Starting phenix.real_space_refine on Tue Sep 15 06:49:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7jl2_22370/09_2026/7jl2_22370.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jl2_22370/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7jl2_22370/09_2026/7jl2_22370.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7jl2_22370/09_2026/7jl2_22370.cif" model { file = "/net/cci-nas-00/data/ceres_data/7jl2_22370/09_2026/7jl2_22370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jl2_22370/09_2026/7jl2_22370.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jl2_22370/09_2026/7jl2_22370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jl2_22370/09_2026/7jl2_22370.map" } 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22128 Number of models: 1 Model: "" Number of chains: 11 Chain: "X" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 944 Classifications: {'RNAv2': 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: {'RNAv2': 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: 5.19, per 1000 atoms: 0.23 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: 1.89 Conformation dependent library (CDL) restraints added in 1.2 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: 2.13 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: 4.49 Time building geometry restraints manager: 2.51 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: 13261 34.56 - 69.13: 328 69.13 - 103.69: 30 103.69 - 138.25: 3 138.25 - 172.82: 4 Dihedral angle restraints: 13626 sinusoidal: 6237 harmonic: 7389 Sorted by residual: dihedral pdb=" C4' A X 15 " pdb=" C3' A X 15 " pdb=" C2' A X 15 " pdb=" C1' A X 15 " ideal model delta sinusoidal sigma weight residual 36.34 -31.08 67.43 1 3.10e+00 1.04e-01 6.16e+02 dihedral pdb=" O4' A X 15 " pdb=" C4' A X 15 " pdb=" C3' A X 15 " pdb=" C2' A X 15 " ideal model delta sinusoidal sigma weight residual -35.15 18.03 -53.18 1 4.00e+00 6.25e-02 2.40e+02 dihedral pdb=" O4' A X 15 " pdb=" C2' A X 15 " pdb=" C1' A X 15 " pdb=" C3' A X 15 " ideal model delta sinusoidal sigma weight residual 25.59 -34.16 59.75 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 13623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3100 0.072 - 0.145: 350 0.145 - 0.217: 52 0.217 - 0.290: 45 0.290 - 0.362: 4 Chirality restraints: 3551 Sorted by residual: chirality pdb=" C2' A X 15 " pdb=" C3' A X 15 " pdb=" O2' A X 15 " pdb=" C1' A X 15 " both_signs ideal model delta sigma weight residual False -2.79 -2.43 -0.36 2.00e-01 2.50e+01 3.28e+00 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 ... (remaining 3548 not shown) Planarity restraints: 3631 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A X 15 " 0.042 2.00e-02 2.50e+03 1.88e-02 9.73e+00 pdb=" N9 A X 15 " -0.043 2.00e-02 2.50e+03 pdb=" C8 A X 15 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A X 15 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A X 15 " 0.002 2.00e-02 2.50e+03 pdb=" C6 A X 15 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A X 15 " 0.010 2.00e-02 2.50e+03 pdb=" N1 A X 15 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A X 15 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A X 15 " -0.007 2.00e-02 2.50e+03 pdb=" C4 A X 15 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 790 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.91e+00 pdb=" C THR A 790 " 0.034 2.00e-02 2.50e+03 pdb=" O THR A 790 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL A 791 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 790 " -0.010 2.00e-02 2.50e+03 1.96e-02 3.83e+00 pdb=" C THR C 790 " 0.034 2.00e-02 2.50e+03 pdb=" O THR C 790 " -0.013 2.00e-02 2.50e+03 pdb=" N VAL C 791 " -0.011 2.00e-02 2.50e+03 ... (remaining 3628 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 209 2.49 - 3.09: 16866 3.09 - 3.70: 35180 3.70 - 4.30: 48551 4.30 - 4.90: 75054 Nonbonded interactions: 175860 Sorted by model distance: nonbonded pdb=" F4 ALF C1103 " pdb="MG MG C1104 " model vdw 1.889 2.120 nonbonded pdb=" F4 ALF E1103 " pdb="MG MG E1104 " model vdw 1.889 2.120 nonbonded pdb=" F4 ALF A1103 " pdb="MG MG A1104 " model vdw 1.889 2.120 nonbonded pdb=" F1 ALF E1103 " pdb="MG MG E1104 " model vdw 1.891 2.120 nonbonded pdb=" F1 ALF A1103 " pdb="MG MG A1104 " model vdw 1.892 2.120 ... (remaining 175855 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) selection = (chain 'D' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) selection = (chain 'F' and (resid 321 through 387 or resid 389 through 432 or resid 434 thro \ ugh 502)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 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: 0.040 Process input model: 25.530 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 22748 Z= 0.300 Angle : 1.376 70.785 31143 Z= 0.578 Chirality : 0.057 0.362 3551 Planarity : 0.004 0.034 3631 Dihedral : 15.177 172.817 8820 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.55 % Allowed : 0.87 % Favored : 98.59 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2466 helix: 0.45 (0.16), residues: 927 sheet: 0.18 (0.23), residues: 501 loop : -1.38 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 323 TYR 0.030 0.002 TYR E 732 PHE 0.020 0.002 PHE A 724 TRP 0.030 0.002 TRP F 386 HIS 0.013 0.002 HIS D 343 Details of bonding type rmsd/Z covalent geometry : bond 0.00617 / 0.30 (22736) covalent geometry : angle 1.36610 / 0.58 (31125) hydrogen bonds : bond 0.16850 / 8.71 ( 1035) hydrogen bonds : angle 7.01083 / 2.84 ( 2857) metal coordination : bond 0.00789 / 0.40 ( 12) metal coordination : angle 6.93425 / 2.31 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.931 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: 0.1561 time to fit residues: 52.6097 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 : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.0770 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 7.