Starting phenix.real_space_refine on Fri Aug 7 16:01:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui4_64183/08_2026/9ui4_64183.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui4_64183/08_2026/9ui4_64183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ui4_64183/08_2026/9ui4_64183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui4_64183/08_2026/9ui4_64183.map" model { file = "/net/cci-nas-00/data/ceres_data/9ui4_64183/08_2026/9ui4_64183.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui4_64183/08_2026/9ui4_64183.cif" } resolution = 2.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.071 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 54 5.49 5 Mg 9 5.21 5 S 117 5.16 5 C 13649 2.51 5 N 3861 2.21 5 O 4365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22055 Number of models: 1 Model: "" Number of chains: 19 Chain: "L" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 540 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2365 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "B" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2327 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 8, 'TRANS': 293} Chain breaks: 2 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "F" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2357 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "I" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2365 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "E" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2357 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "H" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2365 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "D" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2357 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "G" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2365 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "C" 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: "B" 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: "A" 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: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" 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: "E" 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: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6123 SG CYS A 137 71.233 27.225 27.402 1.00111.42 S Time building chain proxies: 5.19, per 1000 atoms: 0.24 Number of scatterers: 22055 At special positions: 0 Unit cell: (112.88, 112.88, 202.52, 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 117 16.00 P 54 15.00 Mg 9 11.99 O 4365 8.00 N 3861 7.00 C 13649 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 848.9 milliseconds 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5026 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 27 sheets defined 44.3% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'C' and resid 26 through 31 Processing helix chain 'C' and resid 34 through 45 removed outlier: 3.516A pdb=" N GLY C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 56 through 62 Processing helix chain 'C' and resid 70 through 80 removed outlier: 4.246A pdb=" N GLU C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 99 removed outlier: 3.581A pdb=" N SER C 97 " --> pdb=" O HIS C 93 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLU C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE C 99 " --> pdb=" O ARG C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 132 through 145 Processing helix chain 'C' and resid 167 through 179 removed outlier: 3.595A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU C 176 " --> pdb=" O LEU C 172 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ARG C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR C 178 " --> pdb=" O VAL C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 187 removed outlier: 3.745A pdb=" N ASP C 187 " --> pdb=" O SER C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 213 removed outlier: 3.509A pdb=" N GLN C 200 " --> pdb=" O ASN C 196 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASP C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 232 removed outlier: 3.638A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.513A pdb=" N PHE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 296 removed outlier: 3.577A pdb=" N ALA C 295 " --> pdb=" O ILE C 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 31 Processing helix chain 'B' and resid 36 through 44 Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 58 through 63 removed outlier: 4.053A pdb=" N ASN B 62 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 63' Processing helix chain 'B' and resid 67 through 78 removed outlier: 3.570A pdb=" N ASP B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 96 removed outlier: 4.134A pdb=" N PHE B 92 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 95 " --> pdb=" O GLU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 115 removed outlier: 3.728A pdb=" N GLN B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLY B 115 " --> pdb=" O LEU B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 111 through 115' Processing helix chain 'B' and resid 132 through 138 removed outlier: 3.501A pdb=" N HIS B 138 " --> pdb=" O THR B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.923A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 196 through 212 removed outlier: 4.784A pdb=" N GLN B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU B 203 " --> pdb=" O HIS B 199 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLU B 208 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET B 210 " --> pdb=" O GLN B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 236 through 260 removed outlier: 4.373A pdb=" N ALA B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 28 removed outlier: 4.070A pdb=" N ARG A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 43 Processing helix chain 'A' and resid 56 through 64 removed outlier: 3.929A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 75 removed outlier: 3.856A pdb=" N ILE A 74 " --> pdb=" O LYS A 70 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 70 through 75' Processing helix chain 'A' and resid 88 through 99 removed outlier: 3.984A pdb=" N SER A 97 " --> pdb=" O HIS A 93 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 99 " --> pdb=" O ARG A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 196 through 208 Processing helix chain 'A' and resid 209 through 211 No H-bonds generated for 'chain 'A' and resid 209 through 211' Processing helix chain 'A' and resid 223 through 227 removed outlier: 3.779A pdb=" N LEU A 227 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 259 Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.663A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 44 Processing helix chain 'F' and resid 68 through 79 Processing helix chain 'F' and resid 93 through 98 Processing helix chain 'F' and resid 133 through 146 removed outlier: 3.902A pdb=" N THR F 139 " --> pdb=" O GLN F 135 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 removed outlier: 3.695A pdb=" N ARG F 150 " --> pdb=" O PRO F 147 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY F 151 " --> pdb=" O ILE F 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 147 through 151' Processing helix chain 'F' and resid 170 through 178 removed outlier: 3.993A pdb=" N VAL F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N TYR F 178 " --> pdb=" O VAL F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 189 Processing helix chain 'F' and resid 197 through 206 Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'F' and resid 224 through 232 removed outlier: 4.483A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 259 removed outlier: 3.506A pdb=" N MET F 251 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP F 257 " --> pdb=" O LEU F 253 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE F 259 " --> pdb=" O LEU F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.859A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 293 " --> pdb=" O GLY F 289 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N HIS F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 32 Processing helix chain 'I' and resid 34 through 45 removed outlier: 3.996A pdb=" N LEU I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 62 removed outlier: 3.652A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.796A pdb=" N LYS I 73 " --> pdb=" O ALA I 69 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA I 79 " --> pdb=" O LEU I 75 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS I 80 " --> pdb=" O THR I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 94 Processing helix chain 'I' and resid 95 through 98 removed outlier: 4.420A pdb=" N GLU I 98 " --> pdb=" O ARG I 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 95 through 98' Processing helix chain 'I' and resid 106 through 113 Processing helix chain 'I' and resid 135 through 144 removed outlier: 4.327A pdb=" N LEU I 140 " --> pdb=" O ILE I 136 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA I 141 " --> pdb=" O CYS I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 178 removed outlier: 4.025A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 199 through 212 removed outlier: 3.619A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU I 208 " --> pdb=" O LEU I 204 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ASP I 209 " --> pdb=" O TYR I 205 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N MET I 210 " --> pdb=" O GLN I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 259 Processing helix chain 'I' and resid 289 through 295 Processing helix chain 'E' and resid 34 through 38 Processing helix chain 'E' and resid 41 through 45 removed outlier: 4.026A pdb=" N GLY E 45 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 62 Processing helix chain 'E' and resid 67 through 80 Processing helix chain 'E' and resid 90 through 96 removed outlier: 3.950A pdb=" N GLN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 141 removed outlier: 3.510A pdb=" N ILE E 136 " --> pdb=" O GLY E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 179 removed outlier: 4.475A pdb=" N VAL E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 187 removed outlier: 3.816A pdb=" N VAL E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 207 Processing helix chain 'E' and resid 207 through 212 Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.599A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 259 removed outlier: 3.822A pdb=" N PHE E 259 " --> pdb=" O LEU E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 294 removed outlier: 3.505A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 43 Processing helix chain 'H' and resid 