Starting phenix.real_space_refine on Tue May 13 12:50:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j62_35999/05_2025/8j62_35999.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j62_35999/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8j62_35999/05_2025/8j62_35999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j62_35999/05_2025/8j62_35999.map" model { file = "/net/cci-nas-00/data/ceres_data/8j62_35999/05_2025/8j62_35999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j62_35999/05_2025/8j62_35999.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 1, 'ARG:plan': 2} 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: {'GLU:plan': 1, 'ARG:plan': 2} 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: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 59 Chain: "Y" 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: J, X, H, I, B, G Time building chain proxies: 7.19, per 1000 atoms: 0.69 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: 2.64 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.00 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: 3.26 Time building geometry restraints manager: 3.09 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: 0.05 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'Y' selection = chain 'X' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'G' } 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: 4.770 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: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 31.620 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:12.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.770 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (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 TRP 0.033 0.001 TRP F 113 HIS 0.002 0.000 HIS H 37 PHE 0.007 0.001 PHE A 58 TYR 0.014 0.001 TYR D 85 ARG 0.006 0.000 ARG H 118 Details of bonding type rmsd hydrogen bonds : bond 0.13887 ( 512) hydrogen bonds : angle 6.21967 ( 1566) metal coordination : bond 0.00103 ( 6) covalent geometry : bond 0.00184 (10822) covalent geometry : angle 0.46417 (14854) *********************** 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 : 1.115 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: 1.3365 time to fit residues: 485.0833 Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 261 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 97 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 9.9990 chunk 30 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.8784 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.120892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.093539 restraints weight = 17977.296| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.51 r_work: 0.3387 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10828 Z= 0.182 Angle : 0.568 5.777 14854 Z= 0.301 Chirality : 0.044 0.152 1594 Planarity : 0.004 0.028 1728 Dihedral : 15.130 163.411 1868 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 5.31 % Allowed : 26.25 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1130 helix: 1.74 (0.26), residues: 374 sheet: 0.53 (0.26), residues: 330 loop : 1.08 (0.33), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 113 HIS 0.004 0.001 HIS G 43 PHE 0.008 0.001 PHE B 140 TYR 0.017 0.001 TYR J 29 ARG 0.006 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03441 ( 512) hydrogen bonds : angle 5.08304 ( 1566) metal coordination : bond 0.00381 ( 6) covalent geometry : bond 0.00411 (10822) covalent geometry : angle 0.56754 (14854) *********************** 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 313 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 260 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7858 (ttm110) REVERT: A 136 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7803 (m110) REVERT: C 167 ARG cc_start: 0.8413 (mtm-85) cc_final: 0.8167 (ttm-80) REVERT: D 28 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8193 (ptmm) REVERT: D 122 MET cc_start: 0.8834 (mmp) cc_final: 0.8576 (mmp) REVERT: E 17 ARG cc_start: 0.8742 (mtt-85) cc_final: 0.8391 (ttp-170) REVERT: E 88 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6683 (tm-30) REVERT: G 99 ASP cc_start: 0.8074 (p0) cc_final: 0.7834 (p0) REVERT: G 101 ASP cc_start: 0.8609 (m-30) cc_final: 0.8221 (p0) REVERT: G 108 HIS cc_start: 0.8457 (m-70) cc_final: 0.8189 (t-90) REVERT: H 122 MET cc_start: 0.8801 (mmp) cc_final: 0.8530 (mmp) REVERT: I 17 ARG cc_start: 0.8735 (mtt-85) cc_final: 0.8483 (mtt-85) REVERT: I 88 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6609 (tm-30) outliers start: 53 outliers final: 28 residues processed: 289 average time/residue: 1.3661 time to fit residues: 420.4312 Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 244 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 41 ARG Chi-restraints excluded: chain C residue 47 THR 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 30 THR 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 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 97 LEU 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 95 SER Chi-restraints excluded: chain G residue 107 ILE 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 88 GLU Chi-restraints excluded: chain I residue 169 LEU 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 69 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 83 optimal weight: 6.