk 170 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 253 optimal weight: 8.9990 chunk 208 optimal weight: 20.0000 chunk 144 optimal weight: 0.8980 chunk 249 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 862 GLN A 966 GLN B 428 GLN B 478 HIS ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 415 ASN ** E 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.057712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.044468 restraints weight = 262940.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.046303 restraints weight = 123230.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.047127 restraints weight = 65424.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047175 restraints weight = 49000.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.047283 restraints weight = 47237.334| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 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 = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22748 Z= 0.191 Angle : 0.669 12.352 31143 Z= 0.335 Chirality : 0.043 0.169 3551 Planarity : 0.004 0.035 3631 Dihedral : 14.322 163.956 4076 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % 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: -0.05 (0.17), residues: 2466 helix: 1.50 (0.17), residues: 972 sheet: -0.31 (0.24), residues: 513 loop : -1.45 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 689 TYR 0.017 0.002 TYR A 461 PHE 0.017 0.002 PHE B 379 TRP 0.039 0.002 TRP B 386 HIS 0.009 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00408 (22736) covalent geometry : angle 0.64616 (31125) hydrogen bonds : bond 0.04430 ( 1035) hydrogen bonds : angle 4.83704 ( 2857) metal coordination : bond 0.01032 ( 12) metal coordination : angle 7.22481 ( 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 218 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7521 (tpp) cc_final: 0.7143 (tpt) REVERT: A 567 MET cc_start: 0.6205 (mmm) cc_final: 0.5584 (mmm) REVERT: A 677 MET cc_start: 0.8886 (mpp) cc_final: 0.8684 (mpp) REVERT: A 854 MET cc_start: 0.9111 (tmm) cc_final: 0.8392 (tmm) REVERT: A 878 MET cc_start: 0.8923 (mtm) cc_final: 0.8669 (mtm) REVERT: A 968 TRP cc_start: 0.6613 (m-10) cc_final: 0.6243 (m-10) REVERT: B 415 ASN cc_start: 0.7214 (m-40) cc_final: 0.6956 (m-40) REVERT: B 453 MET cc_start: 0.7305 (ppp) cc_final: 0.6561 (ppp) REVERT: B 489 PHE cc_start: 0.9351 (m-10) cc_final: 0.9092 (m-10) REVERT: B 497 LEU cc_start: 0.9016 (tp) cc_final: 0.8765 (tp) REVERT: C 313 MET cc_start: 0.7897 (tpp) cc_final: 0.7691 (tpt) REVERT: C 709 MET cc_start: 0.8998 (mmm) cc_final: 0.8772 (mmm) REVERT: C 766 MET cc_start: 0.8660 (ttp) cc_final: 0.8269 (tmm) REVERT: C 854 MET cc_start: 0.9080 (tmm) cc_final: 0.8740 (ppp) REVERT: C 864 MET cc_start: 0.7595 (mtp) cc_final: 0.6858 (ttm) REVERT: C 908 LYS cc_start: 0.6969 (mtpt) cc_final: 0.6576 (mttt) REVERT: C 926 MET cc_start: 0.8630 (mmt) cc_final: 0.8327 (tpp) REVERT: C 968 TRP cc_start: 0.6715 (m-10) cc_final: 0.5901 (m100) REVERT: C 971 MET cc_start: 0.7877 (tpt) cc_final: 0.7451 (tpt) REVERT: D 343 HIS cc_start: 0.8159 (m-70) cc_final: 0.7760 (m90) REVERT: D 368 PHE cc_start: 0.7916 (m-80) cc_final: 0.7566 (m-10) REVERT: D 408 ARG cc_start: 0.8098 (ptm160) cc_final: 0.7828 (tmm-80) REVERT: D 415 ASN cc_start: 0.7439 (m-40) cc_final: 0.7175 (m-40) REVERT: D 453 MET cc_start: 0.7388 (ppp) cc_final: 0.7012 (ppp) REVERT: D 461 CYS cc_start: 0.6418 (m) cc_final: 0.6099 (m) REVERT: E 313 MET cc_start: 0.7419 (tpp) cc_final: 0.7077 (tpp) REVERT: E 445 CYS cc_start: 0.7814 (p) cc_final: 