Starting phenix.real_space_refine on Wed Mar 4 16:39:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy9_11555/03_2026/6zy9_11555.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy9_11555/03_2026/6zy9_11555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zy9_11555/03_2026/6zy9_11555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy9_11555/03_2026/6zy9_11555.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy9_11555/03_2026/6zy9_11555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy9_11555/03_2026/6zy9_11555.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 P 6 5.49 5 Mg 2 5.21 5 S 69 5.16 5 C 9647 2.51 5 N 2513 2.21 5 O 2736 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 65 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14973 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 966 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 801 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "I" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 957 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 2 Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'ASP:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 41 Chain: "J" Number of atoms: 1041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1041 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 966 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 925 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 4, 'GLU:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 712 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 1954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1954 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 240} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1971 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 242} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1927 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "H" Number of atoms: 1946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 1946 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 251} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.26, per 1000 atoms: 0.22 Number of scatterers: 14973 At special positions: 0 Unit cell: (99.372, 130.806, 147.03, 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) S 69 16.00 P 6 15.00 Mg 2 11.99 O 2736 8.00 N 2513 7.00 C 9647 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 668.0 milliseconds 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 20 sheets defined 40.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 3 through 24 removed outlier: 4.077A pdb=" N GLU A 7 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ILE A 8 " --> pdb=" O LYS A 4 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 21 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 152 removed outlier: 3.873A pdb=" N GLN A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.620A pdb=" N ILE D 8 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N TRP D 9 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLY D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'I' and resid 5 through 24 removed outlier: 4.263A pdb=" N TRP I 9 " --> pdb=" O LYS I 5 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL I 10 " --> pdb=" O ASN I 6 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY I 11 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 147 removed outlier: 3.632A pdb=" N LEU I 146 " --> pdb=" O VAL I 142 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 142 through 147' Processing helix chain 'J' and resid 5 through 29 removed outlier: 3.692A pdb=" N TRP J 9 " --> pdb=" O LYS J 5 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLY J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE J 12 " --> pdb=" O ILE J 8 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA J 17 " --> pdb=" O PHE J 13 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU J 18 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LYS J 27 " --> pdb=" O PHE J 23 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA J 29 " --> pdb=" O CYS J 25 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 152 removed outlier: 3.585A pdb=" N LEU J 146 " --> pdb=" O VAL J 142 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU J 151 " --> pdb=" O ILE J 147 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 24 removed outlier: 3.636A pdb=" N LEU K 15 " --> pdb=" O GLY K 11 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 151 removed outlier: 3.605A pdb=" N LEU K 151 " --> pdb=" O ILE K 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 19 removed outlier: 4.181A pdb=" N TRP L 9 " --> pdb=" O LYS L 5 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL L 10 " --> pdb=" O ASN L 6 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLY L 11 " --> pdb=" O GLU L 7 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA L 17 " --> pdb=" O PHE L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 23 Processing helix chain 'L' and resid 142 through 152 Processing helix chain 'B' and resid 25 through 30 removed outlier: 3.805A pdb=" N GLU B 30 " --> pdb=" O LEU B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 60 removed outlier: 4.358A pdb=" N LEU B 57 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 89 removed outlier: 4.240A pdb=" N TYR B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS B 86 " --> pdb=" O TYR B 82 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 51 through 69 removed outlier: 3.670A pdb=" N LEU C 57 " --> pdb=" O GLY C 53 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP C 63 " --> pdb=" O LEU C 59 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLN C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 84 removed outlier: 3.795A pdb=" N LEU C 84 " --> pdb=" O LYS C 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 56 removed outlier: 3.994A pdb=" N LEU F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU F 53 " --> pdb=" O THR F 49 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.513A pdb=" N ARG F 86 " --> pdb=" O VAL F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 107 Processing helix chain 'F' and resid 117 through 122 removed outlier: 3.736A pdb=" N HIS F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 127 removed outlier: 3.674A pdb=" N MET F 126 " --> pdb=" O HIS F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 133 removed outlier: 4.160A pdb=" N VAL F 132 " --> pdb=" O LYS F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 159 removed outlier: 3.911A pdb=" N ARG F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 193 removed outlier: 3.580A pdb=" N VAL F 182 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL F 184 " --> pdb=" O MET F 180 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 185 " --> pdb=" O GLY F 181 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN F 191 " --> pdb=" O ILE F 187 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 Processing helix chain 'F' and resid 239 through 244 removed outlier: 3.561A pdb=" N PHE F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU F 244 " --> pdb=" O VAL F 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 239 through 244' Processing helix chain 'G' and resid 47 through 56 removed outlier: 4.014A pdb=" N LEU G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 81 removed outlier: 3.679A pdb=" N TYR G 81 " --> pdb=" O ARG G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'G' and resid 101 through 107 removed outlier: 3.553A pdb=" N VAL G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA G 107 " --> pdb=" O PHE G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 133 removed outlier: 3.709A pdb=" N SER G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET G 126 " --> pdb=" O HIS G 122 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLU G 130 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL G 132 " --> pdb=" O LYS G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 145 removed outlier: 3.691A pdb=" N LEU G 145 " --> pdb=" O PRO G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 159 removed outlier: 4.088A pdb=" N ARG G 151 " --> pdb=" O GLY G 147 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE G 159 " --> pdb=" O LEU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 189 removed outlier: 3.848A pdb=" N VAL G 182 " --> pdb=" O ILE G 178 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER G 188 " --> pdb=" O VAL G 184 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 Processing helix chain 'G' and resid 239 through 244 removed outlier: 4.212A pdb=" N PHE G 243 " --> pdb=" O ARG G 239 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU G 244 " --> pdb=" O VAL G 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 239 through 244' Processing helix chain 'E' and resid 10 through 30 removed outlier: 3.781A pdb=" N LYS E 15 " --> pdb=" O HIS E 11 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR E 16 " --> pdb=" O LYS E 12 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU E 17 " --> pdb=" O GLY E 13 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY E 24 " --> pdb=" O PHE E 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 removed outlier: 3.969A pdb=" N VAL E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG E 46 " --> pdb=" O PRO E 42 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN E 47 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 Processing helix chain 'E' and resid 56 through 78 removed outlier: 3.675A pdb=" N SER E 62 " --> pdb=" O ILE E 58 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE E 65 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 112 removed outlier: 3.752A pdb=" N LEU E 106 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 110 " --> pdb=" O LEU E 106 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG E 111 " --> pdb=" O LEU E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 126 removed outlier: 4.358A pdb=" N MET E 123 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG E 124 " --> pdb=" O ILE E 120 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA E 125 " --> pdb=" O GLY E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 136 removed outlier: 3.583A pdb=" N SER E 131 " --> pdb=" O GLU E 127 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N MET E 135 " --> pdb=" O SER E 131 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA E 136 " --> pdb=" O MET E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 removed outlier: 3.631A pdb=" N ARG E 141 " --> pdb=" O ASP E 138 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARG E 142 " --> pdb=" O PRO E 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 138 through 142' Processing helix chain 'E' and resid 144 through 149 removed outlier: 3.538A pdb=" N TRP E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 167 removed outlier: 3.804A pdb=" N VAL E 160 " --> pdb=" O PRO E 156 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE E 161 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY E 166 " --> pdb=" O PHE E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 169 through 174 Processing helix chain 'E' and resid 181 through 191 removed outlier: 3.628A pdb=" N SER E 187 " --> pdb=" O GLY E 183 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ALA E 188 " --> pdb=" O PHE E 184 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N MET E 189 " --> pdb=" O PHE E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 221 removed outlier: 3.699A pdb=" N THR E 212 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE E 216 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE E 219 " --> pdb=" O TRP E 215 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY E 221 " --> pdb=" O SER E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 247 removed outlier: 3.648A pdb=" N SER E 232 " --> pdb=" O SER E 228 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL E 239 " --> pdb=" O THR E 235 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL E 240 " --> pdb=" O THR E 236 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA E 245 " --> pdb=" O HIS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 247 through 252 removed outlier: 4.089A pdb=" N PHE E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL E 252 " --> pdb=" O GLY E 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 247 through 252' Processing helix chain 'E' and resid 253 through 256 removed outlier: 3.617A pdb=" N LEU E 256 " --> pdb=" O LEU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 256' Processing helix chain 'H' and resid 3 through 30 removed outlier: 3.867A pdb=" N SER H 8 " --> pdb=" O ASN H 4 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU H 9 " --> pdb=" O ALA H 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N HIS H 11 " --> pdb=" O ALA H 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY H 24 " --> pdb=" O PHE H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 50 removed outlier: 3.856A pdb=" N VAL H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASN H 50 " --> pdb=" O ARG H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 55 Processing helix chain 'H' and resid 56 through 61 removed outlier: 3.558A pdb=" N VAL H 61 " --> pdb=" O LEU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 78 removed outlier: 3.566A pdb=" N MET H 68 " --> pdb=" O VAL H 64 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU H 70 " --> pdb=" O ILE H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 85 No H-bonds generated for 'chain 'H' and resid 83 through 85' Processing helix chain 'H' and resid 86 through 98 removed outlier: 3.502A pdb=" N LEU H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU H 93 " --> pdb=" O MET H 89 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU H 96 " --> pdb=" O ALA H 92 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU H 98 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 126 removed outlier: 3.625A pdb=" N LEU H 106 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER H 114 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA H 115 " --> pdb=" O ARG H 111 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE H 120 " --> pdb=" O LEU H 116 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU H 122 " --> pdb=" O ALA H 118 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR H 126 " --> pdb=" O LEU H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 138 through 143 removed outlier: 3.750A pdb=" N ARG H 142 " --> pdb=" O ASP H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 153 removed outlier: 3.717A pdb=" N GLY H 151 " --> pdb=" O ARG H 147 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE H 153 " --> pdb=" O TRP H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 176 removed outlier: 3.794A pdb=" N VAL H 160 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE H 167 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER H 176 " --> pdb=" O LEU H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 186 removed outlier: 3.686A pdb=" N TRP H 186 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 186 through 191 Processing helix chain 'H' and resid 199 through 223 removed outlier: 3.576A pdb=" N LEU H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 208 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE H 211 " --> pdb=" O VAL H 207 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR H 212 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL H 213 " --> pdb=" O PHE H 209 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N THR H 214 " --> pdb=" O ALA H 210 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ILE H 216 " --> pdb=" O THR H 212 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY H 221 " --> pdb=" O SER H 217 