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 524 ASN ** A 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 966 GLN C 524 ASN ** C 835 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 966 GLN ** D 415 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 ASN E 835 HIS E 966 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.060359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.046758 restraints weight = 329989.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.048875 restraints weight = 132753.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050233 restraints weight = 63586.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.050060 restraints weight = 48291.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.050336 restraints weight = 44603.039| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 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 = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22748 Z= 0.123 Angle : 0.663 8.430 31143 Z= 0.317 Chirality : 0.045 0.248 3551 Planarity : 0.004 0.028 3631 Dihedral : 10.261 163.495 3774 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: 0.35 (0.17), residues: 2466 helix: 1.61 (0.17), residues: 948 sheet: 0.28 (0.24), residues: 522 loop : -1.15 (0.20), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 348 TYR 0.012 0.001 TYR C 623 PHE 0.015 0.001 PHE C 680 TRP 0.021 0.001 TRP B 386 HIS 0.006 0.001 HIS B 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (22736) covalent geometry : angle 0.64648 / 0.32 (31125) hydrogen bonds : bond 0.04322 / 2.23 ( 1035) hydrogen bonds : angle 4.83732 / 1.96 ( 2857) metal coordination : bond 0.00633 / 0.35 ( 12) metal coordination : angle 6.09300 / 2.03 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4932 Ramachandran restraints generated. 2466 Oldfield, 0 Emsley, 2466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 1.046 Fit side-chains revert: symmetry clash REVERT: A 313 MET cc_start: 0.7419 (tpp) cc_final: 0.6987 (tpt) REVERT: A 526 ASP cc_start: 0.8260 (t0) cc_final: 0.7943 (p0) REVERT: A 567 MET cc_start: 0.5516 (mmp) cc_final: 0.5227 (mmm) REVERT: A 854 MET cc_start: 0.9012 (tmm) cc_final: 0.8229 (tmm) REVERT: A 968 TRP cc_start: 0.6669 (m-10) cc_final: 0.6259 (m-10) REVERT: B 343 HIS cc_start: 0.7975 (m170) cc_final: 0.7622 (m170) REVERT: B 345 TYR cc_start: 0.7246 (m-80) cc_final: 0.6936 (m-80) REVERT: B 415 ASN cc_start: 0.7273 (m-40) cc_final: 0.7016 (m-40) REVERT: B 453 MET cc_start: 0.7402 (ppp) cc_final: 0.6696 (ppp) REVERT: C 306 LEU cc_start: 0.7948 (mp) cc_final: 0.7284 (tp) REVERT: C 313 MET cc_start: 0.7613 (tpp) cc_final: 0.7377 (tpt) REVERT: C 567 MET cc_start: 0.5140 (mmp) cc_final: 0.4912 (mmp) REVERT: C 854 MET cc_start: 0.9054 (tmm) cc_final: 0.8751 (tmm) REVERT: C 864 MET cc_start: 0.7556 (mtp) cc_final: 0.6885 (ttm) REVERT: C 878 MET cc_start: 0.8933 (mtp) cc_final: 0.8589 (mtp) REVERT: C 879 GLN cc_start: 0.8822 (tt0) cc_final: 0.8604 (mm-40) REVERT: C 926 MET cc_start: 0.8495 (mmt) cc_final: 0.8158 (tpp) REVERT: C 968 TRP cc_start: 0.6998 (m-10) cc_final: 0.6473 (m-10) REVERT: D 415 ASN cc_start: 0.7300 (m-40) cc_final: 0.6966 (m-40) REVERT: D 461 CYS cc_start: 0.6513 (m) cc_final: 0.6242 (m) REVERT: D 478 HIS cc_start: 0.8151 (m-70) cc_final: 0.7572 (m-70) REVERT: E 313 MET cc_start: 0.7457 (tpp) cc_final: 0.7126 (tpp) REVERT: E 854 MET cc_start: 0.8928 (tmm) cc_final: 0.8214 (tmm) REVERT: E 878 MET cc_start: 0.8717 (mtp) cc_final: 0.8401 (mtp) REVERT: E 968 TRP cc_start: 0.6673 (m-10) cc_final: 0.5956 (m-10) REVERT: F 343 HIS cc_start: 0.8163 (m170) cc_final: 0.7760 (m170) REVERT: F 354 LYS cc_start: 0.7489 (pttt) cc_final: 0.7213 (pttm) REVERT: F 368 PHE cc_start: 0.7871 (m-10) cc_final: 0.7660 (m-80) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1505 time to fit residues: 56.0847 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 : 0.845 ------------------------------------------------------------------------------- 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: 8.9990 chunk 145 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 180 optimal weight: 8.9990 chunk 177 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 56 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** E 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.058912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.045524 restraints weight = 318782.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047542 restraints weight = 128928.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.048492 restraints weight = 64712.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.048353 restraints weight = 50877.