Starting phenix.real_space_refine on Sat Aug 23 07:27:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j62_35999/08_2025/8j62_35999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j62_35999/08_2025/8j62_35999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2025/8j62_35999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2025/8j62_35999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2025/8j62_35999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j62_35999/08_2025/8j62_35999.map" } resolution = 2.5 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= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 36 5.49 5 S 48 5.16 5 C 6578 2.51 5 N 1826 2.21 5 O 1958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10448 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1521 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 7, 'TRANS': 172} Chain: "C" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1075 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 844 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 912 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "F" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 480 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain breaks: 4 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 96 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "X" Number of atoms: 391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 391 Classifications: {'RNA': 19} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 7, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 5} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%rna3p_pyr:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 749 SG CYS A 84 32.319 53.134 49.548 1.00 41.85 S ATOM 771 SG CYS A 87 33.682 51.225 51.830 1.00 42.44 S Restraints were copied for chains: B, G, H, I, J, Y Time building chain proxies: 2.55, per 1000 atoms: 0.24 Number of scatterers: 10448 At special positions: 0 Unit cell: (86.0096, 109.933, 105.376, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 48 16.00 P 36 15.00 O 1958 8.00 N 1826 7.00 C 6578 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: 0.98 Conformation dependent library (CDL) restraints added in 364.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" ND1 HIS A 53 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 87 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 84 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 87 " pdb="ZN ZN B 401 " - pdb=" ND1 HIS B 53 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 84 " 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2240 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 14 sheets defined 35.9% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 2 through 10 Processing helix chain 'A' and resid 53 through 66 removed outlier: 3.656A pdb=" N LYS A 66 " --> pdb=" O VAL A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 98 Processing helix chain 'A' and resid 115 through 128 Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 160 through 177 Processing helix chain 'C' and resid 14 through 31 Processing helix chain 'C' and resid 42 through 46 removed outlier: 3.566A pdb=" N SER C 46 " --> pdb=" O HIS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 111 Processing helix chain 'C' and resid 165 through 171 Processing helix chain 'D' and resid 18 through 24 removed outlier: 3.898A pdb=" N GLU D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 50 Processing helix chain 'D' and resid 72 through 74 No H-bonds generated for 'chain 'D' and resid 72 through 74' Processing helix chain 'E' and resid 14 through 31 Processing helix chain 'E' and resid 42 through 46 removed outlier: 3.516A pdb=" N GLU E 45 " --> pdb=" O HIS E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 111 removed outlier: 3.659A pdb=" N GLN E 105 " --> pdb=" O ASP E 101 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 171 removed outlier: 3.556A pdb=" N LEU E 169 " --> pdb=" O SER E 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 51 Processing helix chain 'F' and resid 70 through 74 Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 53 through 66 removed outlier: 3.656A pdb=" N LYS B 66 " --> pdb=" O VAL B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 98 Processing helix chain 'B' and resid 115 through 128 Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 160 through 177 Processing helix chain 'G' and resid 14 through 31 Processing helix chain 'G' and resid 42 through 46 removed outlier: 3.566A pdb=" N SER G 46 " --> pdb=" O HIS G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 111 Processing helix chain 'G' and resid 165 through 171 Processing helix chain 'H' and resid 18 through 24 removed outlier: 3.898A pdb=" N GLU H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 50 Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'I' and resid 14 through 31 Processing helix chain 'I' and resid 42 through 46 removed outlier: 3.516A pdb=" N GLU I 45 " --> pdb=" O HIS I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 111 removed outlier: 3.659A pdb=" N GLN I 105 " --> pdb=" O ASP I 101 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N HIS I 110 " --> pdb=" O LEU I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 171 removed outlier: 3.558A pdb=" N LEU I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 38 through 51 Processing helix chain 'J' and resid 70 through 74 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 38 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 38 removed outlier: 6.897A pdb=" N TRP A 81 " --> pdb=" O ALA A 108 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 39 through 41 removed outlier: 4.876A pdb=" N ILE C 87 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE C 9 