Starting phenix.real_space_refine on Fri Jun 13 10:26:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zy9_11555/06_2025/6zy9_11555.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zy9_11555/06_2025/6zy9_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_11555/06_2025/6zy9_11555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zy9_11555/06_2025/6zy9_11555.map" model { file = "/net/cci-nas-00/data/ceres_data/6zy9_11555/06_2025/6zy9_11555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zy9_11555/06_2025/6zy9_11555.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2} 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: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2, '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: {'GLU:plan': 3, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} 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: {'GLN:plan1': 1, 'ASP:plan': 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: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 4} 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: 9.46, per 1000 atoms: 0.63 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: 3.44 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.62 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: 4.07 Time building geometry restraints manager: 4.08 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 264 or resid 401 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: 0.730 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 34.860 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.100 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.220 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.010 0.001 TRP E 168 HIS 0.003 0.000 HIS G 203 PHE 0.018 0.001 PHE F 254 TYR 0.012 0.001 TYR L 40 ARG 0.003 0.000 ARG C 49 Details of bonding type rmsd hydrogen bonds : bond 0.32078 ( 440) hydrogen bonds : angle 10.69657 ( 1272) covalent geometry : bond 0.00385 (15231) covalent geometry : angle 0.80616 (20726) *********************** 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 : 1.548 Fit side-chains revert: symmetry clash REVERT: J 14 LEU cc_start: 0.7140 (mt) cc_final: 0.6918 (mt) REVERT: L 59 SER cc_start: 0.4315 (t) cc_final: 0.4097 (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: 0.3235 time to fit residues: 172.4753 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 : 1.931 ------------------------------------------------------------------------------- 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 162 optimal weight: 0.7980 chunk 145 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 chunk 91 optimal weight: 0.0060 chunk 112 optimal weight: 0.0570 chunk 174 optimal weight: 0.9990 overall best weight: 0.5316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 91 ASN L 88 GLN L 110 GLN C 9 GLN F 7 ASN F 175 GLN G 57 GLN G 175 GLN E 11 HIS E 191 ASN ** H 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 241 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.221065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.177431 restraints weight = 18809.939| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 3.00 r_work: 0.3609 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15231 Z= 0.127 Angle : 0.568 7.638 20726 Z= 0.284 Chirality : 0.041 0.150 2538 Planarity : 0.005 0.064 2570 Dihedral : 6.462 47.486 2167 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.09 % Allowed : 14.75 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.15), residues: 1935 helix: -3.05 (0.13), residues: 723 sheet: -1.54 (0.35), residues: 215 loop : -2.86 (0.16), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 168 HIS 0.006 0.001 HIS F 122 PHE 0.022 0.001 PHE F 254 TYR 0.012 0.001 TYR K 111 ARG 0.006 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 440) hydrogen bonds : angle 5.33009 ( 1272) covalent geometry : bond 0.00248 (15231) covalent geometry : angle 0.56774 (20726) *********************** 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 298 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 265 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 99 LEU cc_start: 0.5723 (mt) cc_final: 0.5478 (tp) REVERT: J 14 LEU cc_start: 0.7843 (mt) cc_final: 0.7575 (mt) REVERT: L 99 LEU cc_start: 0.6928 (tp) cc_final: 0.6445 (mp) REVERT: B 12 ASP cc_start: 0.7996 (p0) cc_final: 0.7765 (p0) REVERT: B 43 ASP cc_start: 0.7820 (t70) cc_final: 0.7478 (t70) REVERT: C 59 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8428 (mp) REVERT: F 29 LEU cc_start: 0.8796 (mp) cc_final: 0.8557 (mm) REVERT: F 220 ASP