0.7553 (p) REVERT: E 854 MET cc_start: 0.8993 (tmm) cc_final: 0.8235 (tmm) REVERT: E 878 MET cc_start: 0.8901 (mtp) cc_final: 0.8441 (mtp) REVERT: E 968 TRP cc_start: 0.6740 (m-10) cc_final: 0.5798 (m100) REVERT: F 354 LYS cc_start: 0.7417 (pttt) cc_final: 0.7151 (pttm) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1510 time to fit residues: 52.4892 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 : 0.922 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 101 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 153 optimal weight: 6.9990 chunk 166 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.058118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.044872 restraints weight = 336497.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046718 restraints weight = 137655.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.047344 restraints weight = 68983.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047417 restraints weight = 57002.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.047587 restraints weight = 55287.764| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 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 = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22748 Z= 0.162 Angle : 0.642 10.922 31143 Z= 0.320 Chirality : 0.043 0.174 3551 Planarity : 0.004 0.035 3631 Dihedral : 14.219 164.019 4076 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % 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: 0.11 (0.17), residues: 2466 helix: 1.70 (0.17), residues: 954 sheet: -0.31 (0.24), residues: 510 loop : -1.34 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 689 TYR 0.015 0.002 TYR A 461 PHE 0.022 0.001 PHE D 379 TRP 0.044 0.001 TRP B 386 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00345 (22736) covalent geometry : angle 0.62208 (31125) hydrogen bonds : bond 0.04237 ( 1035) hydrogen bonds : angle 4.74157 ( 2857) metal coordination : bond 0.00847 ( 12) metal coordination : angle 6.67734 ( 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 212 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7569 (tpp) cc_final: 0.7196 (tpt) REVERT: A 567 MET cc_start: 0.6220 (mmm) cc_final: 0.5623 (mmm) REVERT: A 677 MET cc_start: 0.8897 (mpp) cc_final: 0.8678 (mpp) REVERT: A 766 MET cc_start: 0.8559 (tmm) cc_final: 0.8320 (tmm) REVERT: A 854 MET cc_start: 0.9046 (tmm) cc_final: 0.8770 (tmm) REVERT: A 878 MET cc_start: 0.8910 (mtm) cc_final: 0.8549 (mtp) REVERT: A 968 TRP cc_start: 0.6510 (m-10) cc_final: 0.6136 (m-10) REVERT: B 345 TYR cc_start: 0.7454 (m-80) cc_final: 0.7131 (m-80) REVERT: B 368 PHE cc_start: 0.8107 (m-80) cc_final: 0.7380 (m-80) REVERT: B 415 ASN cc_start: 0.7262 (m-40) cc_final: 0.6988 (m-40) REVERT: B 453 MET cc_start: 0.7582 (ppp) cc_final: 0.6781 (ppp) REVERT: C 306 LEU cc_start: 0.7986 (mp) cc_final: 0.7154 (tt) REVERT: C 313 MET cc_start: 0.7931 (tpp) cc_final: 0.7564 (tpt) REVERT: C 864 MET cc_start: 0.7562 (mtp) cc_final: 0.6799 (ttm) REVERT: C 882 MET cc_start: 0.5173 (mpp) cc_final: 0.4769 (mpp) REVERT: C 926 MET cc_start: 0.8608 (mmt) cc_final: 0.8309 (tpp) REVERT: C 968 TRP cc_start: 0.6669 (m-10) cc_final: 0.5839 (m100) REVERT: D 343 HIS cc_start: 0.8148 (m-70) cc_final: 0.7754 (m90) REVERT: D 408 ARG cc_start: 0.8080 (ptm160) cc_final: 0.7805 (tmm-80) REVERT: D 415 ASN cc_start: 0.7383 (m-40) cc_final: 0.7103 (m-40) REVERT: D 461 CYS cc_start: 0.6375 (m) cc_final: 0.6053 (m) REVERT: D 489 PHE cc_start: 0.9089 (m-80) cc_final: 0.8669 (m-80) REVERT: E 313 MET cc_start: 0.7456 (tpp) cc_final: 0.7103 (tpp) REVERT: E 445 CYS cc_start: 0.7815 (p) cc_final: 0.7501 (p) REVERT: E 854 MET cc_start: 0.8927 (tmm) cc_final: 0.8283 (tmm) REVERT: E 968 TRP cc_start: 0.6662 (m-10) cc_final: 0.5652 (m-10) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1464 time to fit residues: 50.0267 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 : 0.854 ------------------------------------------------------------------------------- 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: 10.0000 chunk 174 optimal weight: 6.9990 chunk 100 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 112 optimal weight: 0.0870 chunk 250 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.045871 restraints weight = 279486.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.048026 restraints weight = 126946.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048627 restraints weight = 63681.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.048892 restraints weight = 50048.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048999 restraints weight = 45960.387| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 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 = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22748 Z= 0.114 Angle : 0.591 9.449 31143 Z= 0.291 Chirality : 0.041 0.161 3551 Planarity : 0.004 0.036 3631 Dihedral : 13.938 163.450 4076 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % 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: 0.39 (0.18), residues: 2466 helix: 1.92 (0.17), residues: 960 sheet: -0.15 (0.24), residues: 507 loop : -1.18 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 689 TYR 0.013 0.001 TYR E 939 PHE 0.009 0.001 PHE C 680 TRP 0.034 0.001 TRP B 386 HIS 0.006 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00239 (22736) covalent geometry : angle 0.57611 (31125) hydrogen bonds : bond 0.03697 ( 1035) hydrogen bonds : angle 4.49386 ( 2857) metal coordination : bond 0.00684 ( 12) metal coordination : angle 5.58633 ( 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 218 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7602 (tpp) cc_final: 0.7197 (tpt) REVERT: A 526 ASP cc_start: 0.8121 (t0) cc_final: 0.7698 (p0) REVERT: A 567 MET cc_start: 0.6154 (mmm) cc_final: 0.5568 (mmm) REVERT: A 766 MET cc_start: 0.8540 (tmm) cc_final: 0.8283 (tmm) REVERT: A 854 MET cc_start: 0.9076 (tmm) cc_final: 0.8801 (tmm) REVERT: A 878 MET cc_start: 0.8883 (mtm) cc_final: 0.8507 (mtp) REVERT: A 968 TRP cc_start: 0.6497 (m-10) cc_final: 0.6134 (m-10) REVERT: B 345 TYR cc_start: 0.7435 (m-80) cc_final: 0.7122 (m-80) REVERT: B 415 ASN cc_start: 0.7226 (m-40) cc_final: 0.6935 (m-40) REVERT: B 453 MET cc_start: 0.7438 (ppp) cc_final: 0.6595 (ppp) REVERT: B 461 CYS cc_start: 0.6260 (m) cc_final: 0.5977 (m) REVERT: B 475 TYR cc_start: 0.6336 (t80) cc_final: 0.6134 (t80) REVERT: C 313 MET cc_start: 0.7837 (tpp) cc_final: 0.7468 (tpt) REVERT: C 766 MET cc_start: 0.8569 (ttp) cc_final: 0.8256 (tmm) REVERT: C 882 MET cc_start: 0.4851 (mpp) cc_final: 0.4525 (mpp) REVERT: C 908 LYS cc_start: 0.6838 (mtpt) cc_final: 0.6452 (mttt) REVERT: C 926 MET cc_start: 0.8569 (mmt) cc_final: 0.8332 (tpp) REVERT: C 968 TRP cc_start: 0.6574 (m-10) cc_final: 0.5698 (m100) REVERT: D 343 HIS cc_start: 0.8172 (m-70) cc_final: 0.7809 (m90) REVERT: D 368 PHE cc_start: 0.7982 (m-80) cc_final: 0.7764 (m-80) REVERT: D 408 ARG cc_start: 0.8004 (ptm160) cc_final: 0.7729 (tmm-80) REVERT: D 415 ASN cc_start: 0.7356 (m-40) cc_final: 0.7089 (m-40) REVERT: D 461 CYS cc_start: 0.6542 (m) cc_final: 0.6229 (m) REVERT: D 475 TYR