48 through 54 removed outlier: 3.715A pdb=" N ALA H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 58 through 62 removed outlier: 3.504A pdb=" N ILE H 61 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN H 62 " --> pdb=" O GLU H 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 58 through 62' Processing helix chain 'H' and resid 67 through 82 removed outlier: 3.596A pdb=" N LYS H 73 " --> pdb=" O ALA H 69 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS H 80 " --> pdb=" O THR H 76 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 93 Processing helix chain 'H' and resid 94 through 99 Processing helix chain 'H' and resid 106 through 113 Processing helix chain 'H' and resid 132 through 144 removed outlier: 3.961A pdb=" N CYS H 137 " --> pdb=" O LYS H 133 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA H 141 " --> pdb=" O CYS H 137 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 169 through 178 Processing helix chain 'H' and resid 181 through 189 Processing helix chain 'H' and resid 196 through 211 removed outlier: 3.506A pdb=" N GLN H 200 " --> pdb=" O ASN H 196 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLN H 202 " --> pdb=" O ASP H 198 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASP H 209 " --> pdb=" O TYR H 205 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET H 210 " --> pdb=" O GLN H 206 " (cutoff:3.500A) Processing helix chain 'H' and resid 223 through 232 removed outlier: 3.963A pdb=" N LEU H 227 " --> pdb=" O SER H 223 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR H 228 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 256 removed outlier: 3.589A pdb=" N LEU H 238 " --> pdb=" O GLY H 234 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER H 239 " --> pdb=" O ARG H 235 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ALA H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET H 251 " --> pdb=" O ARG H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 288 through 296 removed outlier: 3.586A pdb=" N ILE H 292 " --> pdb=" O GLY H 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 45 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 58 through 63 removed outlier: 3.904A pdb=" N ASN D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 58 through 63' Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.844A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 98 Processing helix chain 'D' and resid 108 through 113 Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.564A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.911A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 188 removed outlier: 3.660A pdb=" N LEU D 186 " --> pdb=" O GLY D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 211 Processing helix chain 'D' and resid 227 through 232 Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'D' and resid 289 through 296 Processing helix chain 'G' and resid 24 through 30 removed outlier: 3.688A pdb=" N GLN G 30 " --> pdb=" O ARG G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 41 removed outlier: 3.864A pdb=" N LYS G 40 " --> pdb=" O ASN G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 Processing helix chain 'G' and resid 56 through 62 Processing helix chain 'G' and resid 67 through 82 Processing helix chain 'G' and resid 88 through 97 removed outlier: 3.681A pdb=" N PHE G 92 " --> pdb=" O THR G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 113 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 167 through 176 Processing helix chain 'G' and resid 196 through 208 removed outlier: 3.678A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 214 removed outlier: 3.556A pdb=" N GLU G 213 " --> pdb=" O ASP G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 removed outlier: 3.588A pdb=" N THR G 230 " --> pdb=" O ALA G 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.737A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.756A pdb=" N ALA D 157 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA D 192 " --> pdb=" O ALA D 157 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR D 159 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LYS D 156 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU D 218 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL D 264 " --> pdb=" O ALA D 217 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LEU D 219 " --> pdb=" O VAL D 264 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR D 266 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL D 221 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N THR D 123 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ASN D 267 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N MET D 125 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE D 327 " --> pdb=" O ARG D 310 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA D 328 " --> pdb=" O GLY D 335 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 333 " --> pdb=" O ASN D 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 156 through 160 removed outlier: 6.739A pdb=" N LYS C 156 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N ILE C 220 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N MET C 158 " --> pdb=" O ILE C 220 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 161 removed outlier: 6.359A pdb=" N ILE B 160 " --> pdb=" O ASP B 222 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B 266 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 309 through 310 Processing sheet with id=AA6, first strand: chain 'A' and resid 266 through 267 removed outlier: 6.317A pdb=" N MET A 125 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 156 through 157 removed outlier: 6.411A pdb=" N LYS A 156 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA9, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AB1, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AB2, first strand: chain 'F' and resid 124 through 127 removed outlier: 7.987A pdb=" N GLU F 124 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N LEU F 302 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N PHE F 126 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 301 " --> pdb=" O LYS F 313 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS F 313 " --> pdb=" O TYR F 301 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AB4, first strand: chain 'I' and resid 125 through 126 removed outlier: 6.411A pdb=" N PHE I 126 " --> pdb=" O LEU I 302 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LYS I 304 " --> pdb=" O PHE I 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 157 through 159 removed outlier: 3.947A pdb=" N ALA I 190 " --> pdb=" O ALA I 157 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 220 through 221 Processing sheet with id=AB7, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB8, first strand: chain 'E' and resid 263 through 264 Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AC1, first strand: chain 'E' and resid 328 through 329 removed outlier: 3.560A pdb=" N ALA E 328 " --> pdb=" O GLY E 335 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 265 through 267 removed outlier: 3.681A pdb=" N GLY H 127 " --> pdb=" O ASN H 267 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE H 327 " --> pdb=" O ARG H 310 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 156 through 157 removed outlier: 7.609A pdb=" N LYS H 156 " --> pdb=" O ALA H 217 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'H' and resid 160 through 161 removed outlier: 5.860A pdb=" N ILE H 160 " --> pdb=" O ASP H 222 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'H' and resid 269 through 270 Processing sheet with id=AC6, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AC7, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AC8, first strand: chain 'G' and resid 189 through 193 removed outlier: 6.314A pdb=" N LYS G 156 " --> pdb=" O LEU G 218 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ILE G 220 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N MET G 158 " --> pdb=" O ILE G 220 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA G 262 " --> pdb=" O ALA G 217 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N THR G 123 " --> pdb=" O ILE G 265 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N ASN G 267 " --> pdb=" O THR G 123 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N MET G 125 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR G 298 " --> pdb=" O ILE G 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 269 through 270 764 hydrogen bonds defined for protein. 2187 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.50 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7139 1.34 - 1.46: 3189 1.46 - 1.58: 11809 1.58 - 1.70: 86 1.70 - 1.82: 202 Bond restraints: 22425 Sorted by residual: bond pdb=" CA LYS E 80 " pdb=" C LYS E 80 " ideal model delta sigma weight residual 1.523 1.584 -0.060 1.80e-02 3.09e+03 1.13e+01 bond pdb=" C3' DT L 21 " pdb=" C2' DT L 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.68e+00 bond pdb=" C3' DT L 22 " pdb=" C2' DT L 22 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.41e+00 bond pdb=" C3' DT L 3 " pdb=" C2' DT L 3 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.13e+00 bond pdb=" C3' DA L 12 " pdb=" C2' DA L 12 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.62e+00 ... (remaining 22420 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 30116 2.65 - 5.30: 255 5.30 - 7.96: 31 7.96 - 10.61: 5 10.61 - 13.26: 2 Bond angle restraints: 30409 Sorted by residual: angle pdb=" CA ARG A 215 " pdb=" CB ARG A 215 " pdb=" CG ARG A 215 " ideal model delta sigma weight residual 114.10 122.67 -8.57 2.00e+00 2.50e-01 1.84e+01 angle pdb=" N3 DT L 23 " pdb=" C4 DT L 23 " pdb=" O4 DT L 23 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT L 2 " pdb=" C4 DT L 2 " pdb=" O4 DT L 2 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT L 20 " pdb=" C4 DT L 20 " pdb=" O4 DT L 20 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT L 22 " pdb=" C4 DT L 22 " pdb=" O4 DT L 22 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 30404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.69: 12308 28.69 - 57.38: 1242 57.38 - 86.07: 122 86.07 - 114.76: 12 114.76 - 143.45: 2 Dihedral angle restraints: 13686 sinusoidal: 5824 harmonic: 7862 Sorted by residual: dihedral pdb=" CA ILE F 160 " pdb=" C ILE F 160 " pdb=" N ASP F 161 " pdb=" CA ASP F 161 " ideal model delta harmonic sigma weight residual 180.00 155.87 24.13 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR I 191 " pdb=" C TYR I 191 " pdb=" N ALA I 192 " pdb=" CA ALA I 192 " ideal model delta harmonic sigma weight residual -180.00 -160.01 -19.99 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" O1B ANP G 402 " pdb=" N3B ANP G 402 " pdb=" PB ANP G 402 " pdb=" PG ANP G 402 " ideal model delta sinusoidal sigma weight residual 35.15 153.82 -118.67 1 3.00e+01 1.11e-03 1.58e+01 ... (remaining 13683 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2722 0.049 - 0.097: 602 0.097 - 0.146: 133 0.146 - 0.194: 7 0.194 - 0.243: 2 Chirality restraints: 3466 Sorted by residual: chirality pdb=" CG LEU H 75 " pdb=" CB LEU H 75 " pdb=" CD1 LEU H 75 " pdb=" CD2 LEU H 75 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB ILE I 220 " pdb=" CA ILE I 220 " pdb=" CG1 ILE I 220 " pdb=" CG2 ILE I 220 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CG LEU B 249 " pdb=" CB LEU B 249 " pdb=" CD1 LEU B 249 " pdb=" CD2 LEU B 249 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 3463 not shown) Planarity restraints: 3803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN I 23 " -0.044 5.00e-02 4.00e+02 6.80e-02 7.39e+00 pdb=" N PRO I 24 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 24 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 24 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 146 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.92e+00 pdb=" N PRO E 147 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 147 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 147 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 167 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.08e+00 pdb=" N PRO C 168 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " -0.031 5.00e-02 4.00e+02 ... (remaining 3800 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 39 2.53 - 3.12: 16947 3.12 - 3.72: 36076 3.72 - 4.31: 50549 4.31 - 4.90: 81952 Nonbonded interactions: 185563 Sorted by model distance: nonbonded pdb=" OG1 THR B 134 " pdb="MG MG B 601 " model vdw 1.942 2.170 nonbonded pdb=" O3A ANP D 402 " pdb="MG MG D 403 " model vdw 1.951 2.170 nonbonded pdb=" N GLY G 132 " pdb="MG MG G 403 " model vdw 1.963 2.250 nonbonded pdb=" O ARG B 130 " pdb="MG MG B 601 " model vdw 1.998 2.170 nonbonded pdb="MG MG E 601 " pdb=" O3G ANP D 401 " model vdw 2.009 2.170 ... (remaining 185558 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 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'B' and (resid 22 through 273 or resid 284 through 336)) selection = (chain 'C' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'D' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'E' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'F' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'G' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'H' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) selection = (chain 'I' and (resid 22 through 147 or resid 152 through 273 or resid 284 throu \ gh 336)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 19.300 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6762 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 : 0.003 0.060 22425 Z= 0.179 Angle : 0.656 13.260 30409 Z= 0.371 Chirality : 0.043 0.243 3466 Planarity : 0.004 0.068 3803 Dihedral : 20.401 143.455 8660 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.62 % Favored : 92.13 % Rotamer: Outliers : 5.82 % Allowed : 41.81 % Favored : 52.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.16), residues: 2718 helix: -0.44 (0.16), residues: 1020 sheet: -2.21 (0.27), residues: 365 loop : -2.25 (0.16), residues: 1333 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 170 TYR 0.017 0.001 TYR G 46 PHE 0.025 0.002 PHE E 166 HIS 0.016 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.18 (22425) covalent geometry : angle 0.65595 / 0.37 (30409) hydrogen bonds : bond 0.16259 / 16.14 ( 764) hydrogen bonds : angle 7.38611 / 6.75 ( 2187) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 264 time to evaluate : 0.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 146 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5265 (mp) REVERT: C 187 ASP cc_start: 0.7547 (t0) cc_final: 0.7075 (t0) REVERT: C 219 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6542 (tp) REVERT: C 243 MET cc_start: 0.7216 (mpt) cc_final: 0.6400 (tpt) REVERT: C 330 ASN cc_start: 0.6190 (m-40) cc_final: 0.5810 (t0) REVERT: B 77 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6649 (mp0) REVERT: B 84 MET cc_start: 0.4215 (mtt) cc_final: 0.3761 (mmt) REVERT: B 172 LEU cc_start: 0.6931 (tm) cc_final: 0.6606 (tp) REVERT: B 191 TYR cc_start: 0.6282 (OUTLIER) cc_final: 0.5690 (m-80) REVERT: B 252 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7571 (tt) REVERT: B 327 PHE cc_start: 0.6618 (OUTLIER) cc_final: 0.6082 (m-10) REVERT: A 34 ASN cc_start: 0.7410 (OUTLIER) cc_final: 0.6904 (p0) REVERT: A 101 GLN cc_start: 0.6021 (OUTLIER) cc_final: 0.5787 (pm20) REVERT: A 158 MET cc_start: 0.7131 (ttt) cc_final: 0.6852 (mtp) REVERT: A 187 ASP cc_start: 0.6586 (m-30) cc_final: 0.6174 (t0) REVERT: A 231 ASP cc_start: 0.8008 (t0) cc_final: 0.7728 (t0) REVERT: A 253 LEU cc_start: 0.4517 (OUTLIER) cc_final: 0.3783 (pp) REVERT: A 268 GLN cc_start: 0.6113 (OUTLIER) cc_final: 0.5451 (mm-40) REVERT: F 34 ASN cc_start: 0.8473 (t0) cc_final: 0.8061 (t0) REVERT: F 150 ARG cc_start: 0.4439 (mtm110) cc_final: 0.2030 (ttp-170) REVERT: F 158 MET cc_start: 0.7391 (mtt) cc_final: 0.6931 (ttt) REVERT: F 191 TYR cc_start: 0.3908 (OUTLIER) cc_final: 0.3067 (p90) REVERT: F 193 ARG cc_start: 0.5875 (ttt-90) cc_final: 0.4581 (tpm170) REVERT: F 326 MET cc_start: 0.5766 (mpp) cc_final: 0.5247 (mpp) REVERT: I 64 LYS cc_start: 0.7419 (mmmm) cc_final: 0.6951 (ptmt) REVERT: I 96 ARG cc_start: 0.4059 (ptm160) cc_final: 0.1361 (ptt90) REVERT: I 136 ILE cc_start: 0.6698 (OUTLIER) cc_final: 0.6199 (pp) REVERT: I 243 MET cc_start: 0.5989 (OUTLIER) cc_final: 0.5696 (mpm) REVERT: I 244 HIS cc_start: 0.7340 (OUTLIER) cc_final: 0.7097 (t-170) REVERT: E 42 GLU cc_start: 0.6591 (mt-10) cc_final: 0.6318 (tp30) REVERT: E 84 MET cc_start: 0.3212 (OUTLIER) cc_final: 0.2525 (ppp) REVERT: E 126 PHE cc_start: 0.6352 (p90) cc_final: 0.6119 (p90) REVERT: E 209 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5127 (m-30) REVERT: E 243 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8043 (mtt) REVERT: E 247 ARG cc_start: 0.7557 (mtm180) cc_final: 0.7228 (mmm160) REVERT: E 251 MET cc_start: 0.6229 (tpp) cc_final: 0.5755 (tmm) REVERT: E 265 ILE cc_start: 0.3303 (OUTLIER) cc_final: 0.2895 (mt) REVERT: E 320 LEU cc_start: 0.6527 (OUTLIER) cc_final: 0.6205 (tt) REVERT: H 103 THR cc_start: 0.4319 (OUTLIER) cc_final: 0.3999 (t) REVERT: H 111 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.6600 (mtmt) REVERT: D 39 LYS cc_start: 0.7619 (mmtt) cc_final: 0.7213 (tmtt) REVERT: D 135 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7596 (mp-120) REVERT: D 243 MET cc_start: 0.8275 (tpt) cc_final: 0.7888 (mmm) REVERT: G 43 GLU cc_start: 0.7246 (pt0) cc_final: 0.6469 (tm-30) REVERT: G 118 GLU cc_start: 0.4715 (tt0) cc_final: 0.4389 (mt-10) REVERT: G 306 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.6001 (mmm-85) REVERT: G 310 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.5566 (mpp-170) outliers start: 130 outliers final: 79 residues processed: 361 average time/residue: 0.4590 time to fit residues: 195.9368 Evaluate side-chains 355 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 252 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 121 SER Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 243 MET Chi-restraints excluded: chain I residue 244 HIS Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 84 MET Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 210 MET Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 315 TYR Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 300 LEU Chi-restraints excluded: chain G residue 306 ARG Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 23 GLN C 244 HIS A 93 HIS I 145 GLN H 93 HIS D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.199959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.178386 restraints weight = 39237.385| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 2.25 r_work: 0.4220 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6790 moved from start: 0.0534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22425 Z= 0.159 Angle : 0.622 11.323 30409 Z= 0.327 Chirality : 0.043 0.191 3466 Planarity : 0.004 0.063 3803 Dihedral : 14.147 142.794 3758 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.06 % Favored : 91.72 % Rotamer: Outliers : 9.67 % Allowed : 37.47 % Favored : 52.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.16), residues: 2718 helix: -0.27 (0.16), residues: 1045 sheet: -2.24 (0.27), residues: 363 loop : -2.24 (0.17), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 241 TYR 0.017 0.002 TYR B 191 PHE 0.027 0.002 PHE F 126 HIS 0.010 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (22425) covalent geometry : angle 0.62217 / 0.33 (30409) hydrogen bonds : bond 0.04181 / 4.15 ( 764) hydrogen bonds : angle 5.82853 / 5.36 ( 2187) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 272 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 34 ASN cc_start: 0.7160 (p0) cc_final: 0.6808 (p0) REVERT: C 146 LEU cc_start: 0.5686 (OUTLIER) cc_final: 0.5268 (mp) REVERT: C 187 ASP cc_start: 0.7626 (t0) cc_final: 0.7160 (t0) REVERT: B 66 ILE cc_start: 0.3537 (OUTLIER) cc_final: 0.3334 (mp) REVERT: B 77 GLU cc_start: 0.7064 (mp0) cc_final: 0.6723 (mp0) REVERT: B 84 MET cc_start: 0.4278 (mtt) cc_final: 0.3767 (mmt) REVERT: B 158 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6408 (mpt) REVERT: B 161 ASP cc_start: 0.5951 (t0) cc_final: 0.5444 (t70) REVERT: B 169 GLU cc_start: 0.5923 (OUTLIER) cc_final: 0.5491 (pp20) REVERT: B 191 TYR cc_start: 0.6361 (OUTLIER) cc_final: 0.5685 (m-80) REVERT: B 327 PHE cc_start: 0.6297 (OUTLIER) cc_final: 0.5790 (m-10) REVERT: A 34 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6917 (p0) REVERT: A 84 MET cc_start: 0.3782 (tpt) cc_final: 0.3553 (tpt) REVERT: A 101 GLN cc_start: 0.6031 (OUTLIER) cc_final: 0.5440 (pm20) REVERT: A 158 MET cc_start: 0.7250 (ttt) cc_final: 0.6993 (mtp) REVERT: A 187 ASP cc_start: 0.6714 (m-30) cc_final: 0.6243 (t0) REVERT: A 231 ASP cc_start: 0.8044 (t0) cc_final: 0.7751 (t0) REVERT: A 253 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.3877 (pp) REVERT: A 273 VAL cc_start: 0.7134 (OUTLIER) cc_final: 0.6903 (t) REVERT: F 34 ASN cc_start: 0.8150 (t0) cc_final: 0.7707 (t0) REVERT: F 133 LYS cc_start: 0.5835 (OUTLIER) cc_final: 0.3958 (mttp) REVERT: F 150 ARG cc_start: 0.4470 (mtm110) cc_final: 0.1690 (ttt-90) REVERT: F 158 MET cc_start: 0.7440 (mtt) cc_final: 0.6971 (ttt) REVERT: F 169 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.6281 (mp0) REVERT: F 191 TYR cc_start: 0.3861 (OUTLIER) cc_final: 0.3033 (p90) REVERT: F 193 ARG cc_start: 0.5889 (ttt-90) cc_final: 0.4618 (tpm170) REVERT: F 245 LEU cc_start: 0.7187 (OUTLIER) cc_final: 0.6723 (tp) REVERT: F 326 MET cc_start: 0.5683 (mpp) cc_final: 0.5135 (mpp) REVERT: I 128 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6171 (pp20) REVERT: I 243 MET cc_start: 0.6157 (OUTLIER) cc_final: 0.5950 (mpm) REVERT: I 254 ARG cc_start: 0.6229 (OUTLIER) cc_final: 0.4349 (ptm160) REVERT: E 126 PHE cc_start: 0.6391 (p90) cc_final: 0.6134 (p90) REVERT: E 247 ARG cc_start: 0.7592 (mtm180) cc_final: 0.7279 (mmm160) REVERT: E 251 MET cc_start: 0.6156 (tpp) cc_final: 0.5734 (tmm) REVERT: E 265 ILE cc_start: 0.2964 (OUTLIER) cc_final: 0.2569 (mt) REVERT: E 320 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.6113 (tt) REVERT: H 251 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7249 (ttp) REVERT: D 39 LYS cc_start: 0.7584 (mmtt) cc_final: 0.7195 (tmtt) REVERT: D 84 MET cc_start: 0.5106 (OUTLIER) cc_final: 0.4022 (mmm) REVERT: D 243 MET cc_start: 0.8278 (tpt) cc_final: 0.7875 (mmm) REVERT: D 251 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.8114 (tpp) REVERT: G 30 GLN cc_start: 0.6682 (OUTLIER) cc_final: 0.6212 (mp10) REVERT: G 43 GLU cc_start: 0.7300 (pt0) cc_final: 0.6538 (tm-30) REVERT: G 310 ARG cc_start: 0.8529 (OUTLIER) cc_final: 0.5609 (mpp-170) outliers start: 216 outliers final: 80 residues processed: 438 average time/residue: 0.4918 time to fit residues: 255.4867 Evaluate side-chains 366 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 262 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 186 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 243 MET Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 300 LEU Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 211 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 158 MET Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 246 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 238 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 23 GLN C 244 HIS I 145 GLN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS D 135 GLN D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.200732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.179129 restraints weight = 39313.575| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.30 r_work: 0.4227 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.0661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22425 Z= 0.134 Angle : 0.600 10.721 30409 Z= 0.313 Chirality : 0.042 0.181 3466 Planarity : 0.004 0.064 3803 Dihedral : 13.608 143.011 3669 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.40 % Favored : 92.38 % Rotamer: Outliers : 9.98 % Allowed : 37.47 % Favored : 52.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.16), residues: 2718 helix: -0.20 (0.16), residues: 1048 sheet: -2.21 (0.27), residues: 362 loop : -2.24 (0.17), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 229 TYR 0.016 0.001 TYR B 191 PHE 0.026 0.002 PHE F 126 HIS 0.013 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (22425) covalent geometry : angle 0.59961 / 0.31 (30409) hydrogen bonds : bond 0.03704 / 3.66 ( 764) hydrogen bonds : angle 5.55204 / 5.05 ( 2187) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 280 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 34 ASN cc_start: 0.7021 (p0) cc_final: 0.6760 (p0) REVERT: C 107 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7338 (mtpp) REVERT: C 146 LEU cc_start: 0.5633 (OUTLIER) cc_final: 0.5186 (mp) REVERT: C 187 ASP cc_start: 0.7627 (t0) cc_final: 0.7155 (t0) REVERT: B 66 ILE cc_start: 0.3578 (OUTLIER) cc_final: 0.3355 (mp) REVERT: B 77 GLU cc_start: 0.7076 (mp0) cc_final: 0.6720 (mp0) REVERT: B 84 MET cc_start: 0.4245 (mtt) cc_final: 0.3722 (mmt) REVERT: B 158 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6333 (mpt) REVERT: B 161 ASP cc_start: 0.5948 (t0) cc_final: 0.5430 (t70) REVERT: B 169 GLU cc_start: 0.5802 (OUTLIER) cc_final: 0.5373 (pp20) REVERT: B 172 LEU cc_start: 0.6796 (tm) cc_final: 0.6429 (tp) REVERT: B 191 TYR cc_start: 0.6348 (OUTLIER) cc_final: 0.5671 (m-80) REVERT: B 204 LEU cc_start: 0.8152 (mm) cc_final: 0.7814 (mm) REVERT: B 248 PHE cc_start: 0.6000 (OUTLIER) cc_final: 0.5188 (t80) REVERT: B 327 PHE cc_start: 0.6330 (OUTLIER) cc_final: 0.5841 (m-10) REVERT: A 34 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6896 (p0) REVERT: A 84 MET cc_start: 0.3810 (tpt) cc_final: 0.3582 (tpt) REVERT: A 158 MET cc_start: 0.7236 (ttt) cc_final: 0.6971 (mtp) REVERT: A 187 ASP cc_start: 0.6727 (m-30) cc_final: 0.6278 (t0) REVERT: A 231 ASP cc_start: 0.8018 (t0) cc_final: 0.7743 (t0) REVERT: A 253 LEU cc_start: 0.4575 (OUTLIER) cc_final: 0.3840 (pp) REVERT: F 34 ASN cc_start: 0.8172 (t0) cc_final: 0.7736 (t0) REVERT: F 133 LYS cc_start: 0.5820 (OUTLIER) cc_final: 0.3856 (mttp) REVERT: F 150 ARG cc_start: 0.4420 (mtm110) cc_final: 0.2034 (ttp-170) REVERT: F 158 MET cc_start: 0.7398 (mtt) cc_final: 0.6940 (ttt) REVERT: F 191 TYR cc_start: 0.3830 (OUTLIER) cc_final: 0.2992 (p90) REVERT: F 193 ARG cc_start: 0.5933 (ttt-90) cc_final: 0.4615 (tpm170) REVERT: F 245 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6685 (tp) REVERT: F 326 MET cc_start: 0.5733 (OUTLIER) cc_final: 0.5160 (mpp) REVERT: I 128 GLU cc_start: 0.6466 (OUTLIER) cc_final: 0.5873 (pp20) REVERT: I 136 ILE cc_start: 0.6961 (OUTLIER) cc_final: 0.6531 (pp) REVERT: I 216 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.5053 (t80) REVERT: I 243 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5849 (mpm) REVERT: I 254 ARG cc_start: 0.6207 (OUTLIER) cc_final: 0.4297 (ptm160) REVERT: E 126 PHE cc_start: 0.6354 (p90) cc_final: 0.6145 (p90) REVERT: E 156 LYS cc_start: 0.3673 (OUTLIER) cc_final: 0.3326 (ttpt) REVERT: E 209 ASP cc_start: 0.6163 (OUTLIER) cc_final: 0.5161 (m-30) REVERT: E 218 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5594 (mm) REVERT: E 247 ARG cc_start: 0.7547 (mtm180) cc_final: 0.7264 (mmm160) REVERT: E 251 MET cc_start: 0.6194 (tpp) cc_final: 0.5754 (tmm) REVERT: E 265 ILE cc_start: 0.2961 (OUTLIER) cc_final: 0.2533 (mt) REVERT: E 320 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6066 (tt) REVERT: D 39 LYS cc_start: 0.7562 (mmtt) cc_final: 0.7163 (tmtt) REVERT: D 84 MET cc_start: 0.5017 (OUTLIER) cc_final: 0.3955 (mmm) REVERT: D 135 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7318 (mp-120) REVERT: D 243 MET cc_start: 0.8323 (tpt) cc_final: 0.7944 (mmm) REVERT: D 251 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8142 (tpp) REVERT: G 30 GLN cc_start: 0.6638 (OUTLIER) cc_final: 0.6174 (mp10) REVERT: G 43 GLU cc_start: 0.7287 (pt0) cc_final: 0.6522 (tm-30) outliers start: 223 outliers final: 93 residues processed: 441 average time/residue: 0.4627 time to fit residues: 242.1648 Evaluate side-chains 374 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 253 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 317 SER Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 93 HIS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 243 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 30 GLN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 249 optimal weight: 0.9980 chunk 216 optimal weight: 7.9990 chunk 238 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 60 optimal weight: 6.9990 chunk 204 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 23 GLN C 244 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN I 145 GLN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.198898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.177239 restraints weight = 39325.487| |-----------------------------------------------------------------------------| r_work (start): 0.4285 rms_B_bonded: 2.25 r_work: 0.4206 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22425 Z= 0.169 Angle : 0.637 9.015 30409 Z= 0.331 Chirality : 0.044 0.208 3466 Planarity : 0.004 0.064 3803 Dihedral : 13.547 142.752 3653 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.39 % Favored : 91.39 % Rotamer: Outliers : 11.37 % Allowed : 36.53 % Favored : 52.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.16), residues: 2718 helix: -0.24 (0.16), residues: 1051 sheet: -2.30 (0.27), residues: 360 loop : -2.28 (0.17), residues: 1307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 229 TYR 0.018 0.002 TYR B 191 PHE 0.030 0.002 PHE F 126 HIS 0.010 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (22425) covalent geometry : angle 0.63702 / 0.33 (30409) hydrogen bonds : bond 0.03693 / 3.65 ( 764) hydrogen bonds : angle 5.52124 / 5.03 ( 2187) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 254 poor density : 269 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 34 ASN cc_start: 0.6869 (p0) cc_final: 0.6618 (p0) REVERT: C 96 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.6644 (mtp180) REVERT: C 107 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7334 (mtpp) REVERT: C 146 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5156 (mp) REVERT: C 187 ASP cc_start: 0.7627 (t0) cc_final: 0.7135 (t0) REVERT: B 66 ILE cc_start: 0.3565 (OUTLIER) cc_final: 0.3325 (mp) REVERT: B 77 GLU cc_start: 0.7135 (mp0) cc_final: 0.6792 (mp0) REVERT: B 84 MET cc_start: 0.4412 (mtt) cc_final: 0.3815 (mmt) REVERT: B 161 ASP cc_start: 0.6103 (t0) cc_final: 0.5598 (t70) REVERT: B 169 GLU cc_start: 0.5882 (OUTLIER) cc_final: 0.5427 (pp20) REVERT: B 172 LEU cc_start: 0.6821 (tm) cc_final: 0.6449 (tp) REVERT: B 191 TYR cc_start: 0.6365 (OUTLIER) cc_final: 0.5586 (m-80) REVERT: B 327 PHE cc_start: 0.6362 (OUTLIER) cc_final: 0.5866 (m-10) REVERT: A 34 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.6944 (p0) REVERT: A 158 MET cc_start: 0.7294 (ttt) cc_final: 0.7013 (mtp) REVERT: A 187 ASP cc_start: 0.6854 (m-30) cc_final: 0.6380 (t0) REVERT: A 231 ASP cc_start: 0.8044 (t0) cc_final: 0.7791 (t0) REVERT: A 247 ARG cc_start: 0.7602 (OUTLIER) cc_final: 0.7162 (mtt-85) REVERT: A 253 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.3895 (pp) REVERT: F 34 ASN cc_start: 0.8231 (t0) cc_final: 0.7764 (t0) REVERT: F 128 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7156 (pt0) REVERT: F 133 LYS cc_start: 0.5977 (OUTLIER) cc_final: 0.4015 (mttp) REVERT: F 158 MET cc_start: 0.7378 (mtt) cc_final: 0.6998 (ttt) REVERT: F 169 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6280 (mp0) REVERT: F 178 TYR cc_start: 0.6665 (m-80) cc_final: 0.3627 (m-80) REVERT: F 191 TYR cc_start: 0.3881 (OUTLIER) cc_final: 0.3033 (p90) REVERT: F 193 ARG cc_start: 0.5946 (ttt-90) cc_final: 0.4642 (tpm170) REVERT: F 245 LEU cc_start: 0.7234 (OUTLIER) cc_final: 0.6756 (tp) REVERT: F 326 MET cc_start: 0.5806 (OUTLIER) cc_final: 0.5236 (mpp) REVERT: I 128 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.6231 (pp20) REVERT: I 216 TYR cc_start: 0.6329 (OUTLIER) cc_final: 0.5101 (t80) REVERT: I 254 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.4342 (ptm160) REVERT: E 42 