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** 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 = 0.118056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.090208 restraints weight = 18219.775| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.60 r_work: 0.3326 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10828 Z= 0.238 Angle : 0.600 6.231 14854 Z= 0.318 Chirality : 0.046 0.166 1594 Planarity : 0.004 0.027 1728 Dihedral : 15.141 167.517 1854 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 6.81 % Allowed : 25.65 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1130 helix: 1.74 (0.26), residues: 376 sheet: 0.61 (0.27), residues: 324 loop : 1.06 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 113 HIS 0.004 0.001 HIS J 37 PHE 0.009 0.001 PHE B 140 TYR 0.011 0.001 TYR C 69 ARG 0.007 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 512) hydrogen bonds : angle 5.11294 ( 1566) metal coordination : bond 0.00507 ( 6) covalent geometry : bond 0.00538 (10822) covalent geometry : angle 0.60012 (14854) *********************** 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 311 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 243 time to evaluate : 1.051 Fit side-chains REVERT: A 97 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8191 (mt-10) REVERT: A 166 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8285 (mp10) REVERT: C 167 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8171 (ttm-80) REVERT: D 30 THR cc_start: 0.8268 (OUTLIER) cc_final: 0.8031 (m) REVERT: E 12 GLN cc_start: 0.8360 (mp10) cc_final: 0.8126 (mp10) REVERT: E 17 ARG cc_start: 0.8717 (mtt-85) cc_final: 0.8506 (mtt180) REVERT: E 88 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: E 97 GLN cc_start: 0.7516 (OUTLIER) cc_final: 0.7230 (mp10) REVERT: B 166 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8262 (mp10) REVERT: G 108 HIS cc_start: 0.8530 (m-70) cc_final: 0.8273 (t-90) REVERT: H 21 LEU cc_start: 0.8853 (mp) cc_final: 0.8578 (mp) REVERT: H 30 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8060 (m) REVERT: I 12 GLN cc_start: 0.8336 (mp10) cc_final: 0.8068 (mp10) REVERT: I 97 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.7155 (mp10) outliers start: 68 outliers final: 37 residues processed: 282 average time/residue: 1.3396 time to fit residues: 402.2108 Evaluate side-chains 278 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 233 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL 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 104 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 C residue 166 VAL Chi-restraints excluded: chain D residue 30 THR Chi-restraints excluded: chain D residue 53 SER 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 85 VAL Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 97 GLN Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 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 85 VAL Chi-restraints excluded: chain I residue 97 GLN Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 chunk 3 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 overall best weight: 0.8178 ------------------------------------------------------------------------------- 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 ** G 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.121509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.094318 restraints weight = 17985.364| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.54 r_work: 0.3404 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10828 Z= 0.114 Angle : 0.563 9.632 14854 Z= 0.289 Chirality : 0.042 0.164 1594 Planarity : 0.004 0.031 1728 Dihedral : 15.016 165.600 1854 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 4.51 % Allowed : 28.36 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.25), residues: 1130 helix: 1.91 (0.26), residues: 376 sheet: 0.73 (0.27), residues: 324 loop : 1.02 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 89 HIS 0.003 0.001 HIS C 110 PHE 0.006 0.001 PHE B 113 TYR 0.020 0.001 TYR