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TYR H 222 " --> pdb=" O LEU H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 245 removed outlier: 3.541A pdb=" N THR H 238 " --> pdb=" O ALA H 234 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N VAL H 239 " --> pdb=" O THR H 235 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N VAL H 240 " --> pdb=" O THR H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 255 removed outlier: 3.737A pdb=" N PHE H 251 " --> pdb=" O LEU H 247 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL H 252 " --> pdb=" O GLY H 248 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA H 255 " --> pdb=" O PHE H 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 removed outlier: 3.529A pdb=" N LEU A 84 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.668A pdb=" N SER A 100 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 99 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 41 through 45 removed outlier: 7.116A pdb=" N ARG D 81 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE D 71 " --> pdb=" O ARG D 81 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N THR D 83 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 67 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL D 63 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N VAL D 58 " --> pdb=" O VAL D 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 113 through 115 removed outlier: 3.872A pdb=" N SER D 98 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N LEU D 99 " --> pdb=" O LYS D 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 41 through 45 removed outlier: 3.540A pdb=" N LEU I 84 " --> pdb=" O LEU I 42 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP I 70 " --> pdb=" O THR I 83 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU I 85 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL I 68 " --> pdb=" O GLU I 85 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL I 63 " --> pdb=" O ILE I 60 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N VAL I 58 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG I 102 " --> pdb=" O TYR I 111 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 42 through 45 Processing sheet with id=AA7, first strand: chain 'J' and resid 63 through 66 removed outlier: 6.267A pdb=" N VAL J 64 " --> pdb=" O ILE J 60 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE J 60 " --> pdb=" O VAL J 64 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY J 66 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU J 99 " --> pdb=" O LYS J 138 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 39 through 41 removed outlier: 3.574A pdb=" N TYR K 40 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE K 86 " --> pdb=" O TYR K 40 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 39 through 41 removed outlier: 3.574A pdb=" N TYR K 40 " --> pdb=" O ILE K 86 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE K 86 " --> pdb=" O TYR K 40 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ARG K 81 " --> pdb=" O ILE K 71 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE K 71 " --> pdb=" O ARG K 81 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N THR K 83 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 58 through 59 removed outlier: 7.064A pdb=" N VAL K 58 " --> pdb=" O VAL K 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 109 through 116 removed outlier: 4.566A pdb=" N GLU K 109 " --> pdb=" O SER K 104 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LYS K 138 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU K 99 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 43 through 45 removed outlier: 3.802A pdb=" N ALA L 44 " --> pdb=" O VAL L 82 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 63 through 66 removed outlier: 6.889A pdb=" N VAL L 58 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER L 59 " --> pdb=" O LEU L 114 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER L 100 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 13 through 15 removed outlier: 6.760A pdb=" N LEU B 14 " --> pdb=" O ASP B 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN B 75 " --> pdb=" O ILE B 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.735A pdb=" N GLY B 18 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ARG B 49 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LEU B 20 " --> pdb=" O ARG B 49 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 41 through 43 removed outlier: 5.618A pdb=" N ILE C 42 " --> pdb=" O GLN C 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 27 through 29 removed outlier: 4.849A pdb=" N LEU F 29 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N ARG F 12 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG F 12 " --> pdb=" O GLU F 64 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLU F 64 " --> pdb=" O ARG F 12 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 165 through 167 removed outlier: 4.109A pdb=" N THR F 37 " --> pdb=" O CYS F 198 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE F 217 " --> pdb=" O VAL F 224 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 165 through 168 removed outlier: 6.497A pdb=" N ILE G 166 " --> pdb=" O VAL G 199 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE G 36 " --> pdb=" O HIS G 214 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N TRP G 216 " --> pdb=" O ILE G 36 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ALA G 38 " --> pdb=" O TRP G 216 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU G 218 " --> pdb=" O ALA G 38 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET G 40 " --> pdb=" O LEU G 218 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 66 through 67 removed outlier: 3.924A pdb=" N GLU G 70 " --> pdb=" O PHE G 67 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4778 1.34 - 1.46: 3228 1.46 - 1.58: 7089 1.58 - 1.70: 10 1.70 - 1.81: 126 Bond restraints: 15231 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.05e+01 bond pdb=" O3A ANP G 401 " pdb=" PB ANP G 401 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" N3B ANP G 401 " pdb=" PG ANP G 401 " ideal model delta sigma weight residual 1.795 1.694 0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" O5' ANP G 401 " pdb=" PA ANP G 401 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.33e+01 ... (remaining 15226 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.25: 20511 3.25 - 6.50: 171 6.50 - 9.74: 36 9.74 - 12.99: 4 12.99 - 16.24: 4 Bond angle restraints: 20726 Sorted by residual: angle pdb=" C ASP G 204 " pdb=" N VAL G 205 " pdb=" CA VAL G 205 " ideal model delta sigma weight residual 120.33 124.73 -4.40 8.00e-01 1.56e+00 3.03e+01 angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 110.71 16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" PB ANP G 401 " pdb=" N3B ANP G 401 " pdb=" PG ANP G 401 " ideal model delta sigma weight residual 126.95 110.72 16.23 3.00e+00 1.11e-01 2.93e+01 angle pdb=" C ASP G 10 " pdb=" N MET G 11 " pdb=" CA MET G 11 " ideal model delta sigma weight residual 122.46 129.52 -7.06 1.41e+00 5.03e-01 2.50e+01 angle pdb=" C ASP F 204 " pdb=" N VAL F 205 " pdb=" CA VAL F 205 " ideal model delta sigma weight residual 120.33 124.27 -3.94 8.00e-01 1.56e+00 2.42e+01 ... (remaining 20721 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.92: 8212 16.92 - 33.83: 659 33.83 - 50.75: 151 50.75 - 67.67: 36 67.67 - 84.58: 17 Dihedral angle restraints: 9075 sinusoidal: 3424 harmonic: 5651 Sorted by residual: dihedral pdb=" CA GLN C 68 " pdb=" C GLN C 68 " pdb=" N GLY C 69 " pdb=" CA GLY C 69 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA GLN C 22 " pdb=" C GLN C 22 " pdb=" N ASP C 23 " pdb=" CA ASP C 23 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ASP C 93 " pdb=" CB ASP C 93 " pdb=" CG ASP C 93 " pdb=" OD1 ASP C 93 " ideal model delta sinusoidal sigma