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048704 restraints weight = 49684.086| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3033 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22748 Z= 0.149 Angle : 0.665 9.897 31143 Z= 0.322 Chirality : 0.048 0.288 3551 Planarity : 0.004 0.032 3631 Dihedral : 10.085 161.476 3774 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 10.90 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: 0.31 (0.17), residues: 2466 helix: 1.65 (0.17), residues: 951 sheet: 0.07 (0.23), residues: 528 loop : -1.16 (0.20), residues: 987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 822 TYR 0.014 0.001 TYR A 461 PHE 0.014 0.001 PHE A 681 TRP 0.022 0.001 TRP B 386 HIS 0.009 0.001 HIS D 383 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.15 (22736) covalent geometry : angle 0.64878 / 0.32 (31125) hydrogen bonds : bond 0.04313 / 2.23 ( 1035) hydrogen bonds : angle 4.81604 / 1.94 ( 2857) metal coordination : bond 0.01850 / 0.97 ( 12) metal coordination : angle 6.10262 / 2.03 ( 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 218 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 306 LEU cc_start: 0.7856 (mp) cc_final: 0.7277 (tp) REVERT: A 313 MET cc_start: 0.7471 (tpp) cc_final: 0.7072 (tpt) REVERT: A 526 ASP cc_start: 0.8274 (t0) cc_final: 0.8058 (p0) REVERT: A 567 MET cc_start: 0.5872 (mmp) cc_final: 0.5501 (mmm) REVERT: A 854 MET cc_start: 0.9064 (tmm) cc_final: 0.8289 (tmm) REVERT: A 968 TRP cc_start: 0.6800 (m-10) cc_final: 0.6366 (m-10) REVERT: B 343 HIS cc_start: 0.8100 (m170) cc_final: 0.7683 (m170) REVERT: B 368 PHE cc_start: 0.8186 (m-80) cc_final: 0.7551 (m-80) REVERT: B 369 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7208 (tm-30) REVERT: B 453 MET cc_start: 0.7148 (ppp) cc_final: 0.6247 (ppp) REVERT: C 306 LEU cc_start: 0.7991 (mp) cc_final: 0.7438 (tp) REVERT: C 313 MET cc_start: 0.7794 (tpp) cc_final: 0.7555 (tpt) REVERT: C 632 GLU cc_start: 0.8767 (pt0) cc_final: 0.8557 (pt0) REVERT: C 854 MET cc_start: 0.9081 (tmm) cc_final: 0.8810 (ppp) REVERT: C 864 MET cc_start: 0.7624 (mtp) cc_final: 0.6918 (ttm) REVERT: C 878 MET cc_start: 0.9004 (mtp) cc_final: 0.8724 (mtp) REVERT: C 968 TRP cc_start: 0.6839 (m-10) cc_final: 0.6317 (m-10) REVERT: D 368 PHE cc_start: 0.7864 (m-80) cc_final: 0.7298 (m-80) REVERT: D 415 ASN cc_start: 0.7287 (m110) cc_final: 0.6862 (m-40) REVERT: D 461 CYS cc_start: 0.6405 (m) cc_final: 0.6078 (m) REVERT: D 478 HIS cc_start: 0.8026 (m-70) cc_final: 0.7383 (m-70) REVERT: E 313 MET cc_start: 0.7411 (tpp) cc_final: 0.7122 (tpp) REVERT: E 445 CYS cc_start: 0.7744 (p) cc_final: 0.7452 (p) REVERT: E 854 MET cc_start: 0.8999 (tmm) cc_final: 0.8497 (tmm) REVERT: E 878 MET cc_start: 0.8901 (mtp) cc_final: 0.8574 (mtp) REVERT: E 968 TRP cc_start: 0.6786 (m-10) cc_final: 0.6163 (m-10) REVERT: F 343 HIS cc_start: 0.8208 (m170) cc_final: 0.7781 (m170) REVERT: F 354 LYS cc_start: 0.7454 (pttt) cc_final: 0.7101 (pttm) REVERT: F 368 PHE cc_start: 0.7826 (m-10) cc_final: 0.7536 (m-80) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1456 time to fit residues: 51.8986 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 : 0.873 ------------------------------------------------------------------------------- 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: 6.9990 chunk 69 optimal weight: 9.9990 chunk 210 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 144 optimal weight: 0.0570 chunk 152 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN A 862 GLN B 393 HIS B 415 ASN C 531 GLN C 862 GLN ** C 966 GLN ** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.059045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.045538 restraints weight = 352808.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.047597 restraints weight = 143971.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048313 restraints weight = 70050.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.048700 restraints weight = 55163.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.048793 restraints weight = 53804.331| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 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 = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2683 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= 0.142 Angle : 0.646 9.117 31143 Z= 0.310 Chirality : 0.046 0.283 3551 Planarity : 0.003 0.031 3631 Dihedral : 9.843 160.490 3774 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % 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: 0.35 (0.17), residues: 2466 helix: 1.78 (0.17), residues: 954 sheet: 0.04 (0.24), residues: 507 loop : -1.19 (0.20), residues: 1005 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 0.011 0.001 PHE A 681 TRP 0.033 0.001 TRP B 386 HIS 0.004 0.001 HIS D 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (22736) covalent geometry : angle 0.63287 / 0.31 (31125) hydrogen bonds : bond 0.03980 / 2.06 ( 1035) hydrogen bonds : angle 4.62463 / 1.88 ( 2857) metal coordination : bond 0.00751 / 0.40 ( 12) metal coordination : angle 5.43051 / 1.81 ( 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 224 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7498 (tpp) cc_final: 0.7114 (tpt) REVERT: A 526 ASP cc_start: 0.8340 (t0) cc_final: 0.8045 (p0) REVERT: A 766 MET cc_start: 0.8541 (tmm) cc_final: 0.8226 (tmm) REVERT: A 854 MET cc_start: 0.9033 (tmm) cc_final: 0.8798 (tmm) REVERT: A 878 MET cc_start: 0.8867 (mtm) cc_final: 0.8439 (mtp) REVERT: A 968 TRP cc_start: 0.6729 (m-10) cc_final: 0.6361 (m-10) REVERT: B 344 PHE cc_start: 0.8262 (m-10) cc_final: 0.8060 (m-10) REVERT: B 