cc_start: 0.6952 (t80) cc_final: 0.6731 (t80) REVERT: E 313 MET cc_start: 0.7481 (tpp) cc_final: 0.7113 (tpp) REVERT: E 567 MET cc_start: 0.5878 (mmt) cc_final: 0.5491 (mmm) REVERT: E 854 MET cc_start: 0.9022 (tmm) cc_final: 0.8773 (tmm) REVERT: E 878 MET cc_start: 0.8882 (mtp) cc_final: 0.8473 (mtp) REVERT: E 968 TRP cc_start: 0.6638 (m-10) cc_final: 0.5613 (m-10) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1416 time to fit residues: 50.1082 Evaluate side-chains 172 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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: 20.0000 chunk 251 optimal weight: 30.0000 chunk 151 optimal weight: 6.9990 chunk 26 optimal weight: 0.3980 chunk 210 optimal weight: 6.9990 chunk 82 optimal weight: 0.0670 chunk 189 optimal weight: 6.9990 chunk 225 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 246 optimal weight: 6.9990 overall best weight: 2.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 GLN D 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.045738 restraints weight = 194699.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.047293 restraints weight = 103808.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048018 restraints weight = 61519.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.048186 restraints weight = 45584.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.048416 restraints weight = 44173.439| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3033 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3033 r_free = 0.3033 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 = 0.3033 r_free = 0.3033 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3608 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= 0.124 Angle : 0.599 10.094 31143 Z= 0.295 Chirality : 0.042 0.165 3551 Planarity : 0.004 0.041 3631 Dihedral : 13.850 163.613 4076 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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: 0.41 (0.18), residues: 2466 helix: 1.91 (0.17), residues: 957 sheet: -0.08 (0.24), residues: 507 loop : -1.18 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 689 TYR 0.015 0.001 TYR E 623 PHE 0.010 0.001 PHE B 489 TRP 0.034 0.001 TRP B 386 HIS 0.005 0.001 HIS B 355 Details of bonding type rmsd covalent geometry : bond 0.00262 (22736) covalent geometry : angle 0.58403 (31125) hydrogen bonds : bond 0.03802 ( 1035) hydrogen bonds : angle 4.50459 ( 2857) metal coordination : bond 0.00668 ( 12) metal coordination : angle 5.63848 ( 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 214 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7534 (tpp) cc_final: 0.7134 (tpt) REVERT: A 526 ASP cc_start: 0.8135 (t0) cc_final: 0.7732 (p0) REVERT: A 567 MET cc_start: 0.6172 (mmm) cc_final: 0.5580 (mmm) REVERT: A 766 MET cc_start: 0.8596 (tmm) cc_final: 0.8319 (tmm) REVERT: A 854 MET cc_start: 0.9095 (tmm) cc_final: 0.8806 (tmm) REVERT: A 878 MET cc_start: 0.8935 (mtm) cc_final: 0.8529 (mtp) REVERT: A 968 TRP cc_start: 0.6635 (m-10) cc_final: 0.6252 (m-10) REVERT: B 345 TYR cc_start: 0.7340 (m-80) cc_final: 0.7058 (m-80) REVERT: B 368 PHE cc_start: 0.8039 (m-80) cc_final: 0.7352 (m-80) REVERT: B 415 ASN cc_start: 0.7267 (m-40) cc_final: 0.6980 (m-40) REVERT: B 453 MET cc_start: 0.7197 (ppp) cc_final: 0.6407 (ppp) REVERT: B 461 CYS cc_start: 0.6144 (m) cc_final: 0.5839 (m) REVERT: C 313 MET cc_start: 0.7836 (tpp) cc_final: 0.7475 (tpt) REVERT: C 567 MET cc_start: 0.5782 (mmp) cc_final: 0.5502 (mmp) REVERT: C 766 MET cc_start: 0.8561 (ttp) cc_final: 0.8197 (tmm) REVERT: C 864 