weight residual -30.00 -90.53 60.53 1 2.00e+01 2.50e-03 1.22e+01 ... (remaining 9072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2123 0.060 - 0.119: 352 0.119 - 0.179: 56 0.179 - 0.238: 3 0.238 - 0.298: 4 Chirality restraints: 2538 Sorted by residual: chirality pdb=" CB ILE A 60 " pdb=" CA ILE A 60 " pdb=" CG1 ILE A 60 " pdb=" CG2 ILE A 60 " both_signs ideal model delta sigma weight residual False 2.64 2.94 -0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C3' ANP G 401 " pdb=" C2' ANP G 401 " pdb=" C4' ANP G 401 " pdb=" O3' ANP G 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 2535 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 176 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.39e+00 pdb=" N PRO G 177 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO G 177 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 177 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA G 118 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO G 119 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO G 119 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 119 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 155 " -0.035 5.00e-02 4.00e+02 5.15e-02 4.25e+00 pdb=" N PRO H 156 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 156 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 156 " -0.029 5.00e-02 4.00e+02 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 459 2.72 - 3.26: 13437 3.26 - 3.81: 22671 3.81 - 4.35: 28163 4.35 - 4.90: 46516 Nonbonded interactions: 111246 Sorted by model distance: nonbonded pdb=" OG1 THR G 48 " pdb="MG MG G 402 " model vdw 2.174 2.170 nonbonded pdb=" OG1 THR F 48 " pdb="MG MG F 402 " model vdw 2.259 2.170 nonbonded pdb=" OH TYR J 40 " pdb=" OD1 ASN J 91 " model vdw 2.319 3.040 nonbonded pdb=" O SER H 86 " pdb=" OG SER H 86 " model vdw 2.331 3.040 nonbonded pdb=" O ALA E 234 " pdb=" OG1 THR E 238 " model vdw 2.338 3.040 ... (remaining 111241 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 69 or (resid \ 70 through 71 and (name N or name CA or name C or name O or name CB )) or resid \ 72 through 80 or (resid 81 and (name N or name CA or name C or name O or name C \ B )) or resid 82 through 88 or (resid 89 and (name N or name CA or name C or nam \ e O or name CB )) or resid 90 or (resid 91 and (name N or name CA or name C or n \ ame O or name CB )) or resid 92 through 94 or (resid 95 and (name N or name CA o \ r name C or name O or name CB )) or resid 96 through 115 or (resid 127 through 1 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 133 or (resid 134 through 135 and (name N or name CA or name C or name O or nam \ e CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C \ or name O or name CB )) or resid 139 through 142 or (resid 143 through 145 and ( \ name N or name CA or name C or name O or name CB )) or resid 146 or (resid 147 a \ nd (name N or name CA or name C or name O or name CB )) or resid 148 through 150 \ or (resid 151 and (name N or name CA or name C or name O or name CB )) or resid \ 152)) selection = (chain 'I' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 72 or (resid \ 73 and (name N or name CA or name C or name O or name CB )) or resid 74 through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or res \ id 77 through 94 or (resid 95 and (name N or name CA or name C or name O or name \ CB )) or resid 96 through 98 or (resid 99 and (name N or name CA or name C or n \ ame O or name CB )) or resid 100 through 106 or (resid 107 and (name N or name C \ A or name C or name O or name CB )) or resid 108 through 115 or (resid 127 throu \ gh 130 and (name N or name CA or name C or name O or name CB )) or resid 131 thr \ ough 134 or (resid 135 and (name N or name CA or name C or name O or name CB )) \ or resid 136 through 142 or (resid 143 through 145 and (name N or name CA or nam \ e C or name O or name CB )) or resid 146 or (resid 147 and (name N or name CA or \ name C or name O or name CB )) or resid 148 through 150 or (resid 151 and (name \ N or name CA or name C or name O or name CB )) or resid 152)) selection = (chain 'J' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 54 or (resid \ 55 and (name N or name CA or name C or name O or name CB )) or resid 56 through \ 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or res \ id 68 through 69 or (resid 70 through 71 and (name N or name CA or name C or nam \ e O or name CB )) or resid 72 or (resid 73 and (name N or name CA or name C or n \ ame O or name CB )) or resid 74 through 75 or (resid 76 and (name N or name CA o \ r name C or name O or name CB )) or resid 77 through 80 or (resid 81 and (name N \ or name CA or name C or name O or name CB )) or resid 82 through 84 or (resid 8 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 86 or (resid \ 87 and (name N or name CA or name C or name O or name CB )) or resid 88 or (res \ id 89 and (name N or name CA or name C or name O or name CB )) or resid 90 or (r \ esid 91 and (name N or name CA or name C or name O or name CB )) or resid 92 thr \ ough 94 or (resid 95 and (name N or name CA or name C or name O or name CB )) or \ resid 96 through 98 or (resid 99 and (name N or name CA or name C or name O or \ name CB )) or resid 100 through 106 or (resid 107 and (name N or name CA or name \ C or name O or name CB )) or resid 108 or (resid 109 and (name N or name CA or \ name C or name O or name CB )) or resid 110 through 115 or (resid 127 through 13 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 131 through \ 133 or (resid 134 through 135 and (name N or name CA or name C or name O or name \ CB )) or resid 136 through 137 or (resid 138 and (name N or name CA or name C o \ r name O or name CB )) or resid 139 through 142 or (resid 143 through 145 and (n \ ame N or name CA or name C or name O or name CB )) or resid 146 or (resid 147 an \ d (name N or name CA or name C or name O or name CB )) or resid 148 through 150 \ or (resid 151 and (name N or name CA or name C or name O or name CB )) or resid \ 152)) selection = (chain 'K' and (resid 4 through 24 or resid 40 through 52 or (resid 53 through 5 \ 5 and (name N or name CA or name C or name O or name CB )) or resid 56 through 6 \ 6 or (resid 67 and (name N or name CA or name C or name O or name CB )) or resid \ 68 through 69 or (resid 70 through 71 and (name N or name CA or name C or name \ O or name CB )) or resid 72 or (resid 73 and (name N or name CA or name C or nam \ e O or name CB )) or resid 74 through 80 or (resid 81 and (name N or name CA or \ name C or name O or name CB )) or resid 82 through 84 or (resid 85 and (name N o \ r name CA or name C or name O or name CB )) or resid 86 or (resid 87 and (name N \ or name CA or name C or name O or name CB )) or resid 88 or (resid 89 and (name \ N or name CA or name C or name O or name CB )) or resid 90 or (resid 91 and (na \ me N or name CA or name C or name O or name CB )) or resid 92 through 94 or (res \ id 95 and (name N or name CA or name C or name O or name CB )) or resid 96 throu \ gh 98 or (resid 99 and (name N or name CA or name C or name O or name CB )) or r \ esid 100 through 106 or (resid 107 and (name N or name CA or name C or name O or \ name CB )) or resid 108 or (resid 109 and (name N or name CA or name C or name \ O or name CB )) or resid 110 through 115 or (resid 127 through 130 and (name N o \ r name CA or name C or name O or name CB )) or resid 131 through 133 or (resid 1 \ 34 through 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 137 or (resid 138 and (name N or name CA or name C or name O or nam \ e CB )) or resid 139 through 142 or (resid 143 through 145 and (name N or name C \ A or name C or name O or name CB )) or resid 146 or (resid 147 and (name N or na \ me CA or name C or name O or name CB )) or resid 148 through 150 or (resid 151 a \ nd (name N or name CA or name C or name O or