J 29 ARG 0.008 0.001 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 512) hydrogen bonds : angle 4.88227 ( 1566) metal coordination : bond 0.00129 ( 6) covalent geometry : bond 0.00253 (10822) covalent geometry : angle 0.56286 (14854) *********************** 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 311 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 1.116 Fit side-chains REVERT: A 50 LEU cc_start: 0.9034 (mt) cc_final: 0.8792 (mm) REVERT: A 57 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7837 (ttm110) REVERT: A 136 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7949 (m110) REVERT: A 166 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8167 (mp10) REVERT: C 33 ARG cc_start: 0.8161 (mtp85) cc_final: 0.7944 (mtp85) REVERT: C 167 ARG cc_start: 0.8446 (mtm-85) cc_final: 0.8205 (ttm-80) REVERT: E 12 GLN cc_start: 0.8306 (mp10) cc_final: 0.8068 (mp10) REVERT: E 17 ARG cc_start: 0.8737 (mtt-85) cc_final: 0.8427 (mtt180) REVERT: E 45 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8713 (mt-10) REVERT: E 88 GLU cc_start: 0.7190 (OUTLIER) cc_final: 0.6627 (tm-30) REVERT: E 171 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7763 (pm20) REVERT: B 50 LEU cc_start: 0.9015 (mt) cc_final: 0.8769 (mm) REVERT: B 166 GLN cc_start: 0.8790 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: G 108 HIS cc_start: 0.8469 (m-70) cc_final: 0.8260 (t-90) REVERT: H 35 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.8092 (mmm-85) REVERT: I 12 GLN cc_start: 0.8334 (mp10) cc_final: 0.7967 (mp10) REVERT: I 17 ARG cc_start: 0.8698 (mtt-85) cc_final: 0.8165 (ttp-170) REVERT: J 69 PHE cc_start: 0.8468 (m-10) cc_final: 0.8160 (m-10) outliers start: 45 outliers final: 26 residues processed: 294 average time/residue: 1.4418 time to fit residues: 449.8345 Evaluate side-chains 277 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 245 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 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 D residue 30 THR 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 15 ARG Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 67 THR 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 88 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain H residue 125 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 98 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 3 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.0070 chunk 7 optimal weight: 0.9980 overall best weight: 0.7202 ------------------------------------------------------------------------------- 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 F 41 GLN B 96 GLN H 45 GLN ** 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 = 0.4032 r_free = 0.4032 target = 0.122341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.095043 restraints weight = 17849.568| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.55 r_work: 0.3412 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10828 Z= 0.110 Angle : 0.558 9.302 14854 Z= 0.286 Chirality : 0.042 0.159 1594 Planarity : 0.004 0.037 1728 Dihedral : 14.906 163.354 1854 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.31 % Allowed : 28.86 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1130 helix: 2.14 (0.27), residues: 364 sheet: 0.77 (0.28), residues: 326 loop : 0.92 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 89 HIS 0.006 0.001 HIS C 110 PHE 0.006 0.001 PHE F 69 TYR 0.010 0.001 TYR G 69 ARG 0.009 0.001 ARG D 49 Details of bonding type rmsd hydrogen bonds : bond 0.02818 ( 512) hydrogen bonds : angle 4.76391 ( 1566) metal coordination : bond 0.00126 ( 6) covalent geometry : bond 0.00247 (10822) covalent geometry : angle 0.55782 (14854) *********************** 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 293 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 250 time to evaluate : 1.048 Fit side-chains REVERT: A 50 LEU cc_start: 0.9006 (mt) cc_final: 0.8797 (mm) REVERT: A 57 ARG cc_start: 0.8396 (OUTLIER) cc_final: 0.7793 (ttm110) REVERT: A 89 ARG cc_start: 0.8620 (ttp-110) cc_final: 0.8359 (mtm110) REVERT: A 136 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.7963 (m110) REVERT: A 166 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: C 33 ARG cc_start: 0.8217 (mtp85) cc_final: 0.7990 (mtp85) REVERT: C 167 ARG cc_start: 0.8465 (mtm-85) cc_final: 0.8219 (ttm-80) REVERT: D 21 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8430 (mp) REVERT: E 12 GLN cc_start: 0.8291 (mp10) cc_final: 0.7999 (mp10) REVERT: E 17 ARG cc_start: 0.8722 (mtt-85) cc_final: 0.8419 (mtt180) REVERT: E 45 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8652 (mt-10) REVERT: E 88 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6617 (tm-30) REVERT: E 171 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7646 (pm20) REVERT: F 68 PHE cc_start: 0.8067 (m-80) cc_final: 0.6063 (t80) REVERT: B 50 LEU cc_start: 0.9014 (mt) cc_final: 0.8796 (mm) REVERT: B 89 ARG cc_start: 0.8624 (ttp-110) cc_final: 0.8359 (mtm110) REVERT: B 166 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: I 12 GLN cc_start: 0.8294 (mp10) cc_final: 0.7838 (mp10) REVERT: I 17 ARG cc_start: 0.8597 (mtt-85) cc_final: 0.8349 (ttp-170) REVERT: J 68 PHE cc_start: 0.8090 (m-80) cc_final: 0.6045 (t80) outliers start: 43 outliers final: 27 residues processed: 276 average time/residue: 1.4236 time to fit residues: 417.6028 Evaluate side-chains 267 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 233 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 136 ASN Chi-restraints excluded: chain A residue 166 GLN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 21 LEU 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 116 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL 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 67 THR 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 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 76 optimal weight: 0.1980 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 108 optimal weight: 0.0270 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.122755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.095714 restraints weight = 18104.168| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.62 r_work: 0.3425 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10828 Z= 0.102 Angle : 0.561 9.169 14854 Z= 0.284 Chirality : 0.042 0.139 1594 Planarity : 0.004 0.038 1728 Dihedral : 14.805 161.634 1854 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 4.11 % Allowed : 30.16 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.26), residues: 1130 helix: 2.14 (0.27), residues: 376 sheet: 0.83 (0.28), residues: 328 loop : 0.97 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 89 HIS 0.008 0.001 HIS C 110 PHE 0.006 0.001 PHE D 44 TYR 0.020 0.001 TYR J 29 ARG 0.008 0.001 ARG H 90 Details of bonding type rmsd hydrogen bonds : bond 0.02694 ( 512) hydrogen bonds : angle 4.66090 ( 1566) metal coordination : bond 0.00090 ( 6) covalent geometry : bond 0.00230 (10822) covalent geometry : angle 0.56086 (14854) *********************** 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 293 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8355 (OUTLIER) cc_final: 0.7787 (ttm110) REVERT: A 86 LYS cc_start: 0.8695 (mtpp) cc_final: 0.8313 (pttm) REVERT: A 89 ARG cc_start: 0.8625 (ttp-110) cc_final: 0.8238 (mtm110) REVERT: A 136 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7903 (m110) REVERT: C 33 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7984 (mtp85) REVERT: C 167 ARG cc_start: 0.8421 (mtm-85) cc_final: 0.8190 (ttm-80) REVERT: E 12 GLN cc_start: 0.8258 (mp10) cc_final: 0.7904 (mp10) REVERT: E 17 ARG cc_start: 0.8717 (mtt-85) cc_final: 0.8457 (mtt180) REVERT: E 45 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8681 (mt-10) REVERT: E 88 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6583 (tm-30) REVERT: B 86 LYS cc_start: 0.8702 (mtpp) cc_final: 0.8330 (pttm) REVERT: B 89 ARG cc_start: 0.8629 (ttp-110) cc_final: 0.8242 (mtm110) REVERT: H 20 LYS cc_start: 0.9405 (ttpp) cc_final: 0.9181 (tmmt) REVERT: I 12 GLN cc_start: 0.8254 (mp10) cc_final: 0.7906 (mp10) REVERT: I 97 GLN cc_start: 0.7494 (OUTLIER) cc_final: 0.7180 (mp10) outliers start: 41 outliers final: 30 residues processed: 275 average time/residue: 1.4361 time to fit residues: 419.8792 Evaluate side-chains 269 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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 136 ASN Chi-restraints excluded: chain C residue 67 THR Chi-restraints excluded: chain C residue 90 ARG 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 15 ARG Chi-restraints excluded: chain E residue 88 GLU Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 101 VAL 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 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 97 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain I residue 169 LEU Chi-restraints excluded: chain J residue 58 VAL 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 36 optimal weight: 0.0270 chunk 76 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 GLN D 41 GLN ** E 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS B 96 GLN G 110 HIS H 41 GLN ** I 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.118073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.090404 restraints weight = 18108.594| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.57 r_work: 0.3329 