345 TYR cc_start: 0.7743 (m-10) cc_final: 0.7371 (m-80) REVERT: B 368 PHE cc_start: 0.8190 (m-80) cc_final: 0.7434 (m-80) REVERT: B 386 TRP cc_start: 0.6919 (p90) cc_final: 0.6564 (p90) REVERT: B 415 ASN cc_start: 0.7158 (m110) cc_final: 0.6877 (m-40) REVERT: C 306 LEU cc_start: 0.7987 (mp) cc_final: 0.7375 (tp) REVERT: C 313 MET cc_start: 0.7811 (tpp) cc_final: 0.7554 (tpt) REVERT: C 558 MET cc_start: 0.9190 (ppp) cc_final: 0.8971 (ppp) REVERT: C 632 GLU cc_start: 0.8705 (pt0) cc_final: 0.8488 (pt0) REVERT: C 766 MET cc_start: 0.8676 (tmm) cc_final: 0.8417 (tmm) REVERT: C 864 MET cc_start: 0.7515 (mtp) cc_final: 0.7039 (ttm) REVERT: C 878 MET cc_start: 0.8886 (mtp) cc_final: 0.8586 (mtp) REVERT: C 882 MET cc_start: 0.5094 (mpp) cc_final: 0.4847 (mpp) REVERT: C 968 TRP cc_start: 0.6773 (m-10) cc_final: 0.6083 (m100) REVERT: D 343 HIS cc_start: 0.8241 (m90) cc_final: 0.7882 (m90) REVERT: D 368 PHE cc_start: 0.7906 (m-80) cc_final: 0.7254 (m-80) REVERT: D 415 ASN cc_start: 0.7305 (m110) cc_final: 0.6892 (m-40) REVERT: D 461 CYS cc_start: 0.6290 (m) cc_final: 0.6028 (m) REVERT: D 497 LEU cc_start: 0.9170 (tp) cc_final: 0.8956 (tp) REVERT: E 313 MET cc_start: 0.7428 (tpp) cc_final: 0.7168 (tpp) REVERT: E 445 CYS cc_start: 0.7841 (p) cc_final: 0.7509 (p) REVERT: E 567 MET cc_start: 0.5621 (mmp) cc_final: 0.5344 (mmp) REVERT: E 683 ASN cc_start: 0.7350 (m110) cc_final: 0.7132 (m-40) REVERT: E 854 MET cc_start: 0.8951 (tmm) cc_final: 0.8342 (tmm) REVERT: E 878 MET cc_start: 0.8851 (mtp) cc_final: 0.8410 (mtp) REVERT: E 968 TRP cc_start: 0.6793 (m-10) cc_final: 0.6104 (m-10) REVERT: F 343 HIS cc_start: 0.8227 (m170) cc_final: 0.7855 (m170) REVERT: F 354 LYS cc_start: 0.7329 (pttt) cc_final: 0.7007 (pttm) REVERT: F 368 PHE cc_start: 0.7852 (m-10) cc_final: 0.7479 (m-80) REVERT: F 475 TYR cc_start: 0.6870 (t80) cc_final: 0.6528 (t80) outliers start: 2 outliers final: 0 residues processed: 224 average time/residue: 0.1466 time to fit residues: 53.3657 Evaluate side-chains 175 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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: 4.9990 chunk 135 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 140 optimal weight: 10.0000 chunk 254 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 238 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 233 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 GLN ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 HIS B 478 HIS C 371 GLN ** C 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 862 GLN D 393 HIS E 371 GLN ** E 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 862 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.057929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.044494 restraints weight = 355894.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046167 restraints weight = 145636.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047086 restraints weight = 73967.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.047149 restraints weight = 57129.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047335 restraints weight = 55449.934| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 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 = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22748 Z= 0.173 Angle : 0.696 11.418 31143 Z= 0.333 Chirality : 0.048 0.312 3551 Planarity : 0.004 0.036 3631 Dihedral : 10.015 160.442 3774 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 0.05 % Allowed : 2.55 % Favored : 97.40 % 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: 0.13 (0.17), residues: 2466 helix: 1.61 (0.17), residues: 954 sheet: -0.18 (0.24), residues: 510 loop : -1.28 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 689 TYR 0.016 0.002 TYR A 461 PHE 0.016 0.002 PHE F 379 TRP 0.028 0.001 TRP B 386 HIS 0.005 0.001 HIS F 393 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (22736) covalent geometry : angle 0.67955 / 0.33 (31125) hydrogen bonds : bond 0.04333 / 2.24 ( 1035) hydrogen bonds : angle 4.80420 / 1.94 ( 2857) metal coordination : bond 0.00823 / 0.41 ( 12) metal coordination : angle 6.33525 / 2.11 ( 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 217 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 216 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7561 (tpp) cc_final: 0.7194 (tpt) REVERT: A 526 ASP cc_start: 0.8420 (t0) cc_final: 0.8040 (p0) REVERT: A 677 MET cc_start: 0.8881 (mpp) cc_final: 0.8665 (mpp) REVERT: A 854 MET cc_start: 0.9067 (tmm) cc_final: 0.8289 (tmm) REVERT: A 878 MET cc_start: 0.8883 (mtm) cc_final: 0.8648 (mtm) REVERT: A 968 TRP cc_start: 0.6616 (m-10) cc_final: 0.6298 (m-10) REVERT: B 415 ASN cc_start: 0.7201 (m110) cc_final: 0.6946 (m-40) REVERT: B 453 MET cc_start: 0.7543 (ppp) cc_final: 0.6790 (ppp) REVERT: C 306 LEU cc_start: 0.7979 (mp) cc_final: 0.7308 (tp) REVERT: C 313 MET cc_start: 0.7958 (tpp) cc_final: 0.7730 (tpt) REVERT: C 854 MET cc_start: 0.9066 (tmm) cc_final: 0.8763 (ppp) REVERT: C 864 MET cc_start: 0.7648 (mtp) cc_final: 0.6967 (ttm) REVERT: C 926 MET cc_start: 0.8641 (mmt) cc_final: 0.8317 (tpp) REVERT: C 968 TRP cc_start: 0.6648 (m-10) cc_final: 0.5830 (m100) REVERT: C 971 MET cc_start: 0.7523 (tpt) cc_final: 0.7240 (tpt) REVERT: D 343 HIS cc_start: 0.8234 (m90) cc_final: 0.7810 (m170) REVERT: D 415 ASN cc_start: 0.7373 (m110) cc_final: 0.6953 (m-40) REVERT: D 461 CYS