name CB )) or resid 152)) selection = (chain 'L' and (resid 4 through 24 or resid 40 through 46 or (resid 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 72 or (resid \ 73 and (name N or name CA or name C or name O or name CB )) or resid 74 through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or res \ id 77 through 88 or (resid 89 and (name N or name CA or name C or name O or name \ CB )) or resid 90 or (resid 91 and (name N or name CA or name C or name O or na \ me CB )) or resid 92 through 98 or (resid 99 and (name N or name CA or name C or \ name O or name CB )) or resid 100 through 127 or (resid 128 through 130 and (na \ me N or name CA or name C or name O or name CB )) or resid 131 through 133 or (r \ esid 134 through 135 and (name N or name CA or name C or name O or name CB )) or \ resid 136 through 137 or (resid 138 and (name N or name CA or name C or name O \ or name CB )) or resid 139 through 152)) } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 5 through 96 or (resid 97 and (name N or name CA or name C \ or name O or name CB )))) } ncs_group { reference = (chain 'E' and (resid 2 through 97 or (resid 98 and (name N or name CA or name C \ or name O or name CB )) or resid 99 through 257)) selection = (chain 'H' and resid 2 through 257) } ncs_group { reference = (chain 'F' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 402)) selection = (chain 'G' and (resid 7 through 129 or (resid 130 through 131 and (name N or nam \ e CA or name C or name O or name CB )) or resid 132 through 259 or (resid 260 an \ d (name N or name CA or name C or name O or name CB )) or resid 261 through 264 \ or resid 401 through 402)) } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.860 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 : 0.004 0.142 15231 Z= 0.200 Angle : 0.806 16.239 20726 Z= 0.403 Chirality : 0.047 0.298 2538 Planarity : 0.005 0.063 2570 Dihedral : 13.731 84.584 5439 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.25 % Allowed : 7.53 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.76 (0.13), residues: 1935 helix: -4.94 (0.05), residues: 713 sheet: -2.09 (0.32), residues: 220 loop : -3.37 (0.15), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 49 TYR 0.012 0.001 TYR L 40 PHE 0.018 0.001 PHE F 254 TRP 0.010 0.001 TRP E 168 HIS 0.003 0.000 HIS G 203 Details of bonding type rmsd covalent geometry : bond 0.00385 (15231) covalent geometry : angle 0.80616 (20726) hydrogen bonds : bond 0.32078 ( 440) hydrogen bonds : angle 10.69657 ( 1272) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 375 time to evaluate : 0.404 Fit side-chains revert: symmetry clash REVERT: J 14 LEU cc_start: 0.7140 (mt) cc_final: 0.6916 (mt) REVERT: L 59 SER cc_start: 0.4315 (t) cc_final: 0.4095 (t) REVERT: L 99 LEU cc_start: 0.6691 (tp) cc_final: 0.6206 (mp) REVERT: B 95 LEU cc_start: 0.6860 (mm) cc_final: 0.6642 (tp) REVERT: F 207 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5820 (mt-10) outliers start: 4 outliers final: 2 residues processed: 377 average time/residue: 0.1287 time to fit residues: 68.2803 Evaluate side-chains 264 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 262 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain L residue 77 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.0060 chunk 149 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN K 91 ASN L 88 GLN L 110 GLN C 9 GLN F 7 ASN F 175 GLN F 191 ASN G 57 GLN G 175 GLN E 11 HIS E 191 ASN H 241 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.214591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.170195 restraints weight = 18716.234| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 3.44 r_work: 0.3475 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15231 Z= 0.145 Angle : 0.605 7.240 20726 Z= 0.303 Chirality : 0.043 0.220 2538 Planarity : 0.005 0.062 2570 Dihedral : 6.331 43.778 2167 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.15 % Allowed : 15.76 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.17 (0.15), residues: 1935 helix: -3.03 (0.13), residues: 742 sheet: -1.56 (0.34), residues: 222 loop : -2.83 (0.16), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.016 0.001 TYR H 49 PHE 0.024 0.002 PHE F 254 TRP 0.007 0.001 TRP A 9 HIS 0.007 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00337 (15231) covalent geometry : angle 0.60501 (20726) hydrogen bonds : bond 0.03738 ( 440) hydrogen bonds : angle 5.13945 ( 1272) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 266 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 99 LEU cc_start: 0.5647 (mt) cc_final: 0.5390 (tp) REVERT: J 7 GLU cc_start: 0.7809 (tp30) cc_final: 0.7504 (mt-10) REVERT: J 14 LEU cc_start: 0.8149 (mt) cc_final: 0.7904 (mt) REVERT: L 99 LEU cc_start: 0.6991 (tp) cc_final: 0.6487 (mp) REVERT: B 12 ASP cc_start: 0.8164 (p0) cc_final: 0.7946 (p0) REVERT: B 43 ASP cc_start: 0.7896 (t70) cc_final: 0.7563 (t70) REVERT: C 59 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8432 (mp) REVERT: F 29 LEU cc_start: 0.8858 (mp) cc_final: 0.8574 (mm) REVERT: F 100 MET cc_start: 0.9172 (ptp) cc_final: 0.8902 (ptp) REVERT: F 220 ASP cc_start: 0.4730 (OUTLIER) cc_final: 0.4211 (p0) REVERT: F 232 LEU cc_start: 0.7689 (mt) cc_final: 0.7405 (mp) REVERT: E 47 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8491 (mm-40) REVERT: E 233 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8100 (mtp-110) outliers start: 34 outliers final: 24 residues processed: 288 average time/residue: 0.1084 time to fit residues: 46.7387 Evaluate side-chains 261 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 235 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 77 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 52 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 199 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 120 ILE Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 203 LEU Chi-restraints excluded: chain H residue 252 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 58 optimal weight: 0.0370 chunk 151 optimal weight: 0.9990 chunk 102 optimal weight: 0.1980 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN F 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.211889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.166839 restraints weight = 18764.830| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 3.84 r_work: 0.3409 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 15231 Z= 0.100 Angle : 0.510 6.838 20726 Z= 0.256 Chirality : 0.040 0.144 2538 Planarity : 0.004 0.063 2570 Dihedral : 5.084 49.204 2167 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.47 % Allowed : 17.59 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.00 (0.17), residues: 1935 helix: -1.51 (0.18), residues: 753 sheet: -1.39 (0.33), residues: 236 loop : -2.56 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 77 TYR 0.008 0.001 TYR F 261 PHE 0.024 0.001 PHE F 254 TRP 0.009 0.001 TRP E 168 HIS 0.003 0.001 HIS F 122 Details of bonding type rmsd covalent geometry : bond 0.00226 (15231) covalent geometry : angle 0.51036 (20726) hydrogen bonds : bond 0.03250 ( 440) hydrogen bonds : angle 4.35403 ( 1272) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 251 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.6895 (mptt) cc_final: 0.6354 (mmtt) REVERT: A 49 ILE cc_start: 0.7329 (tp) cc_final: 0.6863 (pt) REVERT: J 7 GLU cc_start: 0.7826 (tp30) cc_final: 0.7587 (mt-10) REVERT: L 5 LYS cc_start: 0.7851 (tttt) cc_final: 0.7468 (ttpt) REVERT: L 99 LEU cc_start: 0.7047 (tp) cc_final: 0.6542 (mp) REVERT: B 12 ASP cc_start: 0.8103 (p0) cc_final: 0.7863 (p0) REVERT: B 43 ASP cc_start: 0.7952 (t70) cc_final: 0.7618 (t70) REVERT: C 43 ASP cc_start: 0.8055 (m-30) cc_final: 0.7365 (p0) REVERT: C 66 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7530 (mmtp) REVERT: F 29 LEU cc_start: 0.8851 (mp) cc_final: 