Starting phenix.real_space_refine on Sat Feb 7 12:29:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pf1_71584/02_2026/9pf1_71584.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pf1_71584/02_2026/9pf1_71584.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pf1_71584/02_2026/9pf1_71584.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pf1_71584/02_2026/9pf1_71584.map" model { file = "/net/cci-nas-00/data/ceres_data/9pf1_71584/02_2026/9pf1_71584.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pf1_71584/02_2026/9pf1_71584.cif" } resolution = 3.57 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= 0.001 sd= 0.032 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 14 5.49 5 Mg 2 5.21 5 S 174 5.16 5 C 20577 2.51 5 N 5684 2.21 5 O 6259 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 147 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32711 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 3135 Classifications: {'peptide': 399} Link IDs: {'PTRANS': 22, 'TRANS': 376} Chain breaks: 1 Chain: "C" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3039 Classifications: {'peptide': 383} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 366} Chain breaks: 1 Chain: "G" Number of atoms: 1820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1820 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 230} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1717 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'TRP:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 11, 'PHE:plan': 2, 'ARG:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 82 Chain: "L" Number of atoms: 1850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1850 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 10, 'TRANS': 227} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "M" Number of atoms: 1856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1856 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 234} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "c" Number of atoms: 2162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2162 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 265} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "v" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2917 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 351} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2811 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 336} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2932 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "F" Number of atoms: 2911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2911 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 354} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.22, per 1000 atoms: 0.22 Number of scatterers: 32711 At special positions: 0 Unit cell: (136.24, 192.832, 170.824, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 174 16.00 P 14 15.00 Mg 2 11.99 O 6259 8.00 N 5684 7.00 C 20577 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 113 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 115 " 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7858 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 26 sheets defined 47.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 26 through 34 Processing helix chain 'A' and resid 41 through 64 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.576A pdb=" N TRP A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 173 through 177 Processing helix chain 'A' and resid 180 through 192 removed outlier: 3.637A pdb=" N VAL A 190 " --> pdb=" O LYS A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 197 through 205 removed outlier: 4.249A pdb=" N PHE A 201 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.805A pdb=" N LEU A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 267 Processing helix chain 'A' and resid 277 through 280 Processing helix chain 'A' and resid 293 through 307 Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 362 removed outlier: 4.299A pdb=" N SER A 361 " --> pdb=" O ILE A 357 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 removed outlier: 3.710A pdb=" N LEU A 373 " --> pdb=" O ARG A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 399 Processing helix chain 'A' and resid 405 through 422 Processing helix chain 'C' and resid 22 through 67 removed outlier: 3.552A pdb=" N ALA C 54 " --> pdb=" O ASN C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 133 through 138 Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 154 through 171 Proline residue: C 168 - end of helix Processing helix chain 'C' and resid 171 through 178 removed outlier: 4.547A pdb=" N PHE C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 208 Processing helix chain 'C' and resid 215 through 220 removed outlier: 3.506A pdb=" N LEU C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 215 through 220' Processing helix chain 'C' and resid 225 through 241 removed outlier: 3.786A pdb=" N ARG C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 254 Processing helix chain 'C' and resid 266 through 282 removed outlier: 3.638A pdb=" N GLU C 275 " --> pdb=" O ARG C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 321 through 334 Processing helix chain 'C' and resid 343 through 350 removed outlier: 3.587A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 373 removed outlier: 3.595A pdb=" N GLU C 373 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 392 removed outlier: 3.634A pdb=" N ALA C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS C 389 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN C 392 " --> pdb=" O ALA C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.770A pdb=" N ILE C 401 " --> pdb=" O LYS C 397 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS C 402 " --> pdb=" O ASN C 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 397 through 402' Processing helix chain 'G' and resid 22 through 32 removed outlier: 3.548A pdb=" N GLU G 26 " --> pdb=" O LEU G 22 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS G 30 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA G 31 " --> pdb=" O TYR G 27 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 106 Processing helix chain 'G' and resid 110 through 128 Processing helix chain 'G' and resid 171 through 184 Processing helix chain 'G' and resid 190 through 207 Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 231 through 244 Processing helix chain 'H' and resid 19 through 29 removed outlier: 3.672A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 102 removed outlier: 3.685A pdb=" N TYR H 83 " --> pdb=" O MET H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 121 Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'H' and resid 