MET cc_start: 0.7389 (mtp) cc_final: 0.6877 (ttm) REVERT: C 968 TRP cc_start: 0.6650 (m-10) cc_final: 0.5849 (m100) REVERT: D 343 HIS cc_start: 0.8165 (m-70) cc_final: 0.7747 (m90) REVERT: D 368 PHE cc_start: 0.7970 (m-80) cc_final: 0.7739 (m-80) REVERT: D 408 ARG cc_start: 0.7954 (ptm160) cc_final: 0.7689 (tmm-80) REVERT: D 415 ASN cc_start: 0.7341 (m-40) cc_final: 0.7099 (m-40) REVERT: D 461 CYS cc_start: 0.6487 (m) cc_final: 0.6270 (m) REVERT: D 475 TYR cc_start: 0.7025 (t80) cc_final: 0.6823 (t80) REVERT: E 313 MET cc_start: 0.7489 (tpp) cc_final: 0.7125 (tpp) REVERT: E 567 MET cc_start: 0.5925 (mmt) cc_final: 0.5551 (mmm) REVERT: E 854 MET cc_start: 0.8981 (tmm) cc_final: 0.8684 (tmm) REVERT: E 968 TRP cc_start: 0.6691 (m-10) cc_final: 0.5676 (m-10) outliers start: 0 outliers final: 0 residues processed: 214 average time/residue: 0.1375 time to fit residues: 47.8975 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 : 0.798 ------------------------------------------------------------------------------- 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: 7.9990 chunk 69 optimal weight: 5.9990 chunk 228 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 chunk 216 optimal weight: 1.9990 chunk 76 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 352 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.045106 restraints weight = 323430.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.046641 restraints weight = 135771.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047502 restraints weight = 72022.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.047509 restraints weight = 55168.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.047766 restraints weight = 54446.582| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2998 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2998 r_free = 0.2998 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 = 0.2998 r_free = 0.2998 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.2998 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3618 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= 0.166 Angle : 0.640 10.675 31143 Z= 0.318 Chirality : 0.043 0.176 3551 Planarity : 0.004 0.043 3631 Dihedral : 13.892 164.574 4076 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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 (0.18), residues: 2466 helix: 1.67 (0.17), residues: 975 sheet: -0.25 (0.24), residues: 510 loop : -1.32 (0.20), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 689 TYR 0.016 0.002 TYR A 461 PHE 0.011 0.001 PHE A 629 TRP 0.043 0.002 TRP B 386 HIS 0.007 0.001 HIS D 355 Details of bonding type rmsd covalent geometry : bond 0.00354 (22736) covalent geometry : angle 0.62515 (31125) hydrogen bonds : bond 0.04110 ( 1035) hydrogen bonds : angle 4.67676 ( 2857) metal coordination : bond 0.00793 ( 12) metal coordination : angle 5.82300 ( 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 205 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7533 (tpp) cc_final: 0.7169 (tpt) REVERT: A 526 ASP cc_start: 0.8314 (t0) cc_final: 0.8049 (t0) REVERT: A 567 MET cc_start: 0.6224 (mmm) cc_final: 0.5622 (mmm) REVERT: A 677 MET cc_start: 0.8896 (mpp) cc_final: 0.8656 (mpp) REVERT: A 766 MET cc_start: 0.8665 (tmm) cc_final: 0.8381 (tmm) REVERT: A 854 MET cc_start: 0.9070 (tmm) cc_final: 0.8760 (tmm) REVERT: A 878 MET cc_start: 0.8943 (mtm) cc_final: 0.8583 (mtp) REVERT: A 968 TRP cc_start: 0.6562 (m-10) cc_final: 0.6191 (m-10) REVERT: B 345 TYR cc_start: 0.7406 (m-80) cc_final: 0.7066 (m-80) REVERT: B 368 PHE