cc_start: 0.4563 (OUTLIER) cc_final: 0.4180 (p0) REVERT: G 144 GLU cc_start: 0.7761 (pp20) cc_final: 0.7524 (pp20) REVERT: E 47 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8384 (mm-40) REVERT: E 233 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7880 (mtp-110) REVERT: H 203 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6934 (mp) outliers start: 33 outliers final: 23 residues processed: 286 average time/residue: 0.2621 time to fit residues: 110.7200 Evaluate side-chains 268 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 220 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 254 PHE Chi-restraints excluded: chain E residue 50 ASN 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 14 ILE Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 129 LEU 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 113 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 187 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 chunk 20 optimal weight: 0.0370 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 overall best weight: 1.1062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN I 135 GLN K 91 ASN F 191 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.205776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150281 restraints weight = 18403.179| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.58 r_work: 0.3443 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15231 Z= 0.145 Angle : 0.600 7.387 20726 Z= 0.300 Chirality : 0.043 0.177 2538 Planarity : 0.005 0.068 2570 Dihedral : 5.347 53.728 2167 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.16 % Allowed : 17.03 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.17), residues: 1935 helix: -1.63 (0.17), residues: 773 sheet: -1.31 (0.34), residues: 235 loop : -2.61 (0.17), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 9 HIS 0.006 0.001 HIS H 40 PHE 0.025 0.002 PHE F 254 TYR 0.018 0.001 TYR F 261 ARG 0.005 0.001 ARG J 55 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 440) hydrogen bonds : angle 4.43054 ( 1272) covalent geometry : bond 0.00342 (15231) covalent geometry : angle 0.59989 (20726) *********************** 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 310 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 260 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7071 (mptt) cc_final: 0.6581 (mmtt) REVERT: A 49 ILE cc_start: 0.7437 (tp) cc_final: 0.6978 (pt) REVERT: D 141 MET cc_start: 0.6095 (tpt) cc_final: 0.5330 (tpt) REVERT: L 5 LYS cc_start: 0.7870 (tttt) cc_final: 0.7510 (ttpt) REVERT: L 12 ILE cc_start: 0.8228 (pt) cc_final: 0.8019 (mt) REVERT: L 99 LEU cc_start: 0.7079 (tp) cc_final: 0.6479 (mp) REVERT: B 12 ASP cc_start: 0.8122 (p0) cc_final: 0.7895 (p0) REVERT: B 43 ASP cc_start: 0.8037 (t70) cc_final: 0.7748 (t70) REVERT: B 86 LYS cc_start: 0.8531 (mtmm) cc_final: 0.8326 (mtmt) REVERT: C 31 MET cc_start: 0.7529 (tpt) cc_final: 0.7326 (tpt) REVERT: C 66 LYS cc_start: 0.7797 (mtmt) cc_final: 0.7559 (mmtp) REVERT: F 29 LEU cc_start: 0.8876 (mp) cc_final: 0.8568 (mp) REVERT: F 180 MET cc_start: 0.8710 (ttm) cc_final: 0.8352 (ttp) REVERT: G 29 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8407 (pp) REVERT: E 43 LEU cc_start: 0.9338 (mt) cc_final: 0.9095 (mt) REVERT: E 233 ARG cc_start: 0.8411 (ttp80) cc_final: 0.8173 (mtp-110) REVERT: H 84 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6116 (tm-30) REVERT: H 134 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6589 (ttm) REVERT: H 250 ASP cc_start: 0.8291 (t0) cc_final: 0.8087 (t0) outliers start: 50 outliers final: 29 residues processed: 291 average time/residue: 0.2807 time to fit residues: 119.4330 Evaluate side-chains 264 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 2.169 ------------------------------------------------------------------------------- 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 19 LEU Chi-restraints excluded: chain J residue 63 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 14 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 99 ASP Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 254 PHE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 230 GLN Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 93 LEU Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 134 MET Chi-restraints excluded: chain H residue 173 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 9.9990 chunk 187 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 158 optimal weight: 0.9980 chunk 181 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 168 