0.8532 (mp) REVERT: F 77 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7699 (ttt90) REVERT: E 47 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8598 (mm-40) REVERT: E 233 ARG cc_start: 0.8459 (ttp80) cc_final: 0.8179 (mtp-110) REVERT: H 134 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.6029 (ttm) outliers start: 39 outliers final: 23 residues processed: 273 average time/residue: 0.1118 time to fit residues: 45.3205 Evaluate side-chains 257 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 147 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 252 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 25 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 124 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.206292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151533 restraints weight = 18503.444| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.82 r_work: 0.3458 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15231 Z= 0.116 Angle : 0.523 6.937 20726 Z= 0.262 Chirality : 0.041 0.145 2538 Planarity : 0.004 0.058 2570 Dihedral : 5.183 59.096 2167 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.59 % Allowed : 19.05 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.34 (0.18), residues: 1935 helix: -0.77 (0.19), residues: 766 sheet: -1.15 (0.34), residues: 233 loop : -2.35 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 77 TYR 0.010 0.001 TYR F 261 PHE 0.027 0.001 PHE J 23 TRP 0.008 0.001 TRP E 168 HIS 0.004 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00273 (15231) covalent geometry : angle 0.52259 (20726) hydrogen bonds : bond 0.02747 ( 440) hydrogen bonds : angle 4.04954 ( 1272) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7012 (mptt) cc_final: 0.6497 (mmtt) REVERT: D 141 MET cc_start: 0.6038 (tpt) cc_final: 0.5297 (tpt) REVERT: J 102 ARG cc_start: 0.6170 (mtt180) cc_final: 0.5391 (mmt180) REVERT: L 5 LYS cc_start: 0.7908 (tttt) cc_final: 0.7562 (ttpt) REVERT: L 99 LEU cc_start: 0.7040 (tp) cc_final: 0.6562 (mp) REVERT: B 12 ASP cc_start: 0.8067 (p0) cc_final: 0.7824 (p0) REVERT: B 43 ASP cc_start: 0.8027 (t70) cc_final: 0.7746 (t70) REVERT: B 86 LYS cc_start: 0.8450 (mtmm) cc_final: 0.8231 (mtmt) REVERT: C 31 MET cc_start: 0.7506 (tpt) cc_final: 0.7104 (tpt) REVERT: C 43 ASP cc_start: 0.8141 (m-30) cc_final: 0.7201 (p0) REVERT: C 66 LYS cc_start: 0.7713 (mtmt) cc_final: 0.7495 (mmtp) REVERT: F 29 LEU cc_start: 0.8887 (mp) cc_final: 0.8553 (mp) REVERT: F 77 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7713 (ttt90) REVERT: F 180 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8112 (ttp) REVERT: F 221 LYS cc_start: 0.8153 (mtmt) cc_final: 0.7791 (mtpt) REVERT: E 233 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8193 (mtp-110) REVERT: E 250 ASP cc_start: 0.8038 (t0) cc_final: 0.7792 (t0) REVERT: H 56 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7576 (mpp) REVERT: H 134 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6649 (ttm) REVERT: H 250 ASP cc_start: 0.8220 (t0) cc_final: 0.7962 (t0) outliers start: 41 outliers final: 28 residues processed: 265 average time/residue: 0.1151 time to fit residues: 45.0628 Evaluate side-chains 258 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 149 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 171 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 138 optimal weight: 0.6980 chunk 147 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 185 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 135 GLN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.204959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.148449 restraints weight = 18543.295| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.83 r_work: 0.3417 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15231 Z= 0.105 Angle : 0.512 8.486 20726 Z= 0.255 Chirality : 0.040 0.142 2538 Planarity : 0.004 0.057 2570 Dihedral : 5.132 57.190 2167 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.23 % Allowed : 18.54 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.19), residues: 1935 helix: -0.37 (0.20), residues: 770 sheet: -1.09 (0.34), residues: 242 loop : -2.12 (0.19), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 49 TYR 0.008 0.001 TYR H 49 PHE 0.018 0.001 PHE F 254 TRP 0.021 0.001 TRP C 7 HIS 0.004 0.001 HIS G 226 Details of bonding type rmsd covalent geometry : bond 0.00253 (15231) covalent geometry : angle 0.51226 (20726) hydrogen bonds : bond 0.02605 ( 440) hydrogen bonds : angle 3.85717 ( 1272) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 243 time to evaluate : 0.522 Fit side-chains REVERT: A 27 LYS cc_start: 0.7083 (mptt) cc_final: 0.6585 (mmtt) REVERT: D 141 MET cc_start: 0.5877 (tpt) cc_final: 0.5108 (tpt) REVERT: J 102 ARG cc_start: 0.6166 (mtt180) cc_final: 0.5392 (mmt180) REVERT: L 5 LYS cc_start: 0.7842 (tttt) cc_final: 0.7470 (ttpt) REVERT: L 99 LEU cc_start: 0.6891 (tp) cc_final: 0.6448 (mp) REVERT: B 12 ASP cc_start: 0.7978 (p0) cc_final: 0.7748 (p0) REVERT: B 43 ASP cc_start: 0.8052 (t70) cc_final: 0.7770 (t70) REVERT: F 77 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7835 (mtp85) REVERT: F 127 MET cc_start: 0.9193 (ptp) cc_final: 0.8932 (ptm) REVERT: F 180 MET cc_start: 0.8648 (ttm) cc_final: 0.8167 (mtt) REVERT: F 207 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7552 (mt-10) REVERT: F 221 LYS cc_start: 0.8221 (mtmt) cc_final: 0.7858 (mtpt) REVERT: E 46 ARG cc_start: 0.8438 (tpt170) cc_final: 0.7808 (tpt-90) REVERT: E 233 ARG cc_start: 0.8463 (ttp80) cc_final: 0.8198 (mtp-110) REVERT: E 250 ASP cc_start: 0.8172 (t0) cc_final: 0.7872 (t0) REVERT: H 50 ASN cc_start: 0.8611 (p0) cc_final: 0.8374 (p0) REVERT: H 134 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6760 (ttm) REVERT: H 250 ASP cc_start: 0.8346 (t0) cc_final: 0.8114 (t0) outliers start: 51 outliers final: 37 residues processed: 272 average time/residue: 0.1189 time to fit residues: 47.3783 Evaluate side-chains 272 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 234 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 129 LYS Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 178 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 101 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 0.3980 chunk 71 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 20.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN G 113 HIS E 40 HIS E 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.202248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.146192 restraints weight = 18577.809| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.78 r_work: 0.3387 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15231 Z= 0.117 Angle : 0.530 9.364 20726 Z= 0.262 Chirality : 0.041 0.140 2538 Planarity : 0.004 0.075 2570 Dihedral : 5.198 57.818 2167 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.23 % Allowed : 19.56 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.19), residues: 1935 helix: -0.14 (0.20), residues: 773 sheet: -1.08 (0.35), residues: 237 loop : -1.95 (0.19), residues: 925 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.011 0.001 TYR C 82 PHE 0.017 0.001 PHE F 254 TRP 0.016 0.001 TRP C 7 HIS 0.004 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00280 (15231) covalent geometry : angle 0.53016 (20726) hydrogen bonds : bond 0.02595 ( 440) hydrogen bonds : angle 3.83117 ( 1272) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 0.451 Fit side-chains REVERT: A 27 LYS cc_start: 0.7131 (mptt) cc_final: 0.6669 (mmtt) REVERT: A 102 ARG cc_start: 0.2772 (mmt90) cc_final: 0.2232 (mmp80) REVERT: D 141 MET cc_start: 0.6005 (tpt) cc_final: 0.5208 (tpt) REVERT: J 79 LEU cc_start: 0.5598 (OUTLIER) cc_final: 0.4645 (pp) REVERT: J 102 ARG cc_start: 0.6255 (mtt180) cc_final: 0.5457 (mmt180) REVERT: K 60 ILE cc_start: 0.6636 (OUTLIER) cc_final: 0.6426 (tp) REVERT: L 5 LYS cc_start: 0.7831 (tttt) cc_final: 0.7466 (ttpt) REVERT: L 99 LEU cc_start: 0.6837 (tp) cc_final: 0.6326 (mp) REVERT: B 12 ASP cc_start: 0.7745 (p0) cc_final: 0.7523 (p0) REVERT: B 43 ASP cc_start: 0.8085 (t70) cc_final: 0.7810 (t70) REVERT: B 86 LYS cc_start: 0.8719 (tppt) cc_final: 0.8516 (tppt) REVERT: C 41 CYS cc_start: 0.7663 (m) cc_final: 0.7309 (t) REVERT: C 43 ASP cc_start: 0.8358 (m-30) cc_final: 0.7053 (p0) REVERT: F 77 ARG cc_start: 0.8148 (ttm-80) cc_final: 0.7853 (mtp85) REVERT: F 180 MET cc_start: 0.8694 (ttm) cc_final: 0.8118 (mtt) REVERT: F 207 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7441 (mt-10) REVERT: F 221 LYS cc_start: 0.8266 (mtmt) cc_final: 0.7941 (mtpt) REVERT: E 167 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7689 (tt) REVERT: E 194 ASP cc_start: 0.5103 (OUTLIER) cc_final: 0.4426 (p0) REVERT: E 233 ARG cc_start: 0.8520 (ttp80) cc_final: 0.8239 (mtp-110) REVERT: E 250 ASP cc_start: 0.8194 (t0) cc_final: 0.7902 (t0) REVERT: H 134 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6950 (ttm) REVERT: H 204 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9059 (mp) outliers start: 51 outliers final: 34 residues processed: 265 average time/residue: 0.1233 time to fit residues: 47.2137 Evaluate side-chains 273 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 232 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 60 ILE Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain K residue 129 LYS Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 204 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 164 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 93 optimal weight: 0.0770 chunk 179 optimal weight: 0.4980 chunk 190 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.204371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.149017 restraints weight = 18234.901| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.79 r_work: 0.3378 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 15231 Z= 0.086 Angle : 0.495 8.342 20726 Z= 0.245 Chirality : 0.039 0.138 2538 Planarity : 0.004 0.062 2570 Dihedral : 5.034 59.859 2167 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.78 % Allowed : 20.06 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.19), residues: 1935 helix: 0.15 (0.20), residues: 779 sheet: -1.03 (0.35), residues: 237 loop : -1.85 (0.19), residues: 919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 49 TYR 0.010 0.001 TYR C 82 PHE 0.017 0.001 PHE F 254 TRP 0.012 0.001 TRP C 7 HIS 0.003 0.001 HIS G 226 Details of bonding type rmsd covalent geometry : bond 0.00197 (15231) covalent geometry : angle 0.49471 (20726) hydrogen bonds : bond 0.02252 ( 440) hydrogen bonds : angle 3.67991 ( 1272) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.508 Fit side-chains REVERT: A 27 LYS cc_start: 0.7126 (mptt) cc_final: 0.6687 (mmtt) REVERT: A 102 ARG cc_start: 0.2771 (mmt90) cc_final: 0.2298 (mmp80) REVERT: D 141 MET cc_start: 0.5724 (tpt) cc_final: 0.4935 (tpt) REVERT: J 79 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.4578 (pp) REVERT: J 102 ARG cc_start: 0.6204 (mtt180) cc_final: 0.5419 (mmt180) REVERT: L 5 LYS cc_start: 0.7825 (tttt) cc_final: 0.7448 (ttpt) REVERT: L 99 LEU cc_start: 0.6801 (tp) cc_final: 0.6382 (mp) REVERT: B 12 ASP cc_start: 0.7734 (p0) cc_final: 0.7512 (p0) REVERT: B 43 ASP cc_start: 0.8055 (t70) cc_final: 0.7766 (t70) REVERT: C 41 CYS cc_start: 0.7506 (m) cc_final: 0.6999 (t) REVERT: C 43 ASP cc_start: 0.8339 (m-30) cc_final: 0.7030 (p0) REVERT: F 77 ARG cc_start: 0.8049 (ttm-80) cc_final: 0.7675 (ttt90) REVERT: F 180 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7985 (mtt) REVERT: F 207 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7402 (mt-10) REVERT: F 221 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7885 (mtpt) REVERT: G 221 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7888 (ptpt) REVERT: E 46 ARG cc_start: 0.8352 (tpt170) cc_final: 0.7785 (tpt-90) REVERT: E 233 ARG cc_start: 0.8437 (ttp80) cc_final: 0.8146 (mtp-110) REVERT: E 250 ASP cc_start: 0.8079 (t0) cc_final: 0.7788 (t0) REVERT: H 204 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.8952 (mp) outliers start: 44 outliers final: 33 residues processed: 264 average time/residue: 0.1269 time to fit residues: 48.5192 Evaluate side-chains 265 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 202 CYS Chi-restraints excluded: chain H residue 204 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 54 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 152 optimal weight: 0.5980 chunk 118 optimal weight: 0.3980 chunk 97 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 150 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.200920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 99)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.140852 restraints weight = 18390.229| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.20 r_work: 0.3348 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15231 Z= 0.116 Angle : 0.530 8.227 20726 Z= 0.262 Chirality : 0.041 0.139 2538 Planarity : 0.004 0.058 2570 Dihedral : 5.145 59.768 2167 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 2.97 % Allowed : 20.25 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.19), residues: 1935 helix: 0.21 (0.20), residues: 786 sheet: -0.93 (0.35), residues: 235 loop : -1.84 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 49 TYR 0.010 0.001 TYR C 82 PHE 0.016 0.001 PHE F 254 TRP 0.011 0.001 TRP I 9 HIS 0.004 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00281 (15231) covalent geometry : angle 0.53029 (20726) hydrogen bonds : bond 0.02596 ( 440) hydrogen bonds : angle 3.72677 ( 1272) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 0.514 Fit side-chains REVERT: A 27 LYS cc_start: 0.7102 (mptt) cc_final: 0.6626 (mmtt) REVERT: A 81 ARG cc_start: 0.7561 (mtt90) cc_final: 0.7271 (mtt180) REVERT: A 102 ARG cc_start: 0.2788 (mmt90) cc_final: 0.2394 (mmp80) REVERT: D 141 MET cc_start: 0.5559 (tpt) cc_final: 0.4793 (tpt) REVERT: J 79 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.4473 (pp) REVERT: J 102 ARG cc_start: 0.6110 (mtt180) cc_final: 0.5306 (mmt180) REVERT: L 5 LYS cc_start: 0.7817 (tttt) cc_final: 0.7421 (ttpt) REVERT: L 99 LEU cc_start: 0.6715 (tp) cc_final: 0.6226 (mp) REVERT: B 12 ASP cc_start: 0.7698 (p0) cc_final: 0.7493 (p0) REVERT: B 43 ASP cc_start: 0.8047 (t70) cc_final: 0.7728 (t70) REVERT: B 93 ASP cc_start: 0.7860 (m-30) cc_final: 0.7655 (m-30) REVERT: C 41 CYS cc_start: 0.7531 (m) cc_final: 0.6982 (t) REVERT: C 43 ASP cc_start: 0.8374 (m-30) cc_final: 0.6890 (p0) REVERT: F 77 ARG cc_start: 0.8218 (ttm-80) cc_final: 0.7917 (mtp85) REVERT: F 180 MET cc_start: 0.8687 (ttm) cc_final: 0.8074 (mtt) REVERT: F 207 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: F 221 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7822 (mtpt) REVERT: E 194 ASP cc_start: 0.5072 (OUTLIER) cc_final: 0.4443 (p0) REVERT: E 233 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8173 (mtp-110) REVERT: E 250 ASP cc_start: 0.8251 (t0) cc_final: 0.7989 (t0) REVERT: H 56 MET cc_start: 0.8555 (tpp) cc_final: 0.8264 (mtt) REVERT: H 134 MET cc_start: 0.7209 (OUTLIER) cc_final: 0.6906 (ttm) outliers start: 47 outliers final: 36 residues processed: 261 average time/residue: 0.1203 time to fit residues: 45.7953 Evaluate side-chains 265 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 225 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 202 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 79 optimal weight: 0.7980 chunk 34 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 190 optimal weight: 0.5980 chunk 71 optimal weight: 20.0000 chunk 17 optimal weight: 0.4980 chunk 27 optimal weight: 20.0000 chunk 108 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.198469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.142056 