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 11.423A pdb=" N TRP C 89 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 14.227A pdb=" N VAL C 7 " --> pdb=" O TRP C 89 " (cutoff:3.500A) removed outlier: 18.909A pdb=" N LYS C 91 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 21.500A pdb=" N TRP C 5 " --> pdb=" O LYS C 91 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU D 64 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 55 " --> pdb=" O PHE D 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP D 120 " --> pdb=" O ASP D 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 41 removed outlier: 11.324A pdb=" N SER C 95 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ILE D 102 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.586A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU E 64 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG E 90 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE E 66 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU E 88 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR E 68 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP E 70 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY E 84 " --> pdb=" O TRP E 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 39 through 41 removed outlier: 6.586A pdb=" N THR E 68 " --> pdb=" O SER E 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU E 54 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE E 66 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS E 56 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU E 64 " --> pdb=" O HIS E 56 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N ALA E 62 " --> pdb=" O PRO E 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU E 64 " --> pdb=" O ARG E 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG E 90 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE E 66 " --> pdb=" O GLU E 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU E 88 " --> pdb=" O ILE E 66 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR E 68 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP E 70 " --> pdb=" O GLY E 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY E 84 " --> pdb=" O TRP E 70 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN E 83 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ILE E 87 " --> pdb=" O ILE E 9 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 9 " --> pdb=" O ILE E 87 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 96 through 103 Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 38 Processing sheet with id=AA9, first strand: chain 'B' and resid 35 through 38 removed outlier: 6.898A pdb=" N TRP B 81 " --> pdb=" O ALA B 108 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41 removed outlier: 4.877A pdb=" N ILE G 87 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ILE G 9 " --> pdb=" O ILE G 87 " (cutoff:3.500A) removed outlier: 11.421A pdb=" N TRP G 89 " --> pdb=" O VAL G 7 " (cutoff:3.500A) removed outlier: 14.228A pdb=" N VAL G 7 " --> pdb=" O TRP G 89 " (cutoff:3.500A) removed outlier: 18.909A pdb=" N LYS G 91 " --> pdb=" O TRP G 5 " (cutoff:3.500A) removed outlier: 21.500A pdb=" N TRP G 5 " --> pdb=" O LYS G 91 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N LEU H 64 " --> pdb=" O ALA H 59 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE H 55 " --> pdb=" O PHE H 68 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASP H 120 " --> pdb=" O ASP H 115 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 39 through 41 removed outlier: 11.323A pdb=" N SER G 95 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE H 102 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 39 through 41 removed outlier: 6.585A pdb=" N THR I 68 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU I 54 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE I 66 " --> pdb=" O GLU I 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS I 56 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 64 " --> pdb=" O HIS I 56 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU I 64 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG I 90 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE I 66 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU I 88 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR I 68 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER I 86 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP I 70 " --> pdb=" O GLY I 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY I 84 " --> pdb=" O TRP I 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 39 through 41 removed outlier: 6.585A pdb=" N THR I 68 " --> pdb=" O SER I 52 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU I 54 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE I 66 " --> pdb=" O GLU I 54 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N HIS I 56 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU I 64 " --> pdb=" O HIS I 56 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LEU I 64 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N ARG I 90 " --> pdb=" O LEU I 64 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ILE I 66 " --> pdb=" O GLU I 88 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU I 88 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N THR I 68 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER I 86 " --> pdb=" O THR I 68 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N TRP I 70 " --> pdb=" O GLY I 84 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLY I 84 " --> pdb=" O TRP I 70 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE I 87 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE I 9 " --> pdb=" O ILE I 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 96 through 103 582 hydrogen bonds defined for protein. 