cc_start: 0.8043 (m-80) cc_final: 0.7304 (m-80) REVERT: B 415 ASN cc_start: 0.7150 (m-40) cc_final: 0.6883 (m-40) REVERT: B 453 MET cc_start: 0.7693 (ppp) cc_final: 0.6540 (ppp) REVERT: B 461 CYS cc_start: 0.6131 (m) cc_final: 0.5859 (m) REVERT: B 489 PHE cc_start: 0.9259 (m-10) cc_final: 0.8939 (m-80) REVERT: B 497 LEU cc_start: 0.8977 (tp) cc_final: 0.8747 (tp) REVERT: C 313 MET cc_start: 0.7943 (tpp) cc_final: 0.7608 (tpt) REVERT: C 766 MET cc_start: 0.8686 (ttp) cc_final: 0.8272 (tmm) REVERT: C 864 MET cc_start: 0.7567 (mtp) cc_final: 0.6995 (ttm) REVERT: C 968 TRP cc_start: 0.6633 (m-10) cc_final: 0.5893 (m-10) REVERT: D 343 HIS cc_start: 0.8102 (m-70) cc_final: 0.7692 (m90) REVERT: D 368 PHE cc_start: 0.7859 (m-80) cc_final: 0.7648 (m-80) REVERT: D 408 ARG cc_start: 0.7996 (ptm160) cc_final: 0.7704 (tmm-80) REVERT: D 415 ASN cc_start: 0.7344 (m-40) cc_final: 0.7129 (m-40) REVERT: D 461 CYS cc_start: 0.6439 (m) cc_final: 0.6143 (m) REVERT: E 313 MET cc_start: 0.7524 (tpp) cc_final: 0.7174 (tpp) REVERT: E 567 MET cc_start: 0.6045 (mmt) cc_final: 0.5662 (mmm) REVERT: E 854 MET cc_start: 0.8913 (tmm) cc_final: 0.8581 (tmm) REVERT: E 968 TRP cc_start: 0.6637 (m-10) cc_final: 0.5708 (m-10) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1372 time to fit residues: 45.2898 Evaluate side-chains 162 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 139 optimal weight: 9.9990 chunk 115 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 217 optimal weight: 8.9990 chunk 168 optimal weight: 0.0040 chunk 180 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 117 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 214 optimal weight: 0.9980 overall best weight: 3.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS E 371 GLN E 693 ASN ** F 332 ASN ** 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 = 0.3317 r_free = 0.3317 target = 0.058197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.044856 restraints weight = 274417.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046670 restraints weight = 128808.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047475 restraints weight = 67044.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.047754 restraints weight = 52097.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.047840 restraints weight = 49817.107| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3011 r_free = 0.3011 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 = 0.3011 r_free = 0.3011 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| r_final: 0.3011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22748 Z= 0.147 Angle : 0.623 10.140 31143 Z= 0.308 Chirality : 0.042 0.167 3551 Planarity : 0.004 0.044 3631 Dihedral : 13.864 164.271 4076 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.05 % Allowed : 0.46 % Favored : 99.50 % 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: 0.24 (0.18), residues: 2466 helix: 1.81 (0.17), residues: 957 sheet: -0.27 (0.24), residues: 519 loop : -1.24 (0.20), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 689 TYR 0.025 0.002 TYR B 475 PHE 0.011 0.001 PHE A 681 TRP 0.041 0.001 TRP B 386 HIS 0.008 0.001 HIS F 355 Details of bonding type rmsd covalent geometry : bond 0.00314 (22736) covalent geometry : angle 0.60761 (31125) hydrogen bonds : bond 0.03988 ( 1035) hydrogen bonds : angle 4.62441 ( 2857) metal coordination : bond 0.00760 ( 12) metal coordination : angle 5.77589 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3508.21 seconds wall clock time: 61 minutes 47.50 seconds (3707.50 seconds total)