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 ASN F 191 ASN G 26 ASN G 113 HIS E 40 HIS E 128 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.201725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.135047 restraints weight = 18346.837| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.08 r_work: 0.3245 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15231 Z= 0.149 Angle : 0.574 7.704 20726 Z= 0.286 Chirality : 0.042 0.145 2538 Planarity : 0.004 0.058 2570 Dihedral : 5.542 59.029 2167 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.10 % Allowed : 18.10 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.18), residues: 1935 helix: -0.95 (0.19), residues: 775 sheet: -1.21 (0.35), residues: 233 loop : -2.35 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 9 HIS 0.006 0.001 HIS H 241 PHE 0.028 0.002 PHE J 23 TYR 0.011 0.001 TYR H 49 ARG 0.006 0.001 ARG J 55 Details of bonding type rmsd hydrogen bonds : bond 0.03095 ( 440) hydrogen bonds : angle 4.24438 ( 1272) covalent geometry : bond 0.00361 (15231) covalent geometry : angle 0.57381 (20726) *********************** 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 300 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 251 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7004 (mptt) cc_final: 0.6451 (mmtt) REVERT: A 102 ARG cc_start: 0.2364 (mmt90) cc_final: 0.2067 (mmp80) REVERT: J 7 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7878 (mt-10) REVERT: J 81 ARG cc_start: 0.6453 (ttp-110) cc_final: 0.6227 (ptm160) REVERT: J 102 ARG cc_start: 0.6030 (mtt180) cc_final: 0.5297 (mmt180) REVERT: L 5 LYS cc_start: 0.7770 (tttt) cc_final: 0.7333 (ttpt) REVERT: L 99 LEU cc_start: 0.6776 (tp) cc_final: 0.6355 (mp) REVERT: B 43 ASP cc_start: 0.8006 (t70) cc_final: 0.7669 (t70) REVERT: C 66 LYS cc_start: 0.7648 (mtmt) cc_final: 0.7424 (mmtp) REVERT: F 221 LYS cc_start: 0.8089 (mtmt) cc_final: 0.7715 (mtpt) REVERT: E 197 MET cc_start: 0.7068 (OUTLIER) cc_final: 0.6755 (ttp) REVERT: E 233 ARG cc_start: 0.8342 (ttp80) cc_final: 0.8071 (mtp-110) REVERT: E 250 ASP cc_start: 0.8284 (t0) cc_final: 0.7955 (t0) REVERT: H 249 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8316 (mp) REVERT: H 250 ASP cc_start: 0.8663 (t0) cc_final: 0.8455 (t0) outliers start: 49 outliers final: 33 residues processed: 276 average time/residue: 0.2711 time to fit residues: 109.0899 Evaluate side-chains 267 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 1.667 ------------------------------------------------------------------------------- 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 141 MET Chi-restraints excluded: chain J residue 31 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 K residue 129 LYS Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 196 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 221 LYS Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 144 ILE Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 197 MET Chi-restraints excluded: chain H residue 53 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 129 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 48 optimal weight: 0.0970 chunk 185 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 102 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 6 ASN ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 191 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.203268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.146170 restraints weight = 18514.880| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.79 r_work: 0.3322 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15231 Z= 0.098 Angle : 0.518 9.645 20726 Z= 0.256 Chirality : 0.040 0.144 2538 Planarity : 0.004 0.073 2570 Dihedral : 5.305 58.886 2167 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.10 % Allowed : 19.37 % Favored : 77.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.19), residues: 1935 helix: -0.40 (0.20), residues: 770 sheet: -1.20 (0.34), residues: 241 loop : -2.12 (0.19), residues: 924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 168 HIS 0.003 0.001 HIS G 226 PHE 0.019 0.001 PHE J 23 TYR 0.008 0.001 TYR E 49 ARG 0.009 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.02597 ( 440) hydrogen bonds : angle 3.95687 ( 1272) covalent geometry : bond 0.00232 (15231) covalent geometry : angle 0.51781 (20726) *********************** 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 286 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 237 time to evaluate : 1.723 Fit side-chains REVERT: A 27 LYS cc_start: 0.7167 (mptt) cc_final: 0.6626 (mmtt) REVERT: A 102 ARG cc_start: 0.2733 (mmt90) cc_final: 0.2359 (mmp80) REVERT: D 141 MET cc_start: 0.5891 (tpt) cc_final: 0.5141 (tpt) REVERT: J 7 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7839 (mt-10) REVERT: J 81 ARG cc_start: 0.6696 (ttp-110) cc_final: 0.6404 (ptm160) REVERT: J 102 ARG cc_start: 0.6183 (mtt180) cc_final: 0.5376 (mmt180) REVERT: L 5 LYS cc_start: 0.7786 (tttt) cc_final: 0.7377 (ttpt) REVERT: L 99 LEU cc_start: 0.6828 (tp) cc_final: 0.6339 (mp) REVERT: B 43 ASP cc_start: 0.8080 (t70) cc_final: 0.7764 (t70) REVERT: F 66 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6812 (mt) REVERT: F 180 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8159 (ttp) REVERT: G 208 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8705 (p) REVERT: E 167 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7595 (tt) REVERT: E 194 ASP cc_start: 0.5084 (OUTLIER) cc_final: 0.4347 (p0) REVERT: E 197 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6760 (ttp) REVERT: E 233 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8109 (mtp-110) REVERT: E 250 ASP cc_start: 0.8146 (t0) cc_final: 0.7883 (t0) REVERT: H 56 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8088 (mtm) REVERT: H 134 MET cc_start: 0.7210 (OUTLIER) cc_final: 0.6687 (ttm) REVERT: H 257 MET cc_start: 0.4821 (mmt) cc_final: 0.4477 (mmt) outliers start: 49 outliers final: 30 residues processed: 263 average time/residue: 0.2863 time to fit residues: 109.5572 Evaluate side-chains 266 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 228 time to evaluate : 1.791 ------------------------------------------------------------------------------- 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 D residue 81 ARG 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 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 14 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 83 VAL 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 208 VAL Chi-restraints excluded: chain G residue 221 LYS Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 144 ILE 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 E residue 197 MET Chi-restraints excluded: chain H residue 56 MET Chi-restraints excluded: chain H residue 129 LEU 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 121 optimal weight: 0.0980 chunk 21 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 115 optimal weight: 0.0870 chunk 30 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 67 optimal weight: 0.0270 chunk 59 optimal weight: 8.9990 chunk 174 optimal weight: 0.7980 overall best weight: 0.4018 ------------------------------------------------------------------------------- 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 = 0.4241 r_free = 0.4241 target = 0.204485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.147911 restraints weight = 18439.708| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.79 r_work: 0.3390 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15231 Z= 0.087 Angle : 0.500 8.285 20726 Z= 0.248 Chirality : 0.039 0.142 2538 Planarity : 0.004 0.060 2570 Dihedral : 5.149 58.724 2167 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.42 % Allowed : 19.68 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.19), residues: 1935 helix: -0.04 (0.20), residues: 772 sheet: -1.13 (0.34), residues: 242 loop : -1.94 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 168 HIS 0.003 0.001 HIS G 226 PHE 0.017 0.001 PHE F 254 TYR 0.007 0.001 TYR E 49 ARG 0.010 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.02308 ( 440) hydrogen bonds : angle 3.77432 ( 1272) covalent geometry : bond 0.00196 (15231) covalent geometry : angle 0.50006 (20726) *********************** 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 280 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 1.532 Fit side-chains REVERT: A 27 LYS cc_start: 0.7178 (mptt) cc_final: 0.6708 (mmtt) REVERT: A 81 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7483 (mtt180) REVERT: A 102 ARG cc_start: 0.2824 (mmt90) cc_final: 0.2414 (mmp80) REVERT: D 141 MET cc_start: 0.5857 (tpt) cc_final: 0.5035 (tpt) REVERT: J 7 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7830 (mt-10) REVERT: J 81 ARG cc_start: 0.6701 (ttp-110) cc_final: 0.6381 (ptm160) REVERT: J 102 ARG cc_start: 0.6213 (mtt180) cc_final: 0.5392 (mmt180) REVERT: K 60 ILE cc_start: 0.6672 (OUTLIER) cc_final: 0.6460 (tp) REVERT: L 5 LYS cc_start: 0.7822 (tttt) cc_final: 0.7433 (ttpt) REVERT: L 99 LEU cc_start: 0.6866 (tp) cc_final: 0.6372 (mp) REVERT: B 43 ASP cc_start: 0.8084 (t70) cc_final: 