cc_start: 0.6235 (m) cc_final: 0.5917 (m) REVERT: D 497 LEU cc_start: 0.9146 (tp) cc_final: 0.8912 (tp) REVERT: E 313 MET cc_start: 0.7571 (tpp) cc_final: 0.7339 (tpp) REVERT: E 445 CYS cc_start: 0.7829 (p) cc_final: 0.7523 (p) REVERT: E 567 MET cc_start: 0.5739 (mmp) cc_final: 0.5504 (mmp) REVERT: E 854 MET cc_start: 0.8960 (tmm) cc_final: 0.8213 (tmm) REVERT: E 968 TRP cc_start: 0.6763 (m-10) cc_final: 0.5868 (m100) REVERT: F 408 ARG cc_start: 0.7895 (ptm160) cc_final: 0.7621 (ptm-80) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1379 time to fit residues: 48.8720 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 : 0.675 ------------------------------------------------------------------------------- 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: 7.9990 chunk 122 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 chunk 170 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 208 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN ** C 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 HIS D 415 ASN ** E 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.057232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.043851 restraints weight = 263677.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.045898 restraints weight = 122355.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046527 restraints weight = 64374.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.046768 restraints weight = 48762.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.046834 restraints weight = 47242.857| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 22748 Z= 0.213 Angle : 0.744 12.846 31143 Z= 0.354 Chirality : 0.050 0.315 3551 Planarity : 0.004 0.035 3631 Dihedral : 10.137 161.795 3774 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: -0.06 (0.17), residues: 2466 helix: 1.49 (0.17), residues: 954 sheet: -0.35 (0.24), residues: 510 loop : -1.39 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 689 TYR 0.019 0.002 TYR A 461 PHE 0.020 0.002 PHE B 379 TRP 0.041 0.002 TRP B 386 HIS 0.011 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.21 (22736) covalent geometry : angle 0.71947 / 0.35 (31125) hydrogen bonds : bond 0.04586 / 2.37 ( 1035) hydrogen bonds : angle 4.94275 / 1.99 ( 2857) metal coordination : bond 0.01367 / 0.69 ( 12) metal coordination : angle 7.87099 / 2.62 ( 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 210 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7573 (tpp) cc_final: 0.7195 (tpt) REVERT: A 567 MET cc_start: 0.6280 (mmm) cc_final: 0.5619 (mmm) REVERT: A 766 MET cc_start: 0.8650 (tmm) cc_final: 0.8407 (tmm) REVERT: A 854 MET cc_start: 0.9082 (tmm) cc_final: 0.8383 (tmm) REVERT: A 878 MET cc_start: 0.9015 (mtm) cc_final: 0.8729 (mtm) REVERT: A 968 TRP cc_start: 0.6588 (m-10) cc_final: 0.6194 (m-10) REVERT: B 345 TYR cc_start: 0.7418 (m-80) cc_final: 0.7120 (m-80) REVERT: B 368 PHE cc_start: 0.8130 (m-80) cc_final: 0.7373 (m-80) REVERT: B 369 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6985 (tm-30) REVERT: B 415 ASN cc_start: 0.7181 (m110) cc_final: 0.6894 (m-40) REVERT: B 453 MET cc_start: 0.7365 (ppp) cc_final: 0.6589 (ppp) REVERT: B 489 PHE cc_start: 0.9441 (m-10) cc_final: 0.9012 (m-10) REVERT: B 497 LEU cc_start: 0.9122 (tp) cc_final: 0.8871 (tp) REVERT: C 313 MET cc_start: 0.7919 (tpp) cc_final: 0.7714 (tpt) REVERT: C 709 MET cc_start: 0.8992 (mmm) cc_final: 0.8758 (mmm) REVERT: C 864 MET cc_start: 0.7660 (mtp) cc_final: 0.6935 (ttm) REVERT: C 908 LYS cc_start: 0.6932 (mtpt) cc_final: 0.6567 (mttt) REVERT: C 926 MET cc_start: 0.8626 (mmt) cc_final: 0.8323 (tpp) REVERT: C 968 TRP cc_start: 0.6685 (m-10) cc_final: 0.5822 (m100) REVERT: D 343 HIS cc_start: 0.8187 (m-70) cc_final: 0.7765 (m90) REVERT: D 368 PHE cc_start: 0.7923 (m-80) cc_final: 0.7627 (m-10) REVERT: D 386 TRP cc_start: 0.6783 (p-90) cc_final: 0.6437 (p90) REVERT: D 408 ARG cc_start: 0.8050 (ptm160) cc_final: 0.7786 (tmm-80) REVERT: D 415 ASN cc_start: 0.7432 (m-40) cc_final: 0.7144 (m-40) REVERT: D 453 MET cc_start: 0.7433 (ppp) cc_final: 0.6478 (ppp) REVERT: D 461 CYS cc_start: 0.6404 (m) cc_final: 0.6159 (m) REVERT: E 313 MET cc_start: 0.7497 (tpp) cc_final: 0.7287 (tpp) REVERT: E 445 CYS cc_start: 0.7847 (p) cc_final: 0.7575 (p) REVERT: E 854 MET cc_start: 0.8995 (tmm) cc_final: 0.8230 (tmm) REVERT: E 878 MET cc_start: 0.8912 (mtp) cc_final: 0.8596 (mtp) REVERT: E 968 TRP cc_start: 0.6682 (m-10) cc_final: 0.5708 (m100) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1486 time to fit residues: 50.3752 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 : 0.715 ------------------------------------------------------------------------------- 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: 8.9990 chunk 103 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 220 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3312 r_free = 0.3312 target = 0.058268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044705 restraints weight = 338128.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.046969 restraints weight = 136737.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.047912 restraints weight = 65650.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.047723 restraints weight = 51633.