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.5996 (mt-10) REVERT: E 209 ASP cc_start: 0.6250 (OUTLIER) cc_final: 0.5282 (m-30) REVERT: E 218 LEU cc_start: 0.6211 (OUTLIER) cc_final: 0.5618 (mm) REVERT: E 243 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8053 (mtt) REVERT: E 247 ARG cc_start: 0.7583 (mtm180) cc_final: 0.7291 (mmm160) REVERT: E 251 MET cc_start: 0.6141 (tpp) cc_final: 0.5714 (tmm) REVERT: E 265 ILE cc_start: 0.2972 (OUTLIER) cc_final: 0.2544 (mt) REVERT: E 320 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6054 (tt) REVERT: H 92 PHE cc_start: 0.4490 (OUTLIER) cc_final: 0.4101 (m-10) REVERT: H 103 THR cc_start: 0.4349 (OUTLIER) cc_final: 0.4005 (t) REVERT: H 251 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7332 (ttp) REVERT: D 39 LYS cc_start: 0.7592 (mmtt) cc_final: 0.7194 (tmtt) REVERT: D 84 MET cc_start: 0.5026 (OUTLIER) cc_final: 0.3945 (mmm) REVERT: D 243 MET cc_start: 0.8298 (tpt) cc_final: 0.7889 (mmm) REVERT: D 251 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8178 (tpp) REVERT: G 43 GLU cc_start: 0.7263 (pt0) cc_final: 0.6543 (tm-30) REVERT: G 58 LYS cc_start: 0.7627 (OUTLIER) cc_final: 0.7104 (ptmt) REVERT: G 310 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.5494 (mpp-170) outliers start: 254 outliers final: 117 residues processed: 455 average time/residue: 0.4772 time to fit residues: 258.7382 Evaluate side-chains 394 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 245 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 148 ILE Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 181 SER Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 119 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 314 ILE Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 84 MET Chi-restraints excluded: chain I residue 93 HIS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 301 TYR Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 201 THR Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 200 GLN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 121 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 233 optimal weight: 4.9990 chunk 8 optimal weight: 0.0170 chunk 197 optimal weight: 0.9980 chunk 69 optimal weight: 0.0050 chunk 151 optimal weight: 4.9990 chunk 175 optimal weight: 0.6980 chunk 155 optimal weight: 0.9990 overall best weight: 0.5434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 23 GLN C 244 HIS A 272 GLN F 23 GLN I 145 GLN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 ASN G 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.201461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.180046 restraints weight = 38933.009| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.25 r_work: 0.4239 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.4239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22425 Z= 0.120 Angle : 0.591 11.170 30409 Z= 0.307 Chirality : 0.041 0.200 3466 Planarity : 0.004 0.065 3803 Dihedral : 13.386 143.153 3648 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.21 % Favored : 92.57 % Rotamer: Outliers : 9.27 % Allowed : 38.41 % Favored : 52.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.15 (0.16), residues: 2718 helix: -0.16 (0.16), residues: 1065 sheet: -2.21 (0.27), residues: 367 loop : -2.29 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 130 TYR 0.016 0.001 TYR B 191 PHE 0.024 0.001 PHE F 126 HIS 0.013 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (22425) covalent geometry : angle 0.59059 / 0.31 (30409) hydrogen bonds : bond 0.03209 / 3.19 ( 764) hydrogen bonds : angle 5.30996 / 4.82 ( 2187) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 267 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 LYS cc_start: 0.5720 (OUTLIER) cc_final: 0.4486 (ptpp) REVERT: C 107 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7273 (mtpp) REVERT: C 146 LEU cc_start: 0.5626 (OUTLIER) cc_final: 0.5172 (mp) REVERT: C 187 ASP cc_start: 0.7600 (t0) cc_final: 0.7101 (t0) REVERT: C 330 ASN cc_start: 0.6173 (m-40) cc_final: 0.5802 (t0) REVERT: B 66 ILE cc_start: 0.3452 (OUTLIER) cc_final: 0.3218 (mp) REVERT: B 77 GLU cc_start: 0.7089 (mp0) cc_final: 0.6688 (mp0) REVERT: B 84 MET cc_start: 0.4303 (mtt) cc_final: 0.3754 (mmt) REVERT: B 158 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6401 (mpt) REVERT: B 169 GLU cc_start: 0.5800 (OUTLIER) cc_final: 0.5382 (pp20) REVERT: B 172 LEU cc_start: 0.6821 (tm) cc_final: 0.6471 (tp) REVERT: B 191 TYR cc_start: 0.6318 (OUTLIER) cc_final: 0.5512 (m-80) REVERT: B 248 PHE cc_start: 0.6003 (OUTLIER) cc_final: 0.5140 (t80) REVERT: B 327 PHE cc_start: 0.6357 (OUTLIER) cc_final: 0.5838 (m-10) REVERT: A 34 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6908 (p0) REVERT: A 158 MET cc_start: 0.7242 (ttt) cc_final: 0.6977 (mtp) REVERT: A 187 ASP cc_start: 0.6777 (m-30) cc_final: 0.6342 (t0) REVERT: A 231 ASP cc_start: 0.8009 (t0) cc_final: 0.7737 (t0) REVERT: A 253 LEU cc_start: 0.4566 (OUTLIER) cc_final: 0.3817 (pp) REVERT: A 268 GLN cc_start: 0.6170 (OUTLIER) cc_final: 0.5483 (mm-40) REVERT: F 34 ASN cc_start: 0.8249 (t0) cc_final: 0.7773 (t0) REVERT: F 133 LYS cc_start: 0.5886 (OUTLIER) cc_final: 0.4158 (mttp) REVERT: F 158 MET cc_start: 0.7391 (mtt) cc_final: 0.6953 (ttt) REVERT: F 169 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: F 178 TYR cc_start: 0.6478 (m-80) cc_final: 0.3630 (m-80) REVERT: F 191 TYR cc_start: 0.3794 (OUTLIER) cc_final: 0.2966 (p90) REVERT: F 193 ARG cc_start: 0.5815 (ttt-90) cc_final: 0.4641 (tpm170) REVERT: F 326 MET cc_start: 0.5645 (OUTLIER) cc_final: 0.5144 (mpp) REVERT: I 84 MET cc_start: 0.6650 (ttp) cc_final: 0.6134 (tpt) REVERT: I 136 ILE cc_start: 0.6907 (OUTLIER) cc_final: 0.6434 (pp) REVERT: I 197 THR cc_start: 0.4083 (p) cc_final: 0.3609 (t) REVERT: I 216 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.5097 (t80) REVERT: I 254 ARG cc_start: 0.6201 (OUTLIER) cc_final: 0.4176 (ptm160) REVERT: E 42 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6033 (mt-10) REVERT: E 101 GLN cc_start: 0.4779 (OUTLIER) cc_final: 0.3849 (mm-40) REVERT: E 158 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.5788 (mtt) REVERT: E 209 ASP cc_start: 0.6169 (OUTLIER) cc_final: 0.5203 (m-30) REVERT: E 218 LEU cc_start: 0.6092 (OUTLIER) cc_final: 0.5542 (mm) REVERT: E 243 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7993 (mtt) REVERT: E 251 MET cc_start: 0.6105 (tpp) cc_final: 0.5744 (tmm) REVERT: E 265 ILE cc_start: 0.2967 (OUTLIER) cc_final: 0.2576 (mt) REVERT: E 320 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6256 (tt) REVERT: H 92 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.4161 (m-10) REVERT: H 111 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.6628 (mtmt) REVERT: D 39 LYS cc_start: 0.7582 (mmtt) cc_final: 0.7186 (tmtt) REVERT: D 84 MET cc_start: 0.4945 (OUTLIER) cc_final: 0.3836 (mmm) REVERT: D 243 MET cc_start: 0.8280 (tpt) cc_final: 0.7914 (mmm) REVERT: D 251 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8128 (tpp) REVERT: G 43 GLU cc_start: 0.7242 (pt0) cc_final: 0.6500 (tm-30) REVERT: G 58 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7125 (ptmt) REVERT: G 299 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7324 (mtm180) outliers start: 207 outliers final: 93 residues processed: 430 average time/residue: 0.4921 time to fit residues: 251.0685 Evaluate side-chains 380 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 254 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 66 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 244 HIS Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 315 TYR Chi-restraints excluded: chain G residue 334 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 175 optimal weight: 0.0170 chunk 227 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 46 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 23 GLN C 242 GLN C 244 HIS I 145 GLN ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 202 GLN G 23 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4548 r_free = 0.4548 target = 0.201983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.180732 restraints weight = 39128.663| |-----------------------------------------------------------------------------| r_work (start): 0.4321 rms_B_bonded: 2.25 r_work: 0.4245 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.0971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22425 Z= 0.117 Angle : 0.599 10.441 30409 Z= 0.308 Chirality : 0.042 0.204 3466 Planarity : 0.004 0.062 3803 Dihedral : 13.314 142.677 3642 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.43 % Favored : 92.35 % Rotamer: Outliers : 9.18 % Allowed : 38.81 % Favored : 52.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.16), residues: 2718 helix: -0.11 (0.16), residues: 1071 sheet: -2.16 (0.27), residues: 375 loop : -2.27 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 130 TYR 0.019 0.001 TYR F 301 PHE 0.024 0.001 PHE F 126 HIS 0.012 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (22425) covalent geometry : angle 0.59864 / 0.31 (30409) hydrogen bonds : bond 0.03077 / 3.05 ( 764) hydrogen bonds : angle 5.19048 / 4.70 ( 2187) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 271 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: C 50 GLU cc_start: 0.5844 (OUTLIER) cc_final: 0.4609 (mp0) REVERT: C 70 LYS cc_start: 0.5750 (OUTLIER) cc_final: 0.4568 (ptpp) REVERT: C 96 ARG cc_start: 0.7635 (OUTLIER) cc_final: 0.6616 (mtp180) REVERT: C 107 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7273 (mtpp) REVERT: C 146 LEU cc_start: 0.5716 (OUTLIER) cc_final: 0.5312 (mp) REVERT: C 159 TYR cc_start: 0.4679 (m-80) cc_final: 0.3926 (m-80) REVERT: C 187 ASP cc_start: 0.7591 (t0) cc_final: 0.7104 (t0) REVERT: C 330 ASN cc_start: 0.6158 (m-40) cc_final: 0.5778 (t0) REVERT: B 77 GLU cc_start: 0.7108 (mp0) cc_final: 0.6713 (mp0) REVERT: B 84 MET cc_start: 0.4347 (mtt) cc_final: 0.3793 (mmt) REVERT: B 169 GLU cc_start: 0.5826 (OUTLIER) cc_final: 0.5403 (pp20) REVERT: B 172 LEU cc_start: 0.6867 (tm) cc_final: 0.6510 (tp) REVERT: B 191 TYR cc_start: 0.6301 (OUTLIER) cc_final: 0.5515 (m-80) REVERT: B 204 LEU cc_start: 0.8165 (mm) cc_final: 0.7751 (mm) REVERT: B 247 ARG cc_start: 0.6413 (OUTLIER) cc_final: 0.5541 (tpp80) REVERT: B 248 PHE cc_start: 0.5988 (OUTLIER) cc_final: 0.5154 (t80) REVERT: B 327 PHE cc_start: 0.6283 (OUTLIER) cc_final: 0.5757 (m-10) REVERT: A 34 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.6853 (p0) REVERT: A 158 MET cc_start: 0.7267 (ttt) cc_final: 0.7020 (mtp) REVERT: A 187 ASP cc_start: 0.6747 (m-30) cc_final: 0.6324 (t0) REVERT: A 231 ASP cc_start: 0.8012 (t0) cc_final: 0.7729 (t0) REVERT: A 253 LEU cc_start: 0.4635 (OUTLIER) cc_final: 0.3869 (pp) REVERT: F 34 ASN cc_start: 0.8277 (t0) cc_final: 0.7806 (t0) REVERT: F 106 SER cc_start: 0.5977 (OUTLIER) cc_final: 0.5590 (t) REVERT: F 133 LYS cc_start: 0.5815 (OUTLIER) cc_final: 0.4797 (mtpp) REVERT: F 158 MET cc_start: 0.7381 (mtt) cc_final: 0.6924 (ttt) REVERT: F 169 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: F 178 TYR cc_start: 0.6438 (m-80) cc_final: 0.3622 (m-80) REVERT: F 191 TYR cc_start: 0.3822 (OUTLIER) cc_final: 0.2919 (p90) REVERT: F 193 ARG cc_start: 0.5861 (ttt-90) cc_final: 0.4633 (tpm170) REVERT: F 326 MET cc_start: 0.5662 (OUTLIER) cc_final: 0.5193 (mpp) REVERT: I 84 MET cc_start: 0.6707 (ttp) cc_final: 0.6139 (tpt) REVERT: I 136 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6425 (pp) REVERT: I 197 THR cc_start: 0.4005 (p) cc_final: 0.3520 (t) REVERT: I 216 TYR cc_start: 0.6307 (OUTLIER) cc_final: 0.5053 (t80) REVERT: I 223 SER cc_start: 0.2071 (OUTLIER) cc_final: 0.1825 (p) REVERT: I 254 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.4205 (ptm160) REVERT: E 42 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6031 (mt-10) REVERT: E 101 GLN cc_start: 0.4849 (OUTLIER) cc_final: 0.3780 (mm-40) REVERT: E 156 LYS cc_start: 0.3600 (OUTLIER) cc_final: 0.3233 (ttpt) REVERT: E 209 ASP cc_start: 0.6148 (OUTLIER) cc_final: 0.5185 (m-30) REVERT: E 218 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5573 (mm) REVERT: E 251 MET cc_start: 0.6101 (tpp) cc_final: 0.5698 (tmm) REVERT: E 265 ILE cc_start: 0.3088 (OUTLIER) cc_final: 0.2751 (mt) REVERT: E 320 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6246 (tt) REVERT: H 103 THR cc_start: 0.4231 (OUTLIER) cc_final: 0.3919 (t) REVERT: H 104 THR cc_start: 0.4742 (OUTLIER) cc_final: 0.4190 (t) REVERT: D 39 LYS cc_start: 0.7623 (mmtt) cc_final: 0.7207 (tmtt) REVERT: D 84 MET cc_start: 0.5001 (OUTLIER) cc_final: 0.3872 (mmm) REVERT: D 243 MET cc_start: 0.8293 (tpt) cc_final: 0.7937 (mmm) REVERT: D 251 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8203 (tpp) REVERT: G 43 GLU cc_start: 0.7244 (pt0) cc_final: 0.6515 (tm-30) REVERT: G 58 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7156 (ptmt) REVERT: G 299 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7443 (mtm180) REVERT: G 310 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.5509 (mpp-170) outliers start: 205 outliers final: 94 residues processed: 433 average time/residue: 0.5063 time to fit residues: 258.8059 Evaluate side-chains 379 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 250 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 211 MET Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 131 THR Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 156 LYS Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 244 HIS Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 23 GLN Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Chi-restraints excluded: chain G residue 334 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 11 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 155 optimal weight: 0.0670 chunk 91 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 241 optimal weight: 9.9990 chunk 259 optimal weight: 5.9990 chunk 236 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 23 GLN C 244 HIS ** A 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 145 GLN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 272 GLN G 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.202506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.180964 restraints weight = 39382.165| |-----------------------------------------------------------------------------| r_work (start): 0.4325 rms_B_bonded: 2.30 r_work: 0.4247 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22425 Z= 0.119 Angle : 0.607 9.757 30409 Z= 0.312 Chirality : 0.042 0.227 3466 Planarity : 0.004 0.062 3803 Dihedral : 13.260 142.966 3639 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.21 % Favored : 92.57 % Rotamer: Outliers : 9.04 % Allowed : 38.85 % Favored : 52.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.16), residues: 2718 helix: -0.11 (0.16), residues: 1072 sheet: -2.14 (0.27), residues: 373 loop : -2.25 (0.17), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 130 TYR 0.021 0.001 TYR E 216 PHE 0.022 0.001 PHE F 126 HIS 0.010 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (22425) covalent geometry : angle 0.60677 / 0.31 (30409) hydrogen bonds : bond 0.03007 / 2.98 ( 764) hydrogen bonds : angle 5.13869 / 4.71 ( 2187) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 261 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: C 50 GLU cc_start: 0.5936 (OUTLIER) cc_final: 0.4722 (mp0) REVERT: C 70 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.4600 (ptpp) REVERT: C 96 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.6611 (mtp180) REVERT: C 107 LYS cc_start: 0.8018 (OUTLIER) cc_final: 0.7273 (mtpp) REVERT: C 146 LEU cc_start: 0.5671 (OUTLIER) cc_final: 0.5280 (mp) REVERT: C 159 TYR cc_start: 0.4634 (m-80) cc_final: 0.4225 (m-80) REVERT: C 187 ASP cc_start: 0.7580 (t0) cc_final: 0.7110 (t0) REVERT: C 330 ASN cc_start: 0.6160 (m-40) cc_final: 0.5777 (t0) REVERT: B 66 ILE cc_start: 0.3543 (OUTLIER) cc_final: 0.3308 (mp) REVERT: B 77 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6713 (mp0) REVERT: B 84 MET cc_start: 0.4462 (mtt) cc_final: 0.3855 (mmt) REVERT: B 158 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6389 (mpt) REVERT: B 169 GLU cc_start: 0.5824 (OUTLIER) cc_final: 0.5359 (pp20) REVERT: B 172 LEU cc_start: 0.6862 (tm) cc_final: 0.6505 (tp) REVERT: B 191 TYR cc_start: 0.6272 (OUTLIER) cc_final: 0.5491 (m-80) REVERT: B 247 ARG cc_start: 0.6484 (OUTLIER) cc_final: 0.5495 (tpp80) REVERT: B 248 PHE cc_start: 0.6056 (OUTLIER) cc_final: 0.5100 (t80) REVERT: B 327 PHE cc_start: 0.6361 (OUTLIER) cc_final: 0.5738 (m-10) REVERT: A 34 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6863 (p0) REVERT: A 158 MET cc_start: 0.7242 (ttt) cc_final: 0.6977 (mtp) REVERT: A 187 ASP cc_start: 0.6755 (m-30) cc_final: 0.6322 (t0) REVERT: A 231 ASP cc_start: 0.8009 (t0) cc_final: 0.7730 (t0) REVERT: A 253 LEU cc_start: 0.4624 (OUTLIER) cc_final: 0.3851 (pp) REVERT: A 268 GLN cc_start: 0.6128 (OUTLIER) cc_final: 0.5427 (mm-40) REVERT: F 34 ASN cc_start: 0.8256 (t0) cc_final: 0.7773 (t0) REVERT: F 106 SER cc_start: 0.5974 (OUTLIER) cc_final: 0.5591 (t) REVERT: F 128 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: F 133 LYS cc_start: 0.5794 (OUTLIER) cc_final: 0.4879 (mtpp) REVERT: F 158 MET cc_start: 0.7379 (mtt) cc_final: 0.6905 (ttt) REVERT: F 169 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: F 178 TYR cc_start: 0.6431 (m-80) cc_final: 0.3583 (m-80) REVERT: F 191 TYR cc_start: 0.3814 (OUTLIER) cc_final: 0.2929 (p90) REVERT: F 193 ARG cc_start: 0.5844 (ttt-90) cc_final: 0.4617 (tpm170) REVERT: F 326 MET cc_start: 0.5686 (OUTLIER) cc_final: 0.5199 (mpp) REVERT: I 84 MET cc_start: 0.6683 (ttp) cc_final: 0.6136 (tpt) REVERT: I 136 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6421 (pp) REVERT: I 197 THR cc_start: 0.3999 (p) cc_final: 0.3504 (t) REVERT: I 216 TYR cc_start: 0.6310 (OUTLIER) cc_final: 0.5008 (t80) REVERT: I 223 SER cc_start: 0.1915 (OUTLIER) cc_final: 0.1708 (p) REVERT: I 254 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.4172 (ptm160) REVERT: E 42 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6064 (mt-10) REVERT: E 101 GLN cc_start: 0.4859 (OUTLIER) cc_final: 0.3755 (mm-40) REVERT: E 209 ASP cc_start: 0.6097 (OUTLIER) cc_final: 0.5115 (m-30) REVERT: E 218 LEU cc_start: 0.6167 (OUTLIER) cc_final: 0.5573 (mm) REVERT: E 235 ARG cc_start: 0.6156 (OUTLIER) cc_final: 0.5920 (ttp-170) REVERT: E 243 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.7981 (mtt) REVERT: E 251 MET cc_start: 0.6207 (tpp) cc_final: 0.5720 (tmm) REVERT: E 265 ILE cc_start: 0.2926 (OUTLIER) cc_final: 0.2616 (mt) REVERT: E 320 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6243 (tt) REVERT: H 92 PHE cc_start: 0.4530 (OUTLIER) cc_final: 0.4180 (m-10) REVERT: H 103 THR cc_start: 0.4263 (OUTLIER) cc_final: 0.3891 (t) REVERT: H 104 THR cc_start: 0.4728 (OUTLIER) cc_final: 0.4210 (t) REVERT: H 111 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.6614 (mtmt) REVERT: H 251 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7002 (ttp) REVERT: D 39 LYS cc_start: 0.7607 (mmtt) cc_final: 0.7180 (tmtt) REVERT: D 84 MET cc_start: 0.4995 (OUTLIER) cc_final: 0.3872 (mmm) REVERT: D 135 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7166 (mp-120) REVERT: D 243 MET cc_start: 0.8282 (tpt) cc_final: 0.7923 (mmm) REVERT: D 251 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8188 (tpp) REVERT: G 43 GLU cc_start: 0.7277 (pt0) cc_final: 0.6520 (tm-30) REVERT: G 58 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.7131 (ptmt) REVERT: G 299 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.7351 (mtm180) REVERT: G 310 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.5498 (mpp-170) outliers start: 202 outliers final: 95 residues processed: 416 average time/residue: 0.4672 time to fit residues: 230.7094 Evaluate side-chains 389 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 249 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 GLN Chi-restraints excluded: chain C residue 50 GLU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 322 GLU Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 223 SER Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 59 GLU Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 201 THR Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 244 HIS Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 82 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 94 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 256 optimal weight: 0.4980 chunk 82 optimal weight: 8.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 222 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 220 optimal weight: 0.5980 chunk 27 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 23 GLN C 244 HIS I 145 GLN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.203083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.181567 restraints weight = 39467.256| |-----------------------------------------------------------------------------| r_work (start): 0.4330 rms_B_bonded: 2.28 r_work: 0.4252 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22425 Z= 0.117 Angle : 0.615 9.717 30409 Z= 0.314 Chirality : 0.042 0.259 3466 Planarity : 0.004 0.062 3803 Dihedral : 13.179 142.863 3635 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.99 % Favored : 92.79 % Rotamer: Outliers : 8.55 % Allowed : 39.21 % Favored : 52.