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10828 Z= 0.242 Angle : 0.642 8.924 14854 Z= 0.329 Chirality : 0.046 0.178 1594 Planarity : 0.004 0.045 1728 Dihedral : 15.056 166.829 1854 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 5.91 % Allowed : 28.76 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.25), residues: 1130 helix: 1.93 (0.27), residues: 376 sheet: 0.73 (0.28), residues: 326 loop : 0.99 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 79 HIS 0.007 0.001 HIS G 110 PHE 0.011 0.001 PHE A 140 TYR 0.011 0.001 TYR C 69 ARG 0.011 0.001 ARG D 90 Details of bonding type rmsd hydrogen bonds : bond 0.03272 ( 512) hydrogen bonds : angle 4.93457 ( 1566) metal coordination : bond 0.00486 ( 6) covalent geometry : bond 0.00555 (10822) covalent geometry : angle 0.64242 (14854) *********************** 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 303 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 244 time to evaluate : 1.213 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7941 (ttm110) REVERT: A 86 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8299 (pttm) REVERT: A 89 ARG cc_start: 0.8690 (ttp-110) cc_final: 0.8309 (mtm110) REVERT: A 136 ASN cc_start: 0.8258 (OUTLIER) cc_final: 0.7980 (m110) REVERT: C 88 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: C 167 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8202 (ttm-80) REVERT: D 30 THR cc_start: 0.8286 (OUTLIER) cc_final: 0.8037 (m) REVERT: D 45 GLN cc_start: 0.8587 (tp-100) cc_final: 0.8357 (tp40) REVERT: D 88 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8137 (mm) REVERT: E 12 GLN cc_start: 0.8299 (mp10) cc_final: 0.7937 (mp10) REVERT: E 17 ARG cc_start: 0.8739 (mtt-85) cc_final: 0.8426 (mtt180) REVERT: F 41 GLN cc_start: 0.8427 (mt0) cc_final: 0.8201 (mp10) REVERT: B 86 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8305 (pttm) REVERT: B 89 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8287 (mtm110) REVERT: H 20 LYS cc_start: 0.9384 (ttpp) cc_final: 0.9133 (tmmt) REVERT: H 30 THR cc_start: 0.8285 (OUTLIER) cc_final: 0.8039 (m) REVERT: I 12 GLN cc_start: 0.8248 (mp10) cc_final: 0.7796 (mp10) REVERT: I 17 ARG cc_start: 0.8591 (ttp-170) cc_final: 0.8373 (ttp-170) REVERT: I 97 GLN cc_start: 0.7580 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: J 68 PHE cc_start: 0.8097 (m-80) cc_final: 0.6056 (t80) outliers start: 59 outliers final: 34 residues processed: 283 average time/residue: 1.3467 time to fit residues: 406.0576 Evaluate side-chains 281 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 136 ASN 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 15 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain B residue 17 SER 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 104 THR 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 G residue 166 VAL Chi-restraints excluded: chain H residue 30 THR 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 97 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 79 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 51 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.120011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.092565 restraints weight = 18121.631| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.62 r_work: 0.3367 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10828 Z= 0.146 Angle : 0.623 11.773 14854 Z= 0.312 Chirality : 0.044 0.156 1594 Planarity : 0.004 0.049 1728 Dihedral : 15.009 166.117 1854 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.71 % Allowed : 31.06 % Favored : 64.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.26), residues: 1130 helix: 2.01 (0.27), residues: 376 sheet: 0.77 (0.28), residues: 324 loop : 0.98 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 89 HIS 0.005 0.001 HIS G 110 PHE 0.008 0.001 PHE H 44 TYR 0.021 0.001 TYR F 29 ARG 0.011 0.001 ARG G 23 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 512) hydrogen bonds : angle 4.79429 ( 1566) metal coordination : bond 0.00217 ( 6) covalent geometry : bond 0.00336 (10822) covalent geometry : angle 0.62302 (14854) *********************** 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 292 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.7854 (ttm110) REVERT: A 89 ARG cc_start: 0.8659 (ttp-110) cc_final: 0.8277 (mtm110) REVERT: A 136 ASN cc_start: 0.8245 (OUTLIER) cc_final: 0.7981 (m110) REVERT: C 33 ARG cc_start: 0.8146 (mtp85) cc_final: 0.7939 (mtp85) REVERT: C 88 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.7410 (pt0) REVERT: C 167 ARG cc_start: 0.8402 (mtm-85) cc_final: 0.8177 (ttm-80) REVERT: E 12 GLN cc_start: 0.8285 (mp10) cc_final: 0.7837 (mp10) REVERT: E 17 ARG cc_start: 0.8713 (mtt-85) cc_final: 