1566 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.00 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3012 1.34 - 1.45: 2237 1.45 - 1.57: 5425 1.57 - 1.69: 72 1.69 - 1.81: 76 Bond restraints: 10822 Sorted by residual: bond pdb=" CA TYR D 85 " pdb=" CB TYR D 85 " ideal model delta sigma weight residual 1.535 1.552 -0.017 2.09e-02 2.29e+03 6.29e-01 bond pdb=" CA TYR H 85 " pdb=" CB TYR H 85 " ideal model delta sigma weight residual 1.535 1.551 -0.016 2.09e-02 2.29e+03 5.61e-01 bond pdb=" CA GLY I 82 " pdb=" C GLY I 82 " ideal model delta sigma weight residual 1.522 1.515 0.007 1.06e-02 8.90e+03 4.67e-01 bond pdb=" CA GLY E 82 " pdb=" C GLY E 82 " ideal model delta sigma weight residual 1.522 1.515 0.007 1.06e-02 8.90e+03 4.47e-01 bond pdb=" CB GLU A 163 " pdb=" CG GLU A 163 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.15e-01 ... (remaining 10817 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.20: 14447 1.20 - 2.40: 304 2.40 - 3.60: 93 3.60 - 4.80: 8 4.80 - 6.00: 2 Bond angle restraints: 14854 Sorted by residual: angle pdb=" C VAL H 86 " pdb=" N ASP H 87 " pdb=" CA ASP H 87 " ideal model delta sigma weight residual 121.75 118.21 3.54 1.73e+00 3.34e-01 4.19e+00 angle pdb=" C3' U Y 11 " pdb=" O3' U Y 11 " pdb=" P U Y 12 " ideal model delta sigma weight residual 120.20 123.24 -3.04 1.50e+00 4.44e-01 4.11e+00 angle pdb=" C VAL D 86 " pdb=" N ASP D 87 " pdb=" CA ASP D 87 " ideal model delta sigma weight residual 121.75 118.25 3.50 1.73e+00 3.34e-01 4.08e+00 angle pdb=" C3' U X 11 " pdb=" O3' U X 11 " pdb=" P U X 12 " ideal model delta sigma weight residual 120.20 123.22 -3.02 1.50e+00 4.44e-01 4.06e+00 angle pdb=" C HIS I 28 " pdb=" N MET I 29 " pdb=" CA MET I 29 " ideal model delta sigma weight residual 121.66 118.60 3.06 1.76e+00 3.23e-01 3.03e+00 ... (remaining 14849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.69: 5926 32.69 - 65.37: 356 65.37 - 98.06: 26 98.06 - 130.74: 0 130.74 - 163.43: 2 Dihedral angle restraints: 6310 sinusoidal: 2858 harmonic: 3452 Sorted by residual: dihedral pdb=" O4' C Y 1 " pdb=" C1' C Y 1 " pdb=" N1 C Y 1 " pdb=" C2 C Y 1 " ideal model delta sinusoidal sigma weight residual 200.00 36.57 163.43 1 1.50e+01 4.44e-03 8.36e+01 dihedral pdb=" O4' C X 1 " pdb=" C1' C X 1 " pdb=" N1 C X 1 " pdb=" C2 C X 1 " ideal model delta sinusoidal sigma weight residual 200.00 36.64 163.36 1 1.50e+01 4.44e-03 8.35e+01 dihedral pdb=" CB GLU I 54 " pdb=" CG GLU I 54 " pdb=" CD GLU I 54 " pdb=" OE1 GLU I 54 " ideal model delta sinusoidal sigma weight residual 0.00 -90.15 90.15 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 6307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 961 0.027 - 0.053: 372 0.053 - 0.080: 126 0.080 - 0.106: 95 0.106 - 0.133: 40 Chirality restraints: 1594 Sorted by residual: chirality pdb=" CA ILE I 57 " pdb=" N ILE I 57 " pdb=" C ILE I 57 " pdb=" CB ILE I 57 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA ILE I 66 " pdb=" N ILE I 66 " pdb=" C ILE I 66 " pdb=" CB ILE I 66 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.29e-01 chirality pdb=" CA ILE E 57 " pdb=" N ILE E 57 " pdb=" C ILE E 57 " pdb=" CB ILE E 57 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 1591 not shown) Planarity restraints: 1728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 113 " -0.011 2.00e-02 2.50e+03 1.21e-02 3.66e+00 pdb=" CG TRP F 113 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP F 113 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP F 113 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 113 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 113 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 113 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 113 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 113 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP F 113 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP J 113 " 0.011 2.00e-02 2.50e+03 1.18e-02 3.50e+00 pdb=" CG TRP J 113 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP J 113 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP J 113 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP J 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP J 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP J 113 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP J 113 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP J 113 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP J 113 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 86 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.18e+00 pdb=" C VAL H 86 " -0.019 2.00e-02 2.50e+03 pdb=" O VAL H 86 " 0.007 2.00e-02 2.50e+03 pdb=" N ASP H 87 " 0.006 2.00e-02 2.50e+03 ... (remaining 1725 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1205 2.75 - 3.29: 9360 3.29 - 3.83: 18363 3.83 - 4.36: 22026 4.36 - 4.90: 37780 Nonbonded interactions: 88734 Sorted by model distance: nonbonded pdb=" OG SER H 53 " pdb=" O6 G Y 10 " model vdw 2.216 3.040 nonbonded pdb=" OG SER D 53 " pdb=" O6 G X 10 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR A 112 " pdb=" OP1 U X 8 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR B 112 " pdb=" OP1 U Y 8 " model vdw 2.227 3.040 nonbonded pdb=" NH2 ARG G 23 " pdb=" OP2 C Y 17 " model vdw 2.239 3.120 ... (remaining 88729 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'X' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.700 Find NCS groups from input model: 0.220 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:7.