0.7777 (t70) REVERT: C 31 MET cc_start: 0.7625 (tpt) cc_final: 0.7425 (tpt) REVERT: F 66 LEU cc_start: 0.7282 (OUTLIER) cc_final: 0.6951 (mt) REVERT: F 221 LYS cc_start: 0.8152 (mtmt) cc_final: 0.7867 (mtpt) REVERT: G 208 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8824 (p) REVERT: E 167 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7617 (tt) REVERT: E 194 ASP cc_start: 0.4973 (OUTLIER) cc_final: 0.4535 (p0) REVERT: E 233 ARG cc_start: 0.8435 (ttp80) cc_final: 0.8155 (mtp-110) REVERT: E 250 ASP cc_start: 0.7995 (t0) cc_final: 0.7762 (t0) REVERT: H 56 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8125 (mtm) REVERT: H 134 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6542 (ttm) REVERT: H 204 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9012 (mp) outliers start: 54 outliers final: 37 residues processed: 260 average time/residue: 0.2732 time to fit residues: 103.7037 Evaluate side-chains 264 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 219 time to evaluate : 1.633 ------------------------------------------------------------------------------- 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 D residue 81 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 60 ILE 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 79 LEU Chi-restraints excluded: chain K residue 45 THR 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 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 20 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU 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 254 PHE Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 144 ILE 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 56 MET Chi-restraints excluded: chain H residue 129 LEU 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 52 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 chunk 9 optimal weight: 20.0000 chunk 131 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 125 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4223 r_free = 0.4223 target = 0.202743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.146934 restraints weight = 18525.481| |-----------------------------------------------------------------------------| r_work (start): 0.3589 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: 3.78 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 15231 Z= 0.098 Angle : 0.503 8.320 20726 Z= 0.249 Chirality : 0.040 0.141 2538 Planarity : 0.004 0.053 2570 Dihedral : 5.124 59.872 2167 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.54 % Allowed : 19.49 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.19), residues: 1935 helix: 0.14 (0.20), residues: 777 sheet: -1.01 (0.34), residues: 242 loop : -1.89 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 9 HIS 0.004 0.001 HIS G 226 PHE 0.017 0.001 PHE F 254 TYR 0.008 0.001 TYR E 49 ARG 0.010 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.02425 ( 440) hydrogen bonds : angle 3.73688 ( 1272) covalent geometry : bond 0.00228 (15231) covalent geometry : angle 0.50284 (20726) *********************** 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 290 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7158 (mptt) cc_final: 0.6704 (mmtt) REVERT: A 102 ARG cc_start: 0.2911 (mmt90) cc_final: 0.2487 (mmp80) REVERT: D 141 MET cc_start: 0.5902 (tpt) cc_final: 0.5030 (tpt) REVERT: J 7 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7903 (mt-10) REVERT: J 79 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.4564 (pp) REVERT: J 81 ARG cc_start: 0.6730 (ttp-110) cc_final: 0.6484 (ptm160) REVERT: J 102 ARG cc_start: 0.6244 (mtt180) cc_final: 0.5432 (mmt180) REVERT: L 5 LYS cc_start: 0.7841 (tttt) cc_final: 0.7465 (ttpt) REVERT: L 99 LEU cc_start: 0.6820 (tp) cc_final: 0.6308 (mp) REVERT: B 43 ASP cc_start: 0.8078 (t70) cc_final: 0.7811 (t70) REVERT: C 41 CYS cc_start: 0.7728 (m) cc_final: 0.7332 (t) REVERT: F 66 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7050 (mt) REVERT: F 221 LYS cc_start: 0.8209 (mtmt) cc_final: 0.7794 (mtpt) REVERT: G 208 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8717 (p) REVERT: E 167 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7636 (tt) REVERT: E 194 ASP cc_start: 0.5010 (OUTLIER) cc_final: 0.4460 (p0) REVERT: E 233 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8192 (mtp-110) REVERT: E 250 ASP cc_start: 0.8059 (t0) cc_final: 0.7827 (t0) REVERT: H 56 MET cc_start: 0.8657 (OUTLIER) cc_final: 0.8190 (mtm) REVERT: H 134 MET cc_start: 0.7292 (OUTLIER) cc_final: 0.6786 (ttm) REVERT: H 204 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9008 (mp) outliers start: 56 outliers final: 37 residues processed: 272 average time/residue: 0.2704 time to fit residues: 107.9168 Evaluate side-chains 271 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 226 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 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 14 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 46 ARG Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 66 LEU 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 254 PHE Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 144 ILE 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 56 MET Chi-restraints excluded: chain H residue 129 LEU 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 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 111 optimal weight: 3.9990 chunk 17 optimal weight: 20.0000 chunk 95 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 174 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 121 optimal weight: 0.0040 chunk 23 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 = 0.4225 r_free = 0.4225 target = 0.202824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147123 restraints weight = 18470.475| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 1.77 r_work: 0.3383 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15231 Z= 0.095 Angle : 0.509 8.228 20726 Z= 0.253 Chirality : 0.040 0.140 2538 Planarity : 0.004 0.051 2570 Dihedral : 5.062 59.249 2167 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.35 % Allowed : 19.81 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 1935 helix: 0.36 (0.20), residues: 776 sheet: -0.96 (0.34), residues: 242 loop : -1.80 (0.19), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 168 HIS 0.003 0.001 HIS G 226 PHE 0.016 0.001 PHE F 254 TYR 0.008 0.001 TYR E 49 ARG 0.009 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.02362 ( 440) hydrogen bonds : angle 3.71912 ( 1272) covalent geometry : bond 0.00223 (15231) covalent geometry : angle 0.50860 (20726) *********************** 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 283 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 230 time to evaluate : 1.649 Fit side-chains REVERT: A 27 LYS cc_start: 0.7193 (mptt) cc_final: 0.6786 (mmtt) REVERT: A 102 ARG cc_start: 0.3002 (mmt90) cc_final: 0.2580 (mmp80) REVERT: A 141 MET cc_start: 0.2909 (tpp) cc_final: 0.2607 (tpp) REVERT: D 141 MET cc_start: 0.5866 (tpt) cc_final: 0.4986 (tpt) REVERT: J 7 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7868 (mt-10) REVERT: J 79 LEU cc_start: 0.5485 (OUTLIER) cc_final: 0.4565 (pp) REVERT: J 81 ARG cc_start: 0.6791 (ttp-110) cc_final: 0.6521 (ptm160) REVERT: J 102 ARG cc_start: 0.6271 (mtt180) cc_final: 0.5428 (mmt180) REVERT: L 5 LYS cc_start: 0.7839 (tttt) cc_final: 0.7461 (ttpt) REVERT: L 99 LEU cc_start: 0.6771 (tp) cc_final: 0.6289 (mp) REVERT: B 43 ASP cc_start: 0.8059 (t70) cc_final: 0.7785 (t70) REVERT: C 41 CYS cc_start: 0.7743 (m) cc_final: 0.7331 (t) REVERT: F 66 LEU cc_start: 0.7229 (pp) cc_final: 0.6993 (mt) REVERT: F 180 MET cc_start: 0.8583 (ttm) cc_final: 0.8247 (ttp) REVERT: F 221 LYS cc_start: 0.8232 (mtmt) cc_final: 0.7837 (mtpt) REVERT: E 167 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7645 (tt) REVERT: E 194 ASP cc_start: 0.4916 (OUTLIER) cc_final: 0.4411 (p0) REVERT: E 233 ARG cc_start: 0.8448 (ttp80) cc_final: 0.8152 (mtp-110) REVERT: E 250 ASP cc_start: 0.7963 (t0) cc_final: 0.7670 (t0) REVERT: H 134 MET cc_start: 0.7289 (OUTLIER) cc_final: 0.6752 (ttm) REVERT: H 204 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8989 (mp) REVERT: H 257 MET cc_start: 0.4976 (mmt) cc_final: 0.4665 (mmt) outliers start: 53 outliers final: 38 residues processed: 269 average time/residue: 0.2841 time to fit residues: 111.1256 Evaluate side-chains 264 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 221 time to evaluate : 1.582 ------------------------------------------------------------------------------- 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 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 20 LEU Chi-restraints excluded: chain B residue 41 CYS Chi-restraints excluded: chain C residue 5 LEU 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 254 PHE Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 189 GLU Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 144 ILE 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 129 LEU 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 202 CYS Chi-restraints excluded: chain H residue 204 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 122 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 26 ASN E 128 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.197749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133279 restraints weight = 18380.159| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.08 r_work: 0.3173 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15231 Z= 0.148 Angle : 0.573 8.937 20726 Z= 0.283 Chirality : 0.042 0.149 2538 Planarity : 0.004 0.054 2570 Dihedral : 5.387 57.916 2167 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 2.91 % Allowed : 20.