0.8364 (mtt180) REVERT: F 41 GLN cc_start: 0.8397 (mt0) cc_final: 0.8167 (mp10) REVERT: B 89 ARG cc_start: 0.8646 (ttp-110) cc_final: 0.8262 (mtm110) REVERT: G 88 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7397 (pt0) REVERT: H 20 LYS cc_start: 0.9410 (ttpp) cc_final: 0.9099 (tmmt) REVERT: H 30 THR cc_start: 0.8187 (OUTLIER) cc_final: 0.7959 (m) REVERT: H 49 ARG cc_start: 0.8381 (tpp80) cc_final: 0.8177 (tpp80) REVERT: I 12 GLN cc_start: 0.8225 (mp10) cc_final: 0.7782 (mp10) REVERT: I 17 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.8351 (ttp-170) REVERT: I 97 GLN cc_start: 0.7508 (OUTLIER) cc_final: 0.7165 (mp10) REVERT: J 68 PHE cc_start: 0.8080 (m-80) cc_final: 0.6030 (t80) outliers start: 47 outliers final: 32 residues processed: 276 average time/residue: 1.3575 time to fit residues: 398.5872 Evaluate side-chains 278 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER 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 104 THR Chi-restraints excluded: chain A residue 136 ASN 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 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 171 GLU 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 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 166 VAL Chi-restraints excluded: chain H residue 30 THR 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 97 GLN Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 8 optimal weight: 0.3980 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 107 optimal weight: 0.0040 chunk 39 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.0596 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.120590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.093145 restraints weight = 18060.661| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.61 r_work: 0.3378 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3145 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= 0.132 Angle : 0.627 11.719 14854 Z= 0.314 Chirality : 0.043 0.154 1594 Planarity : 0.004 0.055 1728 Dihedral : 14.962 165.371 1854 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.01 % Allowed : 31.66 % Favored : 64.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.26), residues: 1130 helix: 2.04 (0.27), residues: 376 sheet: 0.75 (0.28), residues: 324 loop : 0.97 (0.33), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 89 HIS 0.005 0.001 HIS G 110 PHE 0.007 0.001 PHE H 44 TYR 0.010 0.001 TYR C 69 ARG 0.012 0.001 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.02878 ( 512) hydrogen bonds : angle 4.71437 ( 1566) metal coordination : bond 0.00178 ( 6) covalent geometry : bond 0.00304 (10822) covalent geometry : angle 0.62723 (14854) *********************** 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 287 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7828 (ttm110) REVERT: A 86 LYS cc_start: 0.8673 (mtpp) cc_final: 0.8282 (pttm) REVERT: A 89 ARG cc_start: 0.8676 (ttp-110) cc_final: 0.8310 (mtm110) REVERT: A 136 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7959 (m110) REVERT: C 33 ARG cc_start: 0.8150 (mtp85) cc_final: 0.7947 (mtp85) REVERT: C 88 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7382 (pt0) REVERT: C 167 ARG cc_start: 0.8414 (mtm-85) cc_final: 0.8191 (ttm-80) REVERT: D 52 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7817 (mtp-110) REVERT: D 95 VAL cc_start: 0.9219 (t) cc_final: 0.8983 (p) REVERT: E 12 GLN cc_start: 0.8239 (mp10) cc_final: 0.7803 (mp10) REVERT: E 17 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.8356 (mtt180) REVERT: B 86 LYS cc_start: 0.8693 (mtpp) cc_final: 0.8312 (pttm) REVERT: B 89 ARG cc_start: 0.8650 (ttp-110) cc_final: 0.8271 (mtm110) REVERT: G 23 ARG cc_start: 0.8184 (mtm110) cc_final: 0.7789 (mtt-85) REVERT: G 88 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7377 (pt0) REVERT: I 12 GLN cc_start: 0.8211 (mp10) cc_final: 0.7775 (mp10) REVERT: I 17 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8370 (ttp-170) REVERT: J 68 PHE cc_start: 0.8056 (m-80) cc_final: 0.6021 (t80) outliers start: 40 outliers final: 33 residues processed: 272 average time/residue: 1.3663 time to fit residues: 395.1242 Evaluate side-chains 279 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 104 THR Chi-restraints excluded: chain A residue 136 ASN 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 116 LEU Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 107 ILE Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 171 GLU 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 104 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 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 J residue 97 LEU Chi-restraints excluded: chain J residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 