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.16), residues: 2718 helix: -0.06 (0.16), residues: 1070 sheet: -2.06 (0.27), residues: 371 loop : -2.22 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 130 TYR 0.023 0.001 TYR E 216 PHE 0.023 0.001 PHE F 126 HIS 0.015 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (22425) covalent geometry : angle 0.61522 / 0.31 (30409) hydrogen bonds : bond 0.02945 / 2.92 ( 764) hydrogen bonds : angle 5.08250 / 4.66 ( 2187) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 263 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 70 LYS cc_start: 0.5678 (OUTLIER) cc_final: 0.4563 (ptpp) REVERT: C 96 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6645 (mtp180) REVERT: C 107 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7288 (mtpp) REVERT: C 146 LEU cc_start: 0.5723 (OUTLIER) cc_final: 0.5341 (mp) REVERT: C 159 TYR cc_start: 0.4906 (m-80) cc_final: 0.4326 (m-80) REVERT: C 187 ASP cc_start: 0.7564 (t0) cc_final: 0.7098 (t0) REVERT: C 330 ASN cc_start: 0.6131 (m-40) cc_final: 0.5678 (t0) REVERT: B 66 ILE cc_start: 0.3417 (OUTLIER) cc_final: 0.2558 (tt) REVERT: B 77 GLU cc_start: 0.7085 (OUTLIER) cc_final: 0.6705 (mp0) REVERT: B 84 MET cc_start: 0.4444 (mtt) cc_final: 0.3848 (mmt) REVERT: B 142 VAL cc_start: 0.5128 (OUTLIER) cc_final: 0.4914 (m) REVERT: B 158 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6384 (mpt) REVERT: B 169 GLU cc_start: 0.5821 (OUTLIER) cc_final: 0.5361 (pp20) REVERT: B 172 LEU cc_start: 0.6969 (tm) cc_final: 0.6611 (tp) REVERT: B 191 TYR cc_start: 0.6251 (OUTLIER) cc_final: 0.5463 (m-80) REVERT: B 204 LEU cc_start: 0.8086 (mm) cc_final: 0.7636 (mm) REVERT: B 247 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.5462 (tpp80) REVERT: B 248 PHE cc_start: 0.6029 (OUTLIER) cc_final: 0.5085 (t80) REVERT: B 327 PHE cc_start: 0.6377 (OUTLIER) cc_final: 0.5715 (m-10) REVERT: A 34 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.6858 (p0) REVERT: A 158 MET cc_start: 0.7202 (ttt) cc_final: 0.6927 (mtp) REVERT: A 187 ASP cc_start: 0.6760 (m-30) cc_final: 0.6330 (t0) REVERT: A 231 ASP cc_start: 0.8016 (t0) cc_final: 0.7736 (t0) REVERT: A 253 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.3827 (pp) REVERT: A 268 GLN cc_start: 0.6114 (OUTLIER) cc_final: 0.5405 (mm-40) REVERT: F 34 ASN cc_start: 0.8267 (t0) cc_final: 0.7787 (t0) REVERT: F 106 SER cc_start: 0.6017 (OUTLIER) cc_final: 0.5629 (t) REVERT: F 125 MET cc_start: 0.4584 (OUTLIER) cc_final: 0.4237 (mmt) REVERT: F 133 LYS cc_start: 0.5770 (OUTLIER) cc_final: 0.4867 (mtpp) REVERT: F 150 ARG cc_start: 0.4381 (mtm110) cc_final: 0.1457 (ttt-90) REVERT: F 158 MET cc_start: 0.7401 (mtt) cc_final: 0.6907 (ttt) REVERT: F 169 GLU cc_start: 0.6832 (OUTLIER) cc_final: 0.6291 (mp0) REVERT: F 191 TYR cc_start: 0.3769 (OUTLIER) cc_final: 0.2882 (p90) REVERT: F 193 ARG cc_start: 0.5874 (ttt-90) cc_final: 0.4646 (tpm170) REVERT: F 210 MET cc_start: 0.6505 (mmp) cc_final: 0.4599 (mtp) REVERT: F 326 MET cc_start: 0.5678 (OUTLIER) cc_final: 0.5132 (mpp) REVERT: I 84 MET cc_start: 0.6614 (ttp) cc_final: 0.6103 (tpt) REVERT: I 136 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6444 (pp) REVERT: I 197 THR cc_start: 0.4092 (p) cc_final: 0.3614 (t) REVERT: I 216 TYR cc_start: 0.6291 (OUTLIER) cc_final: 0.4985 (t80) REVERT: I 254 ARG cc_start: 0.6144 (OUTLIER) cc_final: 0.4159 (ptm160) REVERT: E 42 GLU cc_start: 0.6636 (OUTLIER) cc_final: 0.6066 (mt-10) REVERT: E 101 GLN cc_start: 0.4936 (OUTLIER) cc_final: 0.3813 (mm-40) REVERT: E 209 ASP cc_start: 0.6145 (OUTLIER) cc_final: 0.5135 (m-30) REVERT: E 218 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5528 (mm) REVERT: E 235 ARG cc_start: 0.6169 (OUTLIER) cc_final: 0.5927 (ttp-170) REVERT: E 243 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.7945 (mtt) REVERT: E 251 MET cc_start: 0.6201 (tpp) cc_final: 0.5713 (tmm) REVERT: E 265 ILE cc_start: 0.2770 (OUTLIER) cc_final: 0.2509 (mt) REVERT: E 320 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6278 (tt) REVERT: H 92 PHE cc_start: 0.4509 (OUTLIER) cc_final: 0.4183 (m-10) REVERT: H 103 THR cc_start: 0.4240 (OUTLIER) cc_final: 0.3919 (t) REVERT: H 104 THR cc_start: 0.4776 (OUTLIER) cc_final: 0.4268 (t) REVERT: H 111 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.6611 (mtmt) REVERT: D 39 LYS cc_start: 0.7617 (mmtt) cc_final: 0.7187 (tmtt) REVERT: D 84 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.3862 (mmm) REVERT: D 243 MET cc_start: 0.8284 (tpt) cc_final: 0.7939 (mmm) REVERT: D 251 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8171 (tpp) REVERT: G 43 GLU cc_start: 0.7250 (pt0) cc_final: 0.6517 (tm-30) REVERT: G 58 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.7161 (ptmt) REVERT: G 299 ARG cc_start: 0.8452 (OUTLIER) cc_final: 0.7431 (mtm180) REVERT: G 310 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.5478 (mpp-170) outliers start: 191 outliers final: 91 residues processed: 410 average time/residue: 0.5034 time to fit residues: 242.9917 Evaluate side-chains 384 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 251 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 247 ARG Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 125 MET Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain E residue 101 GLN Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 ARG Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 244 HIS Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 299 ARG Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Chi-restraints excluded: chain G residue 334 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 60 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 195 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 18 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 161 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS I 145 GLN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.201705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.180513 restraints weight = 38936.908| |-----------------------------------------------------------------------------| r_work (start): 0.4318 rms_B_bonded: 2.23 r_work: 0.4241 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6734 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22425 Z= 0.134 Angle : 0.636 9.598 30409 Z= 0.325 Chirality : 0.043 0.233 3466 Planarity : 0.004 0.062 3803 Dihedral : 13.221 142.671 3634 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.62 % Favored : 92.16 % Rotamer: Outliers : 7.65 % Allowed : 40.11 % Favored : 52.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.16), residues: 2718 helix: -0.03 (0.16), residues: 1058 sheet: -2.08 (0.27), residues: 371 loop : -2.19 (0.17), residues: 1289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 130 TYR 0.019 0.001 TYR E 216 PHE 0.023 0.002 PHE F 126 HIS 0.013 0.001 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (22425) covalent geometry : angle 0.63604 / 0.33 (30409) hydrogen bonds : bond 0.03035 / 2.99 ( 764) hydrogen bonds : angle 5.10508 / 4.68 ( 2187) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 253 time to evaluate : 0.915 Fit side-chains revert: symmetry clash REVERT: C 70 LYS cc_start: 0.5676 (OUTLIER) cc_final: 0.4577 (ptpp) REVERT: C 96 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.6639 (mtp180) REVERT: C 107 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7300 (mtpp) REVERT: C 146 LEU cc_start: 0.5742 (OUTLIER) cc_final: 0.5343 (mp) REVERT: C 159 TYR cc_start: 0.4946 (m-80) cc_final: 0.4353 (m-80) REVERT: C 187 ASP cc_start: 0.7582 (t0) cc_final: 0.7119 (t0) REVERT: C 219 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6585 (tp) REVERT: C 330 ASN cc_start: 0.6160 (m-40) cc_final: 0.5775 (t0) REVERT: B 66 ILE cc_start: 0.3447 (OUTLIER) cc_final: 0.2705 (tt) REVERT: B 77 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6737 (mp0) REVERT: B 84 MET cc_start: 0.4442 (mtt) cc_final: 0.3837 (mmt) REVERT: B 169 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5352 (pp20) REVERT: B 172 LEU cc_start: 0.6927 (tm) cc_final: 0.6569 (tp) REVERT: B 191 TYR cc_start: 0.6281 (OUTLIER) cc_final: 0.5476 (m-80) REVERT: B 200 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: B 204 LEU cc_start: 0.8150 (mm) cc_final: 0.7697 (mm) REVERT: B 248 PHE cc_start: 0.6020 (OUTLIER) cc_final: 0.4954 (t80) REVERT: B 327 PHE cc_start: 0.6397 (OUTLIER) cc_final: 0.5726 (m-10) REVERT: A 34 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.6829 (p0) REVERT: A 158 MET cc_start: 0.7232 (ttt) cc_final: 0.6976 (mtp) REVERT: A 187 ASP cc_start: 0.6767 (m-30) cc_final: 0.6322 (t0) REVERT: A 231 ASP cc_start: 0.7992 (t0) cc_final: 0.7711 (t0) REVERT: A 253 LEU cc_start: 0.4616 (OUTLIER) cc_final: 0.3865 (pp) REVERT: A 268 GLN cc_start: 0.6129 (OUTLIER) cc_final: 0.5435 (mm-40) REVERT: F 34 ASN cc_start: 0.8265 (t0) cc_final: 0.7790 (t0) REVERT: F 106 SER cc_start: 0.6003 (OUTLIER) cc_final: 0.5613 (t) REVERT: F 133 LYS cc_start: 0.5756 (OUTLIER) cc_final: 0.4115 (mttp) REVERT: F 150 ARG cc_start: 0.4419 (mtm110) cc_final: 0.1629 (ttt-90) REVERT: F 158 MET cc_start: 0.7417 (mtt) cc_final: 0.6945 (ttt) REVERT: F 169 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.6252 (mp0) REVERT: F 191 TYR cc_start: 0.3807 (OUTLIER) cc_final: 0.2908 (p90) REVERT: F 193 ARG cc_start: 0.5877 (ttt-90) cc_final: 0.4632 (tpm170) REVERT: F 326 MET cc_start: 0.5627 (OUTLIER) cc_final: 0.5119 (mpp) REVERT: I 136 ILE cc_start: 0.6851 (OUTLIER) cc_final: 0.6439 (pp) REVERT: I 197 THR cc_start: 0.4002 (p) cc_final: 0.3506 (t) REVERT: I 216 TYR cc_start: 0.6310 (OUTLIER) cc_final: 0.5035 (t80) REVERT: I 239 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7534 (p) REVERT: I 254 ARG cc_start: 0.6147 (OUTLIER) cc_final: 0.4156 (ptm160) REVERT: E 42 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.6053 (mt-10) REVERT: E 209 ASP cc_start: 0.6155 (OUTLIER) cc_final: 0.5169 (m-30) REVERT: E 218 LEU cc_start: 0.6062 (OUTLIER) cc_final: 0.5491 (mm) REVERT: E 243 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.7980 (mtt) REVERT: E 251 MET cc_start: 0.6203 (tpp) cc_final: 0.5705 (tmm) REVERT: E 265 ILE cc_start: 0.2980 (OUTLIER) cc_final: 0.2651 (mt) REVERT: E 320 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6165 (tt) REVERT: H 92 PHE cc_start: 0.4540 (OUTLIER) cc_final: 0.4192 (m-10) REVERT: H 103 THR cc_start: 0.4306 (OUTLIER) cc_final: 0.3973 (t) REVERT: H 104 THR cc_start: 0.4790 (OUTLIER) cc_final: 0.4291 (t) REVERT: H 111 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.6631 (mtmt) REVERT: H 251 MET cc_start: 0.7597 (OUTLIER) cc_final: 0.6900 (ttp) REVERT: D 39 LYS cc_start: 0.7654 (mmtt) cc_final: 0.7224 (tmtt) REVERT: D 84 MET cc_start: 0.4907 (OUTLIER) cc_final: 0.3777 (mmm) REVERT: D 243 MET cc_start: 0.8279 (tpt) cc_final: 0.7922 (mmm) REVERT: D 251 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8167 (tpp) REVERT: G 43 GLU cc_start: 0.7235 (pt0) cc_final: 0.6510 (tm-30) REVERT: G 58 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7128 (ptmt) REVERT: G 310 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.5509 (mpp-170) outliers start: 171 outliers final: 93 residues processed: 384 average time/residue: 0.4408 time to fit residues: 201.2022 Evaluate side-chains 377 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 245 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain B residue 332 ASP Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 176 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain F residue 330 ASN Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 239 SER Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 209 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 244 HIS Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 124 GLU Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 251 MET Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 205 TYR Chi-restraints excluded: chain G residue 257 ASP Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Chi-restraints excluded: chain G residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 253 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 263 optimal weight: 0.0070 chunk 217 optimal weight: 7.9990 chunk 208 optimal weight: 4.9990 chunk 268 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 201 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 126 optimal weight: 0.3980 overall best weight: 2.