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1935 helix: 0.18 (0.20), residues: 791 sheet: -0.96 (0.35), residues: 240 loop : -1.81 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP I 9 HIS 0.005 0.001 HIS H 241 PHE 0.019 0.001 PHE J 13 TYR 0.011 0.001 TYR E 49 ARG 0.008 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.02946 ( 440) hydrogen bonds : angle 3.92230 ( 1272) covalent geometry : bond 0.00368 (15231) covalent geometry : angle 0.57266 (20726) *********************** 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 276 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 230 time to evaluate : 1.658 Fit side-chains REVERT: A 27 LYS cc_start: 0.7022 (mptt) cc_final: 0.6488 (mmtt) REVERT: A 102 ARG cc_start: 0.2772 (mmt90) cc_final: 0.2489 (mmp80) REVERT: A 141 MET cc_start: 0.2933 (tpp) cc_final: 0.2571 (tpp) REVERT: D 141 MET cc_start: 0.5659 (tpt) cc_final: 0.4847 (tpt) REVERT: J 7 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8260 (tt0) REVERT: J 81 ARG cc_start: 0.6787 (ttp-110) cc_final: 0.6473 (ptm160) REVERT: J 102 ARG cc_start: 0.6145 (mtt180) cc_final: 0.5383 (mmt180) REVERT: L 5 LYS cc_start: 0.7735 (tttt) cc_final: 0.7425 (tttm) REVERT: L 99 LEU cc_start: 0.6678 (tp) cc_final: 0.6189 (mp) REVERT: B 43 ASP cc_start: 0.8025 (t70) cc_final: 0.7740 (t70) REVERT: B 50 VAL cc_start: 0.8795 (t) cc_final: 0.8487 (p) REVERT: B 75 GLN cc_start: 0.7731 (mm110) cc_final: 0.7331 (pt0) REVERT: C 41 CYS cc_start: 0.7627 (m) cc_final: 0.7058 (t) REVERT: F 127 MET cc_start: 0.9385 (ptp) cc_final: 0.8991 (ptm) REVERT: F 180 MET cc_start: 0.8956 (ttm) cc_final: 0.8494 (ttp) REVERT: F 221 LYS cc_start: 0.8162 (mtmt) cc_final: 0.7776 (mtpt) REVERT: E 46 ARG cc_start: 0.8413 (tpt170) cc_final: 0.8040 (tpt170) REVERT: E 134 MET cc_start: 0.8521 (tpp) cc_final: 0.8297 (tpt) REVERT: E 167 ILE cc_start: 0.8122 (OUTLIER) cc_final: 0.7602 (tt) REVERT: E 194 ASP cc_start: 0.5243 (OUTLIER) cc_final: 0.4082 (p0) REVERT: E 233 ARG cc_start: 0.8371 (ttp80) cc_final: 0.8119 (mtp-110) REVERT: H 134 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7336 (ttm) REVERT: H 204 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8881 (mp) outliers start: 46 outliers final: 36 residues processed: 262 average time/residue: 0.3257 time to fit residues: 125.2845 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 : 1.985 ------------------------------------------------------------------------------- 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 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 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 5 LEU 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 254 PHE Chi-restraints excluded: chain G residue 47 LYS Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 144 ILE 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 129 LEU 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 202 CYS Chi-restraints excluded: chain H residue 204 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 151 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 104 optimal weight: 0.0020 chunk 164 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 22 optimal weight: 0.2980 chunk 143 optimal weight: 0.3980 chunk 190 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 69 optimal weight: 0.4980 chunk 44 optimal weight: 0.2980 overall best weight: 0.2988 ------------------------------------------------------------------------------- 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** E 128 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.201358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.145801 restraints weight = 18421.814| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.75 r_work: 0.3310 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15231 Z= 0.089 Angle : 0.519 8.465 20726 Z= 0.257 Chirality : 0.040 0.141 2538 Planarity : 0.004 0.051 2570 Dihedral : 5.129 59.718 2167 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.19), residues: 1935 helix: 