108 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.117072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.089539 restraints weight = 18050.929| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.53 r_work: 0.3310 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 10828 Z= 0.267 Angle : 0.701 11.847 14854 Z= 0.355 Chirality : 0.048 0.192 1594 Planarity : 0.004 0.057 1728 Dihedral : 15.164 168.965 1854 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 4.51 % Allowed : 30.86 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1130 helix: 1.78 (0.27), residues: 376 sheet: 0.58 (0.28), residues: 322 loop : 0.94 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 79 HIS 0.004 0.001 HIS G 110 PHE 0.013 0.002 PHE A 140 TYR 0.024 0.002 TYR F 29 ARG 0.012 0.001 ARG C 23 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 512) hydrogen bonds : angle 4.94382 ( 1566) metal coordination : bond 0.00548 ( 6) covalent geometry : bond 0.00613 (10822) covalent geometry : angle 0.70059 (14854) ********************** 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 289 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 244 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8042 (ttm110) REVERT: A 86 LYS cc_start: 0.8696 (OUTLIER) cc_final: 0.8277 (pttm) REVERT: A 89 ARG cc_start: 0.8698 (ttp-110) cc_final: 0.8318 (mtm110) REVERT: A 136 ASN cc_start: 0.8178 (OUTLIER) cc_final: 0.7881 (m110) REVERT: A 166 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8216 (mp10) REVERT: C 88 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7536 (pt0) REVERT: C 167 ARG cc_start: 0.8449 (mtm-85) cc_final: 0.8223 (ttm-80) REVERT: D 52 ARG cc_start: 0.8355 (mtp-110) cc_final: 0.8059 (mtp-110) REVERT: E 12 GLN cc_start: 0.8263 (mp10) cc_final: 0.7839 (mp10) REVERT: F 41 GLN cc_start: 0.8371 (mt0) cc_final: 0.8144 (mp10) REVERT: B 86 LYS cc_start: 0.8704 (OUTLIER) cc_final: 0.8302 (pttm) REVERT: B 89 ARG cc_start: 0.8684 (ttp-110) cc_final: 0.8302 (mtm110) REVERT: B 166 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8194 (mp10) REVERT: G 88 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7537 (pt0) REVERT: H 52 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.8114 (mtp-110) REVERT: H 88 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8167 (mm) REVERT: I 12 GLN cc_start: 0.8199 (mp10) cc_final: 0.7708 (mp10) REVERT: I 17 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.7988 (ttp-170) REVERT: J 41 GLN cc_start: 0.8906 (mt0) cc_final: 0.8616 (mp10) outliers start: 45 outliers final: 31 residues processed: 271 average time/residue: 1.3644 time to fit residues: 393.4033 Evaluate side-chains 281 residues out of total 1064 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 240 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 SER 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 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 54 GLU 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 15 ARG Chi-restraints excluded: chain E residue 169 LEU Chi-restraints excluded: chain E residue 171 GLU 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 104 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 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 J residue 97 LEU Chi-restraints excluded: chain J residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 57 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 79 optimal weight: 0.3980 chunk 54 optimal weight: 0.0030 chunk 55 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.121419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.094435 restraints weight = 17978.971| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.56 r_work: 0.3399 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3298 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= 0.117 Angle : 0.643 11.436 14854 Z= 0.323 Chirality : 0.043 0.147 1594 Planarity : 0.005 0.063 1728 Dihedral : 15.000 166.193 1854 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.21 % Allowed : 32.97 % Favored : 63.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.26), residues: 1130 helix: 2.10 (0.28), residues: 364 sheet: 0.68 (0.28), residues: 320 loop : 1.05 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 89 HIS 0.005 0.001 HIS G 110 PHE 0.006 0.001 PHE B 58 TYR 0.010 0.001 TYR C 69 ARG 0.012 0.001 ARG G 23 Details of bonding type rmsd hydrogen bonds : bond 0.02783 ( 512) hydrogen bonds : angle 4.70677 ( 1566) metal coordination : bond 0.00065 ( 6) covalent geometry : bond 0.00272 (10822) covalent geometry : angle 0.64319 (14854) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9555.87 seconds wall clock time: 164 minutes 56.99 seconds (9896.99 seconds total)