restraints weight = 18397.821| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.76 r_work: 0.3267 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15231 Z= 0.133 Angle : 0.563 9.332 20726 Z= 0.277 Chirality : 0.042 0.144 2538 Planarity : 0.004 0.058 2570 Dihedral : 5.329 58.131 2167 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.16 % Allowed : 20.25 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.19), residues: 1935 helix: 0.23 (0.20), residues: 787 sheet: -0.78 (0.35), residues: 236 loop : -1.82 (0.19), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 49 TYR 0.012 0.001 TYR C 82 PHE 0.036 0.001 PHE L 23 TRP 0.014 0.001 TRP I 9 HIS 0.004 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00326 (15231) covalent geometry : angle 0.56257 (20726) hydrogen bonds : bond 0.02754 ( 440) hydrogen bonds : angle 3.83813 ( 1272) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.568 Fit side-chains REVERT: A 27 LYS cc_start: 0.7279 (mptt) cc_final: 0.6803 (mmtt) REVERT: A 81 ARG cc_start: 0.7676 (mtt90) cc_final: 0.7455 (mtt180) REVERT: D 141 MET cc_start: 0.5866 (tpt) cc_final: 0.4999 (tpt) REVERT: J 79 LEU cc_start: 0.5731 (OUTLIER) cc_final: 0.4661 (pp) REVERT: J 102 ARG cc_start: 0.6260 (mtt180) cc_final: 0.5451 (mmt180) REVERT: L 5 LYS cc_start: 0.7811 (tttt) cc_final: 0.7415 (ttpt) REVERT: L 99 LEU cc_start: 0.6790 (tp) cc_final: 0.6256 (mp) REVERT: B 12 ASP cc_start: 0.7767 (p0) cc_final: 0.7552 (p0) REVERT: B 43 ASP cc_start: 0.8059 (t70) cc_final: 0.7779 (t70) REVERT: B 50 VAL cc_start: 0.8755 (t) cc_final: 0.8436 (p) REVERT: B 75 GLN cc_start: 0.7595 (mm110) cc_final: 0.7326 (pt0) REVERT: C 41 CYS cc_start: 0.7386 (m) cc_final: 0.6834 (t) REVERT: F 66 LEU cc_start: 0.7377 (pt) cc_final: 0.6985 (mt) REVERT: F 180 MET cc_start: 0.8785 (ttm) cc_final: 0.8290 (ttm) REVERT: F 207 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7507 (mt-10) REVERT: F 221 LYS cc_start: 0.8165 (mtmt) cc_final: 0.7783 (mtpt) REVERT: E 167 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7505 (tt) REVERT: E 194 ASP cc_start: 0.5115 (OUTLIER) cc_final: 0.3978 (p0) REVERT: E 250 ASP cc_start: 0.8372 (t0) cc_final: 0.8159 (t0) REVERT: H 56 MET cc_start: 0.8741 (tpp) cc_final: 0.8473 (mtt) REVERT: H 134 MET cc_start: 0.7381 (OUTLIER) cc_final: 0.7041 (ttm) outliers start: 50 outliers final: 37 residues processed: 261 average time/residue: 0.1122 time to fit residues: 43.7053 Evaluate side-chains 263 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain E residue 117 THR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 194 ASP Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 202 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 124 optimal weight: 0.0670 chunk 45 optimal weight: 5.9990 chunk 167 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 92 optimal weight: 0.9990 chunk 35 optimal weight: 0.0370 chunk 109 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 68 GLN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.200142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.142047 restraints weight = 18585.392| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.83 r_work: 0.3282 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15231 Z= 0.099 Angle : 0.528 9.781 20726 Z= 0.260 Chirality : 0.040 0.142 2538 Planarity : 0.004 0.055 2570 Dihedral : 5.140 59.767 2167 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.53 % Allowed : 20.95 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.19), residues: 1935 helix: 0.48 (0.20), residues: 781 sheet: -0.77 (0.35), residues: 239 loop : -1.76 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 49 TYR 0.010 0.001 TYR C 82 PHE 0.024 0.001 PHE L 23 TRP 0.007 0.001 TRP I 9 HIS 0.003 0.001 HIS G 226 Details of bonding type rmsd covalent geometry : bond 0.00234 (15231) covalent geometry : angle 0.52780 (20726) hydrogen bonds : bond 0.02373 ( 440) hydrogen bonds : angle 3.70800 ( 1272) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 233 time to evaluate : 0.511 Fit side-chains REVERT: A 27 LYS cc_start: 0.7211 (mptt) cc_final: 0.6744 (mmtt) REVERT: A 81 ARG cc_start: 0.7696 (mtt90) cc_final: 0.7489 (mtt180) REVERT: A 141 MET cc_start: 0.2937 (tpp) cc_final: 0.2630 (tpp) REVERT: D 141 MET cc_start: 0.5737 (tpt) cc_final: 0.4912 (tpt) REVERT: J 79 LEU cc_start: 0.5542 (OUTLIER) cc_final: 0.4608 (pp) REVERT: J 102 ARG cc_start: 0.6145 (mtt180) cc_final: 0.5419 (mmt180) REVERT: L 5 LYS cc_start: 0.7798 (tttt) cc_final: 0.7367 (ttpt) REVERT: L 99 LEU cc_start: 0.6686 (tp) cc_final: 0.6173 (mp) REVERT: B 12 ASP cc_start: 0.7759 (p0) cc_final: 0.7494 (p0) REVERT: B 43 ASP cc_start: 0.8044 (t70) cc_final: 0.7763 (t70) REVERT: B 50 VAL cc_start: 0.8732 (t) cc_final: 0.8409 (p) REVERT: C 41 CYS cc_start: 0.7541 (m) cc_final: 0.6900 (t) REVERT: C 43 ASP cc_start: 0.8405 (m-30) cc_final: 0.6935 (p0) REVERT: F 66 LEU cc_start: 0.7239 (pt) cc_final: 0.6889 (mt) REVERT: F 180 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8068 (mtt) REVERT: F 207 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7495 (mt-10) REVERT: F 221 LYS cc_start: 0.8139 (mtmt) cc_final: 0.7764 (mtpt) REVERT: E 46 ARG cc_start: 0.8326 (tpt170) cc_final: 0.7939 (tpt170) REVERT: E 76 LEU cc_start: 0.8223 (mm) cc_final: 0.7812 (tt) REVERT: E 250 ASP cc_start: 0.8282 (t0) cc_final: 0.8043 (t0) REVERT: H 134 MET cc_start: 0.7182 (OUTLIER) cc_final: 0.6871 (ttm) REVERT: H 257 MET cc_start: 0.4959 (mmt) cc_final: 0.4637 (mmt) outliers start: 40 outliers final: 33 residues processed: 258 average time/residue: 0.1117 time to fit residues: 43.0027 Evaluate side-chains 265 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 228 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain D residue 43 TYR Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain I residue 60 ILE Chi-restraints excluded: chain I residue 90 TYR Chi-restraints excluded: chain I residue 141 MET Chi-restraints excluded: chain J residue 14 LEU Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 31 VAL Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 79 LEU Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain K residue 49 ILE Chi-restraints excluded: chain K residue 101 ILE Chi-restraints excluded: chain K residue 103 THR Chi-restraints excluded: chain K residue 114 LEU Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 180 MET Chi-restraints excluded: chain F residue 194 LEU Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 152 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 202 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 184 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 168 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 189 optimal weight: 0.0270 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.198594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.141283 restraints weight = 18470.092| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.73 r_work: 0.3305 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15231 Z= 0.118 Angle : 0.549 10.175 20726 Z= 0.271 Chirality : 0.041 0.141 2538 Planarity : 0.004 0.055 2570 Dihedral : 5.227 59.550 2167 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.72 % Allowed : 21.14 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.19), residues: 1935 helix: 0.49 (0.20), residues: 785 sheet: -0.73 (0.35), residues: 239 loop : -1.72 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.012 0.001 TYR C 82 PHE 0.021 0.001 PHE L 23 TRP 0.010 0.001 TRP I 9 HIS 0.004 0.001 HIS H 241 Details of bonding type rmsd covalent geometry : bond 0.00287 (15231) covalent geometry : angle 0.54914 (20726) hydrogen bonds : bond 0.02607 ( 440) hydrogen bonds : angle 3.77560 ( 1272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4220.34 seconds wall clock time: 72 minutes 34.32 seconds (4354.32 seconds total)