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.047906 restraints weight = 50351.179| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 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 = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3356 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= 0.142 Angle : 0.669 11.491 31143 Z= 0.315 Chirality : 0.047 0.319 3551 Planarity : 0.004 0.036 3631 Dihedral : 9.757 160.940 3774 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.17), residues: 2466 helix: 1.75 (0.17), residues: 957 sheet: -0.30 (0.24), residues: 510 loop : -1.29 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 689 TYR 0.013 0.001 TYR A 461 PHE 0.018 0.001 PHE D 379 TRP 0.042 0.001 TRP B 386 HIS 0.007 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (22736) covalent geometry : angle 0.64732 / 0.31 (31125) hydrogen bonds : bond 0.04037 / 2.09 ( 1035) hydrogen bonds : angle 4.66654 / 1.89 ( 2857) metal coordination : bond 0.00910 / 0.45 ( 12) metal coordination : angle 7.06663 / 2.36 ( 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 215 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7528 (tpp) cc_final: 0.7164 (tpt) REVERT: A 567 MET cc_start: 0.6207 (mmm) cc_final: 0.5621 (mmm) REVERT: A 677 MET cc_start: 0.8874 (mpp) cc_final: 0.8673 (mpp) REVERT: A 766 MET cc_start: 0.8666 (tmm) cc_final: 0.8381 (tmm) REVERT: A 854 MET cc_start: 0.9076 (tmm) cc_final: 0.8797 (tmm) REVERT: A 878 MET cc_start: 0.8927 (mtm) cc_final: 0.8567 (mtp) REVERT: A 968 TRP cc_start: 0.6492 (m-10) cc_final: 0.6141 (m-10) REVERT: B 345 TYR cc_start: 0.7417 (m-80) cc_final: 0.7145 (m-80) REVERT: B 415 ASN cc_start: 0.7154 (m110) cc_final: 0.6891 (m-40) REVERT: B 453 MET cc_start: 0.7443 (ppp) cc_final: 0.6659 (ppp) REVERT: C 313 MET cc_start: 0.7893 (tpp) cc_final: 0.7540 (tpt) REVERT: C 854 MET cc_start: 0.9049 (tmm) cc_final: 0.8654 (tmm) REVERT: C 864 MET cc_start: 0.7509 (mtp) cc_final: 0.6750 (ttm) REVERT: C 882 MET cc_start: 0.5275 (mpp) cc_final: 0.4928 (mpp) REVERT: C 908 LYS cc_start: 0.6871 (mtpt) cc_final: 0.6452 (mttt) REVERT: C 926 MET cc_start: 0.8573 (mmt) cc_final: 0.8281 (tpp) REVERT: C 968 TRP cc_start: 0.6351 (m-10) cc_final: 0.5325 (m100) REVERT: D 343 HIS cc_start: 0.8140 (m-70) cc_final: 0.7777 (m90) REVERT: D 408 ARG cc_start: 0.8057 (ptm160) cc_final: 0.7778 (tmm-80) REVERT: D 415 ASN cc_start: 0.7359 (m-40) cc_final: 0.7077 (m-40) REVERT: D 461 CYS cc_start: 0.6532 (m) cc_final: 0.6245 (m) REVERT: D 475 TYR cc_start: 0.6951 (t80) cc_final: 0.6742 (t80) REVERT: E 313 MET cc_start: 0.7418 (tpp) cc_final: 0.7073 (tpp) REVERT: E 445 CYS cc_start: 0.7822 (p) cc_final: 0.7478 (p) REVERT: E 854 MET cc_start: 0.8940 (tmm) cc_final: 0.8310 (tmm) REVERT: E 968 TRP cc_start: 0.6614 (m-10) cc_final: 0.5590 (m-10) REVERT: F 408 ARG cc_start: 0.7510 (ptm-80) cc_final: 0.7297 (tmm-80) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.1567 time to fit residues: 54.1337 Evaluate side-chains 175 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.864 ------------------------------------------------------------------------------- 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: 9.9990 chunk 174 optimal weight: 30.0000 chunk 100 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 120 optimal weight: 0.2980 chunk 219 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 250 optimal weight: 9.9990 chunk 173 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS F 352 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.058351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.044841 restraints weight = 282449.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.046854 restraints weight = 128582.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.047668 restraints weight = 66378.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.047938 restraints weight = 48064.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.048057 restraints weight = 46754.614| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 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 = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3474 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= 0.143 Angle : 0.670 10.615 31143 Z= 0.316 Chirality : 0.047 0.301 3551 Planarity : 0.004 0.036 3631 Dihedral : 9.610 161.460 3774 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: 0.22 (0.18), residues: 2466 helix: 1.79 (0.17), residues: 957 sheet: -0.27 (0.24), residues: 510 loop : -1.27 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 689 TYR 0.014 0.001 TYR E 623 PHE 0.011 0.001 PHE A 681 TRP 0.036 0.001 TRP B 386 HIS 0.006 0.001 HIS B 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (22736) covalent geometry : angle 0.65178 / 0.32 (31125) hydrogen bonds : bond 0.03996 / 2.07 ( 1035) hydrogen bonds : angle 4.65491 / 1.88 ( 2857) metal coordination : bond 0.00822 / 0.41 ( 12) metal coordination : angle 6.53167 / 2.18 ( 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 213 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7553 (tpp) cc_final: 0.7154 (tpt) REVERT: A 567 MET cc_start: 0.6221 (mmm) cc_final: 0.5604 (mmm) REVERT: A 766 MET cc_start: 0.8654 (tmm) cc_final: 0.8369 (tmm) REVERT: A 854 MET cc_start: 0.9130 (tmm) cc_final: 0.8830 (tmm) REVERT: A 878 MET cc_start: 0.8935 (mtm) cc_final: 0.8569 (mtp) REVERT: A 968 TRP cc_start: 0.6517 (m-10) cc_final: 0.6154 (m-10) REVERT: B 345 TYR cc_start: 0.7335 (m-80) cc_final: 0.7026 (m-80) REVERT: B 415 ASN cc_start: 0.7214 (m110) cc_final: 0.6995 (m-40) REVERT: B 453 MET cc_start: 0.7549 (ppp) cc_final: 0.6681 (ppp) REVERT: B 489 PHE cc_start: 0.9361 (m-10) cc_final: 0.9055 (m-10) REVERT: B 497 LEU cc_start: 0.9060 (tp) cc_final: 0.8832 (tp) REVERT: C 313 MET cc_start: 0.7857 (tpp) cc_final: 0.7511 (tpt) REVERT: C 854 MET cc_start: 0.9062 (tmm) cc_final: 0.8427 (tmm) REVERT: C 864 MET cc_start: 0.7522 (mtp) cc_final: 0.6730 (ttm) REVERT: C 878 MET cc_start: 0.8853 (mtp) cc_final: 0.8644 (mtp) REVERT: C 882 MET cc_start: 0.5189 (mpp) cc_final: 0.4858 (mpp) REVERT: C 926 MET cc_start: 0.8598 (mmt) cc_final: 0.8326 (tpp) REVERT: C 968 TRP cc_start: 0.6570 (m-10) cc_final: 0.5620 (m100) REVERT: D 343 HIS cc_start: 0.8198 (m-70) cc_final: 0.7763 (m90) REVERT: D 368 PHE cc_start: 0.7970 (m-80) cc_final: 0.7722 (m-80) REVERT: D 408 ARG cc_start: 0.8007 (ptm160) cc_final: 0.7741 (tmm-80) REVERT: D 415 ASN cc_start: 0.7350 (m-40) cc_final: 0.7090 (m-40) REVERT: D 461 CYS cc_start: 0.6513 (m) cc_final: 0.6278 (m) REVERT: D 489 PHE cc_start: 0.9162 (m-80) cc_final: 0.8667 (m-80) REVERT: E 313 MET cc_start: 0.7491 (tpp) cc_final: 0.7138 (tpp) REVERT: E 567 MET cc_start: 0.5902 (mmt) cc_final: 0.5588 (mmm) REVERT: E 854 MET cc_start: 0.8985 (tmm) cc_final: 0.8681 (tmm) REVERT: E 878 MET cc_start: 0.8849 (mtp) cc_final: 0.8471 (mtp) REVERT: E 968 TRP cc_start: 0.6648 (m-10) cc_final: 0.5604 (m-10) REVERT: F 408 ARG cc_start: 0.7852 (ptm-80) cc_final: 0.6473 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1522 time to fit residues: 52.0714 Evaluate side-chains 161 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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: 4.9990 chunk 251 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 225 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 246 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 371 GLN ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS ** E 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.057648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.044739 restraints weight = 194727.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.046222 restraints weight = 104345.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.046919 restraints weight = 62031.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.047135 restraints weight = 45712.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.047321 restraints weight = 44729.143| |-----------------------------------------------------------------------------| 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 22748 Z= 0.184 Angle : 0.718 11.776 31143 Z= 0.341 Chirality : 0.049 0.287 3551 Planarity : 0.004 0.044 3631 Dihedral : 9.729 162.058 3774 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % 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: 0.01 (0.17), residues: 2466 helix: 1.61 (0.17), residues: 954 sheet: -0.42 (0.24), residues: 510 loop : -1.34 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 689 TYR 0.017 0.002 TYR A 461 PHE 0.014 0.001 PHE A 681 TRP 0.033 0.002 TRP B 386 HIS 0.008 0.001 HIS F 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (22736) covalent geometry : angle 0.69881 / 0.34 (31125) hydrogen bonds : bond 0.04346 / 2.25 ( 1035) hydrogen bonds : angle 4.83325 / 1.95 ( 2857) metal coordination : bond 0.00989 / 0.50 ( 12) metal coordination : angle 6.82424 / 2.27 ( 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 202 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7522 (tpp) cc_final: 0.7167 (tpt) REVERT: A 567 MET cc_start: 0.6237 (mmm) cc_final: 0.5666 (mmm) REVERT: A 854 MET cc_start: 0.9106 (tmm) cc_final: 0.8382 (tmm) REVERT: A 968 TRP cc_start: 0.6546 (m-10) cc_final: 0.6163 (m-10) REVERT: B 345 TYR cc_start: 0.7392 (m-80) cc_final: 0.7051 (m-80) REVERT: B 415 ASN cc_start: 0.7195 (m-40) cc_final: 0.6975 (m-40) REVERT: B 453 MET cc_start: 0.7913 (ppp) cc_final: 0.6867 (ppp) REVERT: C 313 MET cc_start: 0.7837 (tpp) cc_final: 0.7498 (tpt) REVERT: C 864 MET cc_start: 0.7504 (mtp) cc_final: 0.6780 (ttm) REVERT: C 926 MET cc_start: 0.8596 (mmt) cc_final: 0.8309 (tpp) REVERT: C 968 TRP cc_start: 0.6635 (m-10) cc_final: 0.5791 (m100) REVERT: D 343 HIS cc_start: 0.8154 (m-70) cc_final: 0.7757 (m90) REVERT: D 368 PHE cc_start: 0.7949 (m-80) cc_final: 0.7678 (m-80) REVERT: D 408 ARG cc_start: 0.8043 (ptm160) cc_final: 0.7758 (tmm-80) REVERT: D 415 ASN cc_start: 0.7336 (m-40) cc_final: 0.7098 (m-40) REVERT: D 475 TYR cc_start: 0.6829 (t80) cc_final: 0.6624 (t80) REVERT: D 489 PHE cc_start: 0.9156 (m-80) cc_final: 0.8599 (m-80) REVERT: E 313 MET cc_start: 0.7429 (tpp) cc_final: 0.7079 (tpp) REVERT: E 567 MET cc_start: 0.6095 (mmt) cc_final: 0.5717 (mmm) REVERT: E 854 MET cc_start: 0.8962 (tmm) cc_final: 0.8613 (tmm) REVERT: E 968 TRP cc_start: 0.6668 (m-10) cc_final: 0.5677 (m-10) REVERT: F 408 ARG cc_start: 0.7547 (ptm-80) cc_final: 0.6315 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1507 time to fit residues: 49.4385 Evaluate side-chains 161 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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: 10.0000 chunk 228 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 chunk 216 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 63 optimal weight: 0.0370 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** C 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN ** E 562 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.057639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.044213 restraints weight = 323596.