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 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 : 0.002 0.020 10828 Z= 0.092 Angle : 0.464 6.001 14854 Z= 0.252 Chirality : 0.041 0.133 1594 Planarity : 0.003 0.027 1728 Dihedral : 18.883 163.427 4070 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 2.91 % Allowed : 24.35 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.53 (0.25), residues: 1130 helix: 1.85 (0.28), residues: 352 sheet: 0.51 (0.27), residues: 326 loop : 0.93 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 118 TYR 0.014 0.001 TYR D 85 PHE 0.007 0.001 PHE A 58 TRP 0.033 0.001 TRP F 113 HIS 0.002 0.000 HIS H 37 Details of bonding type rmsd covalent geometry : bond 0.00184 (10822) covalent geometry : angle 0.46417 (14854) hydrogen bonds : bond 0.13887 ( 512) hydrogen bonds : angle 6.21967 ( 1566) metal coordination : bond 0.00103 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 323 time to evaluate : 0.496 Fit side-chains REVERT: C 99 ASP cc_start: 0.7721 (p0) cc_final: 0.7166 (p0) REVERT: E 88 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7088 (tm-30) REVERT: H 21 LEU cc_start: 0.8074 (mp) cc_final: 0.7857 (mp) outliers start: 29 outliers final: 16 residues processed: 341 average time/residue: 0.7315 time to fit residues: 264.6384 Evaluate side-chains 276 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 260 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 114 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.0050 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 20.0000 chunk 100 optimal weight: 0.9980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 43 HIS D 45 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN G 43 HIS ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.125411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.097823 restraints weight = 18123.842| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 2.63 r_work: 0.3464 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10828 Z= 0.114 Angle : 0.533 5.877 14854 Z= 0.281 Chirality : 0.042 0.147 1594 Planarity : 0.004 0.027 1728 Dihedral : 15.002 160.162 1868 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 3.61 % Allowed : 27.96 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.68 (0.25), residues: 1130 helix: 1.76 (0.27), residues: 374 sheet: 0.72 (0.27), residues: 328 loop : 1.09 (0.33), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 49 TYR 0.017 0.001 TYR J 29 PHE 0.007 0.001 PHE F 44 TRP 0.023 0.001 TRP J 113 HIS 0.004 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00250 (10822) covalent geometry : angle 0.53346 (14854) hydrogen bonds : bond 0.03137 ( 512) hydrogen bonds : angle 4.99310 ( 1566) metal coordination : bond 0.00149 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 273 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.7884 (m110) cc_final: 0.7610 (m110) REVERT: C 167 ARG cc_start: 0.8400 (mtm-85) cc_final: 0.8158 (ttm-80) REVERT: D 122 MET cc_start: 0.8831 (mmp) cc_final: 0.8612 (mmp) REVERT: E 17 ARG cc_start: 0.8693 (mtt-85) cc_final: 0.8311 (ttp80) REVERT: E 88 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6380 (tm-30) REVERT: G 99 ASP cc_start: 0.7732 (p0) cc_final: 0.7406 (p0) REVERT: G 101 ASP cc_start: 0.8583 (m-30) cc_final: 0.8195 (p0) REVERT: G 108 HIS cc_start: 0.8437 (m-70) cc_final: 0.8106 (t-90) REVERT: H 122 MET cc_start: 0.8796 (mmp) cc_final: 0.8541 (mmp) REVERT: I 17 ARG cc_start: 0.8691 (mtt-85) cc_final: 0.8356 (ttp-170) REVERT: I 88 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.6489 (tm-30) outliers start: 36 outliers final: 17 residues processed: 290 average time/residue: 0.7134 time to fit residues: 219.3389 Evaluate side-chains 278 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 259 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 63 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 114 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 88 optimal weight: 20.0000 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN D 45 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 HIS ** 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 = 0.4064 r_free = 0.4064 target = 0.124427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.096694 restraints weight = 18084.021| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 2.65 r_work: 0.3447 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10828 Z= 0.111 Angle : 0.527 6.412 14854 Z= 0.275 Chirality : 0.042 0.172 1594 Planarity : 0.004 0.027 1728 Dihedral : 14.802 160.359 1854 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 5.31 % Allowed : 28.26 % Favored : 66.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.80 (0.25), residues: 1130 helix: 1.92 (0.26), residues: 374 sheet: 0.79 (0.27), residues: 324 loop : 1.08 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 49 TYR 0.010 0.001 TYR G 69 PHE 0.006 0.001 PHE F 57 TRP 0.023 0.001 TRP J 113 HIS 0.003 0.001 HIS G 43 Details of bonding type rmsd covalent geometry : bond 0.00251 (10822) covalent geometry : angle 0.52692 (14854) hydrogen bonds : bond 0.02923 ( 512) hydrogen bonds : angle 4.77507 ( 1566) metal coordination : bond 0.00146 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 271 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 ASN cc_start: 0.8039 (OUTLIER) cc_final: 0.7709 (m110) REVERT: C 167 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.8168 (ttm-80) REVERT: D 28 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8213 (ptmm) REVERT: E 12 GLN cc_start: 0.8388 (mp10) cc_final: 0.8140 (mp10) REVERT: E 88 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: G 91 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8192 (tppt) REVERT: G 99 ASP cc_start: 0.7900 (p0) cc_final: 0.7579 (p0) REVERT: G 101 ASP cc_start: 0.8540 (m-30) cc_final: 0.8171 (p0) REVERT: G 108 HIS cc_start: 0.8430 (m-70) cc_final: 0.8167 (t-90) REVERT: H 21 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8140 (mp) REVERT: I 12 GLN cc_start: 0.8408 (mp10) cc_final: 0.8137 (mp10) REVERT: I 17 ARG cc_start: 0.8631 (mtt-85) cc_final: 0.8422 (ttp-170) REVERT: I 88 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6530 (tm-30) outliers start: 53 outliers final: 27 residues processed: 292 average time/residue: 0.6929 time to fit residues: 214.7474 Evaluate side-chains 283 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 41 ARG Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 28 LYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 8 MET Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 91 LYS Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 107 ILE Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 8 MET Chi-restraints excluded: chain I residue 88 GLU Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 95 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 104 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN B 96 GLN ** I 28 HIS ** 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 = 0.3969 r_free = 0.3969 target = 0.118024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090166 restraints weight = 18265.426| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.61 r_work: 0.3325 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10828 Z= 0.240 Angle : 0.614 7.385 14854 Z= 0.323 Chirality : 0.046 0.158 1594 Planarity : 0.004 0.026 1728 Dihedral : 15.060 166.801 1854 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 6.01 % Allowed : 27.96 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.68 (0.25), residues: 1130 helix: 1.77 (0.26), residues: 378 sheet: 0.69 (0.27), residues: 326 loop : 1.09 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 49 TYR 0.022 0.002 TYR J 29 PHE 0.012 0.002 PHE A 140 TRP 0.019 0.001 TRP I 89 HIS 0.004 0.001 HIS G 56 Details of bonding type rmsd covalent geometry : bond 0.00545 (10822) covalent geometry : angle 0.61379 (14854) hydrogen bonds : bond 0.03372 ( 512) hydrogen bonds : angle 5.00254 ( 1566) metal coordination : bond 0.00525 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 244 time to evaluate : 0.445 Fit side-chains REVERT: A 50 LEU cc_start: 0.9093 (mt) cc_final: 0.8818 (mm) REVERT: A 57 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7990 (ttm110) REVERT: A 97 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8202 (mt-10) REVERT: A 166 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: C 167 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.8184 (ttm-80) REVERT: D 20 LYS cc_start: 0.9350 (ttpp) cc_final: 0.9143 (tmmt) REVERT: D 30 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.8043 (m) REVERT: E 12 GLN cc_start: 0.8269 (mp10) cc_final: 0.7989 (mp10) REVERT: E 17 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8209 (ttp-170) REVERT: E 88 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6901 (tm-30) REVERT: E 97 GLN cc_start: 0.7485 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: B 166 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8230 (mp10) REVERT: G 108 HIS cc_start: 0.8530 (m-70) cc_final: 0.8263 (t-90) REVERT: H 30 THR cc_start: 0.8277 (OUTLIER) cc_final: 0.8034 (m) REVERT: I 12 GLN cc_start: 0.8301 (mp10) cc_final: 0.7992 (mp10) REVERT: I 97 GLN cc_start: 0.7432 (OUTLIER) cc_final: 0.7127 (mp10) outliers start: 60 outliers final: 28 residues processed: 277 average time/residue: 0.7264 time to fit residues: 212.8962 Evaluate side-chains 270 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 85 VAL Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 81 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 97 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN C 110 HIS ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 41 GLN B 96 GLN H 45 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 41 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.120808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.093499 restraints weight = 18059.144| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.58 r_work: 0.3388 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10828 Z= 0.131 Angle : 0.575 10.072 14854 Z= 0.295 Chirality : 0.043 0.152 1594 Planarity : 0.004 0.040 1728 Dihedral : 14.985 165.629 1854 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 5.01 % Allowed : 29.06 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.78 (0.25), residues: 1130 helix: 1.97 (0.27), residues: 376 sheet: 0.74 (0.27), residues: 328 loop : 1.02 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 49 TYR 0.010 0.001 TYR C 69 PHE 0.007 0.001 PHE A 58 TRP 0.017 0.001 TRP I 89 HIS 0.002 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00298 (10822) covalent geometry : angle 0.57450 (14854) hydrogen bonds : bond 0.02946 ( 512) hydrogen bonds : angle 4.82559 ( 1566) metal coordination : bond 0.00186 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 249 time to evaluate : 0.260 Fit side-chains REVERT: A 50 LEU cc_start: 0.9029 (mt) cc_final: 0.8771 (mm) REVERT: A 57 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7909 (ttm110) REVERT: A 136 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7998 (m110) REVERT: A 166 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: C 167 ARG cc_start: 0.8451 (mtm-85) cc_final: 0.8216 (ttm-80) REVERT: D 20 LYS cc_start: 0.9351 (ttpp) cc_final: 0.9107 (tmmt) REVERT: D 35 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8251 (mmm160) REVERT: E 12 GLN cc_start: 0.8281 (mp10) cc_final: 0.7911 (mp10) REVERT: E 17 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8140 (ttp-170) REVERT: E 104 ASP cc_start: 0.7636 (m-30) cc_final: 0.7421 (m-30) REVERT: B 50 LEU cc_start: 0.9014 (mt) cc_final: 0.8678 (mm) REVERT: B 89 ARG cc_start: 0.8664 (ttp-110) cc_final: 0.8234 (mtm110) REVERT: B 166 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8158 (mp10) REVERT: G 108 HIS cc_start: 0.8478 (m-70) cc_final: 0.8258 (t-90) REVERT: H 21 LEU cc_start: 0.8737 (mp) cc_final: 0.8531 (mp) REVERT: I 12 GLN cc_start: 0.8332 (mp10) cc_final: 0.7906 (mp10) REVERT: J 68 PHE cc_start: 0.8099 (m-80) cc_final: 0.6071 (t80) outliers start: 50 outliers final: 29 residues processed: 274 average time/residue: 0.6247 time to fit residues: 181.2293 Evaluate side-chains 271 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 237 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 51 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 98 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS J 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.118925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091394 restraints weight = 18216.590| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.54 r_work: 0.3349 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10828 Z= 0.183 Angle : 0.599 9.720 14854 Z= 0.309 Chirality : 0.044 0.162 1594 Planarity : 0.004 0.039 1728 Dihedral : 15.027 166.385 1854 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 5.11 % Allowed : 28.86 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.74 (0.25), residues: 1130 helix: 1.98 (0.26), residues: 376 sheet: 0.65 (0.28), residues: 330 loop : 1.01 (0.33), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 23 TYR 0.021 0.001 TYR J 29 PHE 0.008 0.001 PHE A 58 TRP 0.012 0.001 TRP I 89 HIS 0.007 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00420 (10822) covalent geometry : angle 0.59881 (14854) hydrogen bonds : bond 0.03168 ( 512) hydrogen bonds : angle 4.90423 ( 1566) metal coordination : bond 0.00344 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9062 (mt) cc_final: 0.8824 (mm) REVERT: A 57 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.7942 (ttm110) REVERT: A 89 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8250 (mtm110) REVERT: A 97 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: A 136 ASN cc_start: 0.8266 (OUTLIER) cc_final: 0.7993 (m110) REVERT: A 166 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8223 (mp10) REVERT: C 167 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8221 (ttm-80) REVERT: D 30 THR cc_start: 0.8249 (OUTLIER) cc_final: 0.8007 (m) REVERT: D 35 ARG cc_start: 0.8430 (mmm-85) cc_final: 0.8156 (mmp-170) REVERT: E 12 GLN cc_start: 0.8283 (mp10) cc_final: 0.7893 (mp10) REVERT: E 17 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8190 (ttp-170) REVERT: E 97 GLN cc_start: 0.7459 (OUTLIER) cc_final: 0.7215 (mp10) REVERT: B 50 LEU cc_start: 0.9042 (mt) cc_final: 0.8734 (mm) REVERT: B 86 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8305 (pttm) REVERT: B 89 ARG cc_start: 0.8667 (ttp-110) cc_final: 0.8262 (mtm110) REVERT: B 166 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8210 (mp10) REVERT: G 88 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7478 (pt0) REVERT: G 99 ASP cc_start: 0.8125 (p0) cc_final: 0.7758 (p0) REVERT: G 101 ASP cc_start: 0.8481 (m-30) cc_final: 0.8165 (p0) REVERT: H 20 LYS cc_start: 0.9381 (ttpp) cc_final: 0.9155 (tmmt) REVERT: I 12 GLN cc_start: 0.8248 (mp10) cc_final: 0.7790 (mp10) REVERT: I 17 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8000 (mtp85) REVERT: I 171 GLU cc_start: 0.8348 (pp20) cc_final: 0.8016 (pp20) outliers start: 51 outliers final: 31 residues processed: 274 average time/residue: 0.6562 time to fit residues: 190.6894 Evaluate side-chains 278 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 97 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS B 96 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.119359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.091788 restraints weight = 17951.634| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.60 r_work: 0.3355 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10828 Z= 0.166 Angle : 0.608 10.721 14854 Z= 0.311 Chirality : 0.044 0.150 1594 Planarity : 0.004 0.045 1728 Dihedral : 15.019 166.446 1854 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 5.31 % Allowed : 28.76 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.77 (0.26), residues: 1130 helix: 2.00 (0.27), residues: 376 sheet: 0.75 (0.28), residues: 324 loop : 0.95 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 90 TYR 0.011 0.001 TYR D 96 PHE 0.007 0.001 PHE A 58 TRP 0.013 0.001 TRP I 89 HIS 0.007 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00379 (10822) covalent geometry : angle 0.60842 (14854) hydrogen bonds : bond 0.03101 ( 512) hydrogen bonds : angle 4.86027 ( 1566) metal coordination : bond 0.00285 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 240 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 50 LEU cc_start: 0.9054 (mt) cc_final: 0.8829 (mm) REVERT: A 57 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7933 (ttm110) REVERT: A 86 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8327 (pttm) REVERT: A 89 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8272 (mtm110) REVERT: A 136 ASN cc_start: 0.8233 (OUTLIER) cc_final: 0.7949 (m110) REVERT: A 166 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: C 88 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: C 167 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.8229 (ttm-80) REVERT: D 30 THR cc_start: 0.8237 (OUTLIER) cc_final: 0.8004 (m) REVERT: D 35 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.8151 (mmp-170) REVERT: E 12 GLN cc_start: 0.8231 (mp10) cc_final: 0.7827 (mp10) REVERT: E 97 GLN cc_start: 0.7405 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: B 50 LEU cc_start: 0.9024 (mt) cc_final: 0.8739 (mm) REVERT: B 89 ARG cc_start: 0.8669 (ttp-110) cc_final: 0.8274 (mtm110) REVERT: B 166 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: G 88 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7448 (pt0) REVERT: G 99 ASP cc_start: 0.8128 (p0) cc_final: 0.7834 (p0) REVERT: G 101 ASP cc_start: 0.8490 (m-30) cc_final: 0.8161 (p0) REVERT: I 12 GLN cc_start: 0.8234 (mp10) cc_final: 0.7774 (mp10) REVERT: I 17 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7625 (mtp85) REVERT: I 171 GLU cc_start: 0.8264 (pp20) cc_final: 0.7477 (pm20) outliers start: 53 outliers final: 33 residues processed: 271 average time/residue: 0.6422 time to fit residues: 184.3673 Evaluate side-chains 279 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 18 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 0.0270 chunk 100 optimal weight: 9.9990 chunk 51 optimal weight: 30.0000 chunk 94 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 overall best weight: 1.4442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN G 110 HIS ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.120125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.092412 restraints weight = 17940.710| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.56 r_work: 0.3365 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10828 Z= 0.152 Angle : 0.610 10.183 14854 Z= 0.311 Chirality : 0.043 0.143 1594 Planarity : 0.004 0.034 1728 Dihedral : 14.981 165.904 1854 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.61 % Allowed : 29.96 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.82 (0.26), residues: 1130 helix: 2.05 (0.27), residues: 376 sheet: 0.79 (0.28), residues: 324 loop : 0.96 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 49 TYR 0.021 0.001 TYR F 29 PHE 0.007 0.001 PHE B 58 TRP 0.013 0.001 TRP G 89 HIS 0.006 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00350 (10822) covalent geometry : angle 0.60977 (14854) hydrogen bonds : bond 0.03019 ( 512) hydrogen bonds : angle 4.82186 ( 1566) metal coordination : bond 0.00240 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 244 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7914 (ttm110) REVERT: A 86 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8347 (pttm) REVERT: A 89 ARG cc_start: 0.8662 (ttp-110) cc_final: 0.8271 (mtm110) REVERT: A 136 ASN cc_start: 0.8218 (OUTLIER) cc_final: 0.7925 (m110) REVERT: A 166 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8186 (mp10) REVERT: C 88 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7427 (pt0) REVERT: C 167 ARG cc_start: 0.8459 (mtm-85) cc_final: 0.8231 (ttm-80) REVERT: E 12 GLN cc_start: 0.8233 (mp10) cc_final: 0.7833 (mp10) REVERT: E 17 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8121 (ttm170) REVERT: E 171 GLU cc_start: 0.8388 (pp20) cc_final: 0.8055 (pp20) REVERT: F 41 GLN cc_start: 0.8317 (mt0) cc_final: 0.8114 (mp10) REVERT: B 50 LEU cc_start: 0.9003 (mt) cc_final: 0.8729 (mm) REVERT: B 89 ARG cc_start: 0.8671 (ttp-110) cc_final: 0.8277 (mtm110) REVERT: B 166 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: G 88 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7452 (pt0) REVERT: G 99 ASP cc_start: 0.8127 (p0) cc_final: 0.7801 (p0) REVERT: G 101 ASP cc_start: 0.8479 (m-30) cc_final: 0.8162 (p0) REVERT: I 12 GLN cc_start: 0.8233 (mp10) cc_final: 0.7766 (mp10) REVERT: I 17 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.7932 (mtp85) REVERT: I 171 GLU cc_start: 0.8213 (pp20) cc_final: 0.7955 (pm20) outliers start: 46 outliers final: 35 residues processed: 270 average time/residue: 0.6548 time to fit residues: 187.3495 Evaluate side-chains 279 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 236 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 10 optimal weight: 2.9990 chunk 21 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS B 96 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 HIS ** 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 = 0.4001 r_free = 0.4001 target = 0.120367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.092668 restraints weight = 17997.801| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.57 r_work: 0.3370 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10828 Z= 0.149 Angle : 0.624 9.863 14854 Z= 0.317 Chirality : 0.044 0.179 1594 Planarity : 0.004 0.053 1728 Dihedral : 14.969 165.790 1854 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.51 % Allowed : 30.46 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.79 (0.26), residues: 1130 helix: 2.03 (0.27), residues: 376 sheet: 0.77 (0.28), residues: 324 loop : 0.95 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 23 TYR 0.010 0.001 TYR D 96 PHE 0.009 0.001 PHE J 69 TRP 0.012 0.001 TRP G 89 HIS 0.005 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00344 (10822) covalent geometry : angle 0.62414 (14854) hydrogen bonds : bond 0.02976 ( 512) hydrogen bonds : angle 4.79652 ( 1566) metal coordination : bond 0.00237 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 238 time to evaluate : 0.346 Fit side-chains REVERT: A 57 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7897 (ttm110) REVERT: A 86 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8347 (pttm) REVERT: A 89 ARG cc_start: 0.8674 (ttp-110) cc_final: 0.8288 (mtm110) REVERT: A 136 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7873 (m110) REVERT: A 166 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8113 (mp10) REVERT: C 88 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: C 167 ARG cc_start: 0.8430 (mtm-85) cc_final: 0.8214 (ttm-80) REVERT: E 12 GLN cc_start: 0.8227 (mp10) cc_final: 0.7833 (mp10) REVERT: E 17 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8018 (ttm170) REVERT: E 171 GLU cc_start: 0.8356 (pp20) cc_final: 0.8014 (pp20) REVERT: F 41 GLN cc_start: 0.8300 (mt0) cc_final: 0.8096 (mp10) REVERT: B 50 LEU cc_start: 0.8993 (mt) cc_final: 0.8736 (mm) REVERT: B 86 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8326 (pttm) REVERT: B 89 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8286 (mtm110) REVERT: B 166 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8156 (mp10) REVERT: G 88 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7451 (pt0) REVERT: H 52 ARG cc_start: 0.8214 (mtp-110) cc_final: 0.7761 (mtp-110) REVERT: I 12 GLN cc_start: 0.8236 (mp10) cc_final: 0.7761 (mp10) REVERT: I 17 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7683 (mtp85) REVERT: I 171 GLU cc_start: 0.8195 (pp20) cc_final: 0.7512 (pm20) REVERT: J 41 GLN cc_start: 0.8293 (mt0) cc_final: 0.8062 (mp10) outliers start: 45 outliers final: 34 residues processed: 261 average time/residue: 0.6602 time to fit residues: 183.0185 Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 233 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 LYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 88 GLU Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 88 GLU Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 95 SER Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 102 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS B 96 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 HIS ** 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 = 0.4020 r_free = 0.4020 target = 0.121628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.094154 restraints weight = 17999.653| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.57 r_work: 0.3398 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10828 Z= 0.123 Angle : 0.616 9.767 14854 Z= 0.313 Chirality : 0.043 0.167 1594 Planarity : 0.004 0.051 1728 Dihedral : 14.875 164.109 1854 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.91 % Allowed : 30.96 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.84 (0.26), residues: 1130 helix: 2.09 (0.27), residues: 376 sheet: 0.77 (0.28), residues: 324 loop : 0.99 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 23 TYR 0.020 0.001 TYR J 29 PHE 0.009 0.001 PHE J 69 TRP 0.015 0.001 TRP G 89 HIS 0.005 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00286 (10822) covalent geometry : angle 0.61640 (14854) hydrogen bonds : bond 0.02817 ( 512) hydrogen bonds : angle 4.70246 ( 1566) metal coordination : bond 0.00148 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 238 time to evaluate : 0.266 Fit side-chains REVERT: A 57 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7839 (ttm110) REVERT: A 86 LYS cc_start: 0.8743 (mtpp) cc_final: 0.8359 (pttm) REVERT: A 89 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8261 (mtm110) REVERT: A 136 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7784 (m110) REVERT: A 166 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8134 (mp10) REVERT: C 23 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7801 (mtt-85) REVERT: C 167 ARG cc_start: 0.8423 (mtm-85) cc_final: 0.8201 (ttm-80) REVERT: E 12 GLN cc_start: 0.8214 (mp10) cc_final: 0.7830 (mp10) REVERT: E 17 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8027 (ttm170) REVERT: E 171 GLU cc_start: 0.8334 (pp20) cc_final: 0.7996 (pp20) REVERT: B 50 LEU cc_start: 0.8948 (mt) cc_final: 0.8718 (mm) REVERT: B 86 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8325 (pttm) REVERT: B 89 ARG cc_start: 0.8650 (ttp-110) cc_final: 0.8273 (mtm110) REVERT: B 166 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8136 (mp10) REVERT: G 23 ARG cc_start: 0.8208 (mtm110) cc_final: 0.7823 (mtt-85) REVERT: G 99 ASP cc_start: 0.8058 (p0) cc_final: 0.7660 (p0) REVERT: G 101 ASP cc_start: 0.8464 (m-30) cc_final: 0.8132 (p0) REVERT: H 52 ARG cc_start: 0.8162 (mtp-110) cc_final: 0.7733 (mtp-110) REVERT: I 12 GLN cc_start: 0.8233 (mp10) cc_final: 0.7854 (mp10) REVERT: I 17 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8074 (mtp85) REVERT: J 41 GLN cc_start: 0.8316 (mt0) cc_final: 0.8108 (mp10) outliers start: 39 outliers final: 31 residues processed: 259 average time/residue: 0.6210 time to fit residues: 170.6314 Evaluate side-chains 270 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 106 VAL Chi-restraints excluded: chain D residue 118 ARG Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 17 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 86 LYS Chi-restraints excluded: chain B residue 101 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 90 ARG Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 54 GLU Chi-restraints excluded: chain H residue 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU Chi-restraints excluded: chain I residue 17 ARG Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 HIS ** 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 = 0.4008 r_free = 0.4008 target = 0.120748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.093065 restraints weight = 18074.229| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 2.57 r_work: 0.3378 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10828 Z= 0.147 Angle : 0.635 10.233 14854 Z= 0.321 Chirality : 0.044 0.171 1594 Planarity : 0.004 0.049 1728 Dihedral : 14.880 164.473 1854 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.11 % Allowed : 31.26 % Favored : 64.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 1.75 (0.26), residues: 1130 helix: 1.96 (0.27), residues: 376 sheet: 0.75 (0.28), residues: 324 loop : 0.97 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 90 TYR 0.011 0.001 TYR C 69 PHE 0.010 0.001 PHE J 69 TRP 0.012 0.001 TRP G 89 HIS 0.005 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00338 (10822) covalent geometry : angle 0.63503 (14854) hydrogen bonds : bond 0.02985 ( 512) hydrogen bonds : angle 4.73118 ( 1566) metal coordination : bond 0.00235 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4590.94 seconds wall clock time: 78 minutes 50.69 seconds (4730.69 seconds total)