0.51 (0.20), residues: 783 sheet: -0.77 (0.36), residues: 230 loop : -1.74 (0.19), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 9 HIS 0.003 0.001 HIS G 226 PHE 0.016 0.001 PHE F 254 TYR 0.009 0.001 TYR K 40 ARG 0.009 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.02287 ( 440) hydrogen bonds : angle 3.73219 ( 1272) covalent geometry : bond 0.00198 (15231) covalent geometry : angle 0.51891 (20726) ********************** 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 : 1.724 Fit side-chains REVERT: A 27 LYS cc_start: 0.7275 (mptt) cc_final: 0.6793 (mmtt) REVERT: A 102 ARG cc_start: 0.2927 (mmt90) cc_final: 0.2627 (mmp80) REVERT: A 141 MET cc_start: 0.2967 (tpp) cc_final: 0.2631 (tpp) REVERT: D 141 MET cc_start: 0.5801 (tpt) cc_final: 0.4939 (tpt) REVERT: J 7 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8085 (tt0) REVERT: J 79 LEU cc_start: 0.5594 (OUTLIER) cc_final: 0.4638 (pp) REVERT: J 81 ARG cc_start: 0.6827 (ttp-110) cc_final: 0.6535 (ptm160) REVERT: J 102 ARG cc_start: 0.6116 (mtt180) cc_final: 0.5334 (mmt180) REVERT: L 5 LYS cc_start: 0.7794 (tttt) cc_final: 0.7506 (tttm) REVERT: L 99 LEU cc_start: 0.6665 (tp) cc_final: 0.6174 (mp) REVERT: B 43 ASP cc_start: 0.8010 (t70) cc_final: 0.7746 (t70) REVERT: B 50 VAL cc_start: 0.8783 (t) cc_final: 0.8512 (p) REVERT: C 41 CYS cc_start: 0.7641 (m) cc_final: 0.7153 (t) REVERT: F 180 MET cc_start: 0.8714 (ttm) cc_final: 0.8321 (ttp) REVERT: F 221 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7772 (mtpt) REVERT: E 46 ARG cc_start: 0.8308 (tpt170) cc_final: 0.7914 (tpt170) REVERT: E 76 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7665 (tt) REVERT: E 167 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7515 (tt) REVERT: E 194 ASP cc_start: 0.5164 (OUTLIER) cc_final: 0.4443 (p0) REVERT: E 233 ARG cc_start: 0.8303 (ttp80) cc_final: 0.8003 (mtp-110) REVERT: H 134 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6686 (ttm) REVERT: H 204 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8849 (mt) outliers start: 40 outliers final: 32 residues processed: 262 average time/residue: 0.3534 time to fit residues: 133.8115 Evaluate side-chains 268 residues out of total 1646 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 230 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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 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 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 5 LEU 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 254 PHE Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain E residue 144 ILE 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 129 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.5908 > 50: distance: 29 - 56: 21.199 distance: 43 - 45: 10.693 distance: 45 - 46: 12.100 distance: 46 - 47: 7.945 distance: 46 - 49: 8.856 distance: 47 - 48: 10.549 distance: 47 - 56: 18.326 distance: 49 - 50: 12.032 distance: 50 - 51: 9.162 distance: 51 - 52: 9.271 distance: 52 - 53: 10.403 distance: 53 - 54: 13.296 distance: 53 - 55: 4.430 distance: 56 - 57: 16.571 distance: 57 - 58: 16.241 distance: 57 - 60: 14.869 distance: 58 - 59: 22.039 distance: 58 - 61: 11.136 distance: 61 - 62: 5.954 distance: 62 - 63: 35.385 distance: 63 - 64: 10.254 distance: 63 - 65: 21.817 distance: 65 - 66: 18.269 distance: 66 - 67: 16.345 distance: 66 - 69: 30.203 distance: 67 - 68: 12.440 distance: 67 - 71: 16.788 distance: 69 - 70: 19.432 distance: 71 - 72: 35.377 distance: 72 - 73: 6.363 distance: 72 - 75: 30.575 distance: 73 - 74: 7.036 distance: 73 - 76: 14.643 distance: 74 - 96: 21.063 distance: 76 - 77: 16.472 distance: 77 - 78: 7.832 distance: 77 - 80: 14.384 distance: 78 - 79: 9.160 distance: 78 - 84: 16.838 distance: 79 - 105: 5.860 distance: 80 - 81: 27.278 distance: 81 - 82: 13.599 distance: 81 - 83: 14.051 distance: 84 - 85: 7.202 distance: 85 - 86: 10.958 distance: 85 - 88: 14.733 distance: 86 - 87: 18.392 distance: 86 - 91: 5.976 distance: 87 - 113: 3.821 distance: 88 - 89: 18.783 distance: 88 - 90: 12.510 distance: 91 - 92: 5.472 distance: 92 - 93: 9.175 distance: 93 - 94: 7.215 distance: 93 - 96: 9.036 distance: 94 - 117: 13.389 distance: 96 - 97: 13.328 distance: 97 - 98: 14.452 distance: 97 - 100: 18.980 distance: 98 - 99: 14.019 distance: 98 - 105: 12.303 distance: 100 - 101: 7.580 distance: 101 - 102: 5.750 distance: 102 - 103: 12.716 distance: 102 - 104: 11.134 distance: 105 - 106: 9.409 distance: 106 - 107: 12.260 distance: 106 - 109: 21.814 distance: 107 - 108: 15.339 distance: 107 - 113: 18.111 distance: 109 - 111: 8.989