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS I 145 GLN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.198659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.176847 restraints weight = 39178.230| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 2.28 r_work: 0.4198 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22425 Z= 0.183 Angle : 0.709 14.199 30409 Z= 0.361 Chirality : 0.045 0.332 3466 Planarity : 0.004 0.062 3803 Dihedral : 13.520 143.424 3634 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.79 % Favored : 90.99 % Rotamer: Outliers : 6.89 % Allowed : 40.91 % Favored : 52.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.16), residues: 2718 helix: -0.21 (0.16), residues: 1057 sheet: -2.19 (0.27), residues: 365 loop : -2.28 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 229 TYR 0.021 0.002 TYR E 216 PHE 0.028 0.002 PHE F 126 HIS 0.013 0.002 HIS A 199 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (22425) covalent geometry : angle 0.70876 / 0.36 (30409) hydrogen bonds : bond 0.03486 / 3.45 ( 764) hydrogen bonds : angle 5.32353 / 4.87 ( 2187) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 258 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: C 70 LYS cc_start: 0.5758 (OUTLIER) cc_final: 0.4691 (ptpp) REVERT: C 96 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.6644 (mtp180) REVERT: C 107 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7392 (mtpp) REVERT: C 146 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5119 (mp) REVERT: C 187 ASP cc_start: 0.7593 (t0) cc_final: 0.7124 (t0) REVERT: C 219 LEU cc_start: 0.7004 (OUTLIER) cc_final: 0.6610 (tp) REVERT: B 66 ILE cc_start: 0.3467 (OUTLIER) cc_final: 0.2642 (tt) REVERT: B 77 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6786 (mp0) REVERT: B 84 MET cc_start: 0.4530 (mtt) cc_final: 0.3880 (mmt) REVERT: B 161 ASP cc_start: 0.6262 (t0) cc_final: 0.5755 (t70) REVERT: B 169 GLU cc_start: 0.5881 (OUTLIER) cc_final: 0.5354 (pp20) REVERT: B 172 LEU cc_start: 0.6916 (tm) cc_final: 0.6554 (tp) REVERT: B 191 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5474 (m-80) REVERT: B 200 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: B 204 LEU cc_start: 0.8178 (mm) cc_final: 0.7789 (mm) REVERT: B 248 PHE cc_start: 0.6070 (OUTLIER) cc_final: 0.5072 (t80) REVERT: B 327 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.5791 (m-10) REVERT: A 34 ASN cc_start: 0.7476 (OUTLIER) cc_final: 0.6887 (p0) REVERT: A 158 MET cc_start: 0.7268 (ttt) cc_final: 0.6996 (mtp) REVERT: A 187 ASP cc_start: 0.6834 (m-30) cc_final: 0.6360 (t0) REVERT: A 231 ASP cc_start: 0.8052 (t0) cc_final: 0.7762 (t0) REVERT: A 253 LEU cc_start: 0.4641 (OUTLIER) cc_final: 0.3873 (pp) REVERT: A 268 GLN cc_start: 0.6215 (OUTLIER) cc_final: 0.5526 (mm-40) REVERT: F 34 ASN cc_start: 0.8260 (t0) cc_final: 0.7811 (t0) REVERT: F 128 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: F 133 LYS cc_start: 0.6004 (OUTLIER) cc_final: 0.4084 (mttp) REVERT: F 150 ARG cc_start: 0.4423 (mtm110) cc_final: 0.1428 (ttt-90) REVERT: F 158 MET cc_start: 0.7416 (mtt) cc_final: 0.7012 (ttt) REVERT: F 169 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: F 191 TYR cc_start: 0.3817 (OUTLIER) cc_final: 0.2936 (p90) REVERT: F 193 ARG cc_start: 0.5912 (ttt-90) cc_final: 0.4565 (tpm170) REVERT: F 326 MET cc_start: 0.5699 (OUTLIER) cc_final: 0.5135 (mpp) REVERT: I 136 ILE cc_start: 0.6928 (OUTLIER) cc_final: 0.6435 (pp) REVERT: I 216 TYR cc_start: 0.6326 (OUTLIER) cc_final: 0.5089 (t80) REVERT: I 254 ARG cc_start: 0.6269 (OUTLIER) cc_final: 0.4324 (ptm160) REVERT: E 42 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5988 (mt-10) REVERT: E 218 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5428 (mm) REVERT: E 243 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8186 (mtt) REVERT: E 251 MET cc_start: 0.6304 (tpp) cc_final: 0.5889 (tmm) REVERT: E 265 ILE cc_start: 0.3063 (OUTLIER) cc_final: 0.2670 (mt) REVERT: E 320 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6119 (tt) REVERT: H 92 PHE cc_start: 0.4647 (OUTLIER) cc_final: 0.4220 (m-10) REVERT: H 103 THR cc_start: 0.4330 (OUTLIER) cc_final: 0.3964 (t) REVERT: H 111 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.6589 (mtmt) REVERT: H 251 MET cc_start: 0.7691 (OUTLIER) cc_final: 0.7050 (ttp) REVERT: D 39 LYS cc_start: 0.7584 (mmtt) cc_final: 0.7172 (tmtt) REVERT: D 84 MET cc_start: 0.5063 (OUTLIER) cc_final: 0.3905 (mmm) REVERT: D 243 MET cc_start: 0.8284 (tpt) cc_final: 0.7874 (mmm) REVERT: G 43 GLU cc_start: 0.7288 (pt0) cc_final: 0.6526 (tm-30) REVERT: G 58 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.7082 (ptmt) REVERT: G 310 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.5414 (mpp-170) REVERT: G 326 MET cc_start: 0.7551 (mpp) cc_final: 0.6821 (mpp) outliers start: 154 outliers final: 89 residues processed: 376 average time/residue: 0.4519 time to fit residues: 202.2736 Evaluate side-chains 373 residues out of total 2234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 249 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 96 ARG Chi-restraints excluded: chain C residue 107 LYS Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 334 VAL Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 191 TYR Chi-restraints excluded: chain B residue 195 PHE Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 248 PHE Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 327 PHE Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 216 TYR Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 PHE Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 46 TYR Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 82 VAL Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 133 LYS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 144 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 297 THR Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain F residue 326 MET Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 136 ILE Chi-restraints excluded: chain I residue 170 ARG Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 216 TYR Chi-restraints excluded: chain I residue 251 MET Chi-restraints excluded: chain I residue 254 ARG Chi-restraints excluded: chain I residue 302 LEU Chi-restraints excluded: chain I residue 309 THR Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 125 MET Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 174 VAL Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 243 MET Chi-restraints excluded: chain E residue 255 LEU Chi-restraints excluded: chain E residue 265 ILE Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 269 VAL Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 92 PHE Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 106 SER Chi-restraints excluded: chain H residue 111 LYS Chi-restraints excluded: chain H residue 131 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 196 ASN Chi-restraints excluded: chain H residue 212 VAL Chi-restraints excluded: chain H residue 222 ASP Chi-restraints excluded: chain H residue 244 HIS Chi-restraints excluded: chain H residue 251 MET Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain H residue 319 CYS Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 62 ASN Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 84 MET Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 131 THR Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 214 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain G residue 48 THR Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 310 ARG Chi-restraints excluded: chain G residue 315 TYR Chi-restraints excluded: chain G residue 334 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 100 optimal weight: 0.0040 chunk 57 optimal weight: 0.7980 chunk 133 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 0.0980 chunk 249 optimal weight: 0.9990 chunk 91 optimal weight: 8.9990 chunk 259 optimal weight: 4.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 244 HIS A 101 GLN F 330 ASN I 145 GLN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN D 202 GLN ** G 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 330 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.202090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.180397 restraints weight = 39383.152| |-----------------------------------------------------------------------------| r_work (start): 0.4320 rms_B_bonded: 2.25 r_work: 0.4244 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22425 Z= 0.124 Angle : 0.654 10.767 30409 Z= 0.334 Chirality : 0.043 0.248 3466 Planarity : 0.004 0.068 3803 Dihedral : 13.352 143.530 3634 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.10 % Favored : 92.64 % Rotamer: Outliers : 6.18 % Allowed : 42.12 % Favored : 51.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.16), residues: 2718 helix: -0.17 (0.16), residues: 1072 sheet: -2.12 (0.27), residues: 371 loop : -2.28 (0.17), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 130 TYR 0.025 0.001 TYR E 216 PHE 0.024 0.002 PHE F 126 HIS 0.015 0.001 HIS H 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (22425) covalent geometry : angle 0.65393 / 0.33 (30409) hydrogen bonds : bond 0.03050 / 3.01 ( 764) hydrogen bonds : angle 5.19081 / 4.73 ( 2187) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7116.91 seconds wall clock time: 122 minutes 15.50 seconds (7335.50 seconds total)