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.046417 restraints weight = 134841.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.047129 restraints weight = 66371.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.047071 restraints weight = 53341.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.047303 restraints weight = 52176.726| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 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 = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22748 Z= 0.193 Angle : 0.728 11.673 31143 Z= 0.346 Chirality : 0.050 0.296 3551 Planarity : 0.004 0.040 3631 Dihedral : 9.721 162.416 3774 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % 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: -0.06 (0.17), residues: 2466 helix: 1.55 (0.17), residues: 954 sheet: -0.48 (0.24), residues: 510 loop : -1.37 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 689 TYR 0.023 0.002 TYR B 475 PHE 0.014 0.002 PHE A 681 TRP 0.041 0.002 TRP B 386 HIS 0.010 0.001 HIS F 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (22736) covalent geometry : angle 0.70977 / 0.34 (31125) hydrogen bonds : bond 0.04377 / 2.26 ( 1035) hydrogen bonds : angle 4.88060 / 1.96 ( 2857) metal coordination : bond 0.01005 / 0.51 ( 12) metal coordination : angle 6.79307 / 2.26 ( 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 202 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.7560 (tpp) cc_final: 0.7200 (tpt) REVERT: A 567 MET cc_start: 0.6251 (mmm) cc_final: 0.5634 (mmm) REVERT: A 677 MET cc_start: 0.8869 (mpp) cc_final: 0.8667 (mpp) REVERT: A 816 MET cc_start: 0.8175 (tmm) cc_final: 0.7754 (tmm) REVERT: A 854 MET cc_start: 0.9035 (tmm) cc_final: 0.8508 (tmm) REVERT: A 968 TRP cc_start: 0.6491 (m-10) cc_final: 0.6106 (m-10) REVERT: B 415 ASN cc_start: 0.7287 (m-40) cc_final: 0.7074 (m-40) REVERT: B 453 MET cc_start: 0.7655 (ppp) cc_final: 0.6573 (ppp) REVERT: B 489 PHE cc_start: 0.9515 (m-10) cc_final: 0.9255 (m-10) REVERT: C 864 MET cc_start: 0.7627 (mtp) cc_final: 0.6877 (ttm) REVERT: C 926 MET cc_start: 0.8631 (mmt) cc_final: 0.8350 (tpp) REVERT: C 968 TRP cc_start: 0.6394 (m-10) cc_final: 0.5366 (m100) REVERT: D 343 HIS cc_start: 0.8135 (m-70) cc_final: 0.7719 (m90) REVERT: D 368 PHE cc_start: 0.8028 (m-80) cc_final: 0.7750 (m-80) REVERT: D 408 ARG cc_start: 0.8061 (ptm160) cc_final: 0.7738 (tmm-80) REVERT: D 415 ASN cc_start: 0.7370 (m-40) cc_final: 0.7112 (m-40) REVERT: D 489 PHE cc_start: 0.9241 (m-80) cc_final: 0.8665 (m-80) REVERT: E 313 MET cc_start: 0.7479 (tpp) cc_final: 0.7134 (tpp) REVERT: E 567 MET cc_start: 0.6122 (mmt) cc_final: 0.5746 (mmm) REVERT: E 854 MET cc_start: 0.8968 (tmm) cc_final: 0.8624 (tmm) REVERT: E 968 TRP cc_start: 0.6577 (m-10) cc_final: 0.5614 (m-10) REVERT: F 408 ARG cc_start: 0.7346 (ptm-80) cc_final: 0.5703 (ptp-110) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1540 time to fit residues: 50.3312 Evaluate side-chains 163 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.852 ------------------------------------------------------------------------------- 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: 10.0000 chunk 115 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 217 optimal weight: 7.9990 chunk 168 optimal weight: 7.9990 chunk 180 optimal weight: 8.9990 chunk 99 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 214 optimal weight: 0.7980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 HIS ** C 966 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.059061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.045532 restraints weight = 272712.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.047663 restraints weight = 124009.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.048287 restraints weight = 64169.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.048453 restraints weight = 50713.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048645 restraints weight = 48572.504| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3027 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3027 r_free = 0.3027 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 = 0.3027 r_free = 0.3027 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 24 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3027 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22748 Z= 0.116 Angle : 0.646 9.154 31143 Z= 0.304 Chirality : 0.046 0.295 3551 Planarity : 0.004 0.037 3631 Dihedral : 9.354 160.861 3774 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % 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: 1.85 (0.17), residues: 960 sheet: -0.41 (0.24), residues: 507 loop : -1.21 (0.20), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 689 TYR 0.016 0.001 TYR E 623 PHE 0.011 0.001 PHE C 629 TRP 0.045 0.001 TRP B 386 HIS 0.008 0.001 HIS F 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 (22736) covalent geometry : angle 0.63065 / 0.30 (31125) hydrogen bonds : bond 0.03790 / 1.96 ( 1035) hydrogen bonds : angle 4.53265 / 1.83 ( 2857) metal coordination : bond 0.00724 / 0.37 ( 12) metal coordination : angle 5.76469 / 1.92 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3609.15 seconds wall clock time: 63 minutes 32.84 seconds (3812.84 seconds total)