183 through 199 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'I' and resid 4 through 8 removed outlier: 3.571A pdb=" N SER I 7 " --> pdb=" O ARG I 4 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG I 8 " --> pdb=" O TYR I 5 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 4 through 8' Processing helix chain 'I' and resid 18 through 29 removed outlier: 3.693A pdb=" N GLU I 22 " --> pdb=" O LEU I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 102 Processing helix chain 'I' and resid 106 through 124 removed outlier: 3.565A pdb=" N PHE I 124 " --> pdb=" O ALA I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 185 through 201 Processing helix chain 'I' and resid 229 through 250 removed outlier: 3.637A pdb=" N VAL I 233 " --> pdb=" O LYS I 229 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU I 250 " --> pdb=" O LYS I 246 " (cutoff:3.500A) Processing helix chain 'J' and resid 16 through 28 Processing helix chain 'J' and resid 76 through 98 Processing helix chain 'J' and resid 103 through 120 Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.602A pdb=" N ARG J 169 " --> pdb=" O ALA J 165 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU J 170 " --> pdb=" O LYS J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 199 removed outlier: 4.010A pdb=" N VAL J 199 " --> pdb=" O LEU J 195 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 237 removed outlier: 3.532A pdb=" N TYR J 228 " --> pdb=" O GLU J 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 removed outlier: 3.812A pdb=" N GLY L 32 " --> pdb=" O ALA L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 100 Processing helix chain 'L' and resid 104 through 118 removed outlier: 3.787A pdb=" N ILE L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 122 Processing helix chain 'L' and resid 165 through 180 removed outlier: 4.472A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 199 removed outlier: 3.779A pdb=" N THR L 198 " --> pdb=" O ALA L 194 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU L 199 " --> pdb=" O LEU L 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 227 No H-bonds generated for 'chain 'L' and resid 225 through 227' Processing helix chain 'L' and resid 228 through 234 removed outlier: 4.195A pdb=" N PHE L 232 " --> pdb=" O ASP L 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 33 removed outlier: 4.011A pdb=" N SER M 33 " --> pdb=" O ALA M 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 103 Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.876A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 178 removed outlier: 4.091A pdb=" N LYS M 178 " --> pdb=" O THR M 174 " (cutoff:3.500A) Processing helix chain 'M' and resid 185 through 200 removed outlier: 4.354A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 242 Processing helix chain 'c' and resid 34 through 49 Processing helix chain 'c' and resid 83 through 87 removed outlier: 3.526A pdb=" N VAL c 87 " --> pdb=" O VAL c 84 " (cutoff:3.500A) Processing helix chain 'c' and resid 88 through 101 Processing helix chain 'c' and resid 124 through 137 removed outlier: 3.582A pdb=" N ASN c 128 " --> pdb=" O GLY c 124 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR c 129 " --> pdb=" O VAL c 125 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN c 130 " --> pdb=" O ASP c 126 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU c 136 " --> pdb=" O SER c 132 " (cutoff:3.500A) Processing helix chain 'c' and resid 165 through 170 Processing helix chain 'c' and resid 188 through 195 Processing helix chain 'c' and resid 216 through 220 removed outlier: 3.609A pdb=" N LEU c 220 " --> pdb=" O LEU c 217 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 229 Processing helix chain 'c' and resid 233 through 260 removed outlier: 3.886A pdb=" N ASN c 254 " --> pdb=" O GLU c 250 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU c 260 " --> pdb=" O ASN c 256 " (cutoff:3.500A) Processing helix chain 'c' and resid 278 through 309 removed outlier: 3.815A pdb=" N ARG c 282 " --> pdb=" O GLN c 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 81 Processing helix chain 'B' and resid 92 through 103 removed outlier: 4.266A pdb=" N ASP B 101 " --> pdb=" O SER B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 168 through 175 Processing helix chain 'B' and resid 190 through 201 Processing helix chain 'B' and resid 201 through 207 removed outlier: 3.700A pdb=" N LEU B 205 " --> pdb=" O VAL B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 215 Processing helix chain 'B' and resid 231 through 243 removed outlier: 3.532A pdb=" N THR B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 Processing helix chain 'B' and resid 261 through 278 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 357 through 371 removed outlier: 4.420A pdb=" N ARG B 371 " --> pdb=" O ILE B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 Processing helix chain 'B' and resid 391 through 410 Processing helix chain 'B' and resid 415 through 429 removed outlier: 3.524A pdb=" N PHE B 419 " --> pdb=" O THR B 415 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 83 removed outlier: 3.930A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 170 through 181 Processing helix chain 'D' and resid 181 through 187 Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.873A pdb=" N TYR D 191 " --> pdb=" O HIS D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 223 removed outlier: 3.644A pdb=" N ALA D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 256 Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.724A pdb=" N ALA D 271 " --> pdb=" O ILE D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 299 Processing helix chain 'D' and resid 339 through 352 removed outlier: 4.114A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 4.061A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'E' and resid 16 through 51 Processing helix chain 'E' and resid 116 through 122 removed outlier: 3.706A pdb=" N TYR E 120 " --> pdb=" O ASP E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 131 through 135 Processing helix chain 'E' and resid 138 through 149 Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.069A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 191 Processing helix chain 'E' and resid 200 through 204 removed outlier: 3.934A pdb=" N VAL E 204 " --> pdb=" O SER E 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 200 through 204' Processing helix chain 'E' and resid 209 through 225 removed outlier: 3.536A pdb=" N ARG E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 Processing helix chain 'E' and resid 251 through 266 Processing helix chain 'E' and resid 281 through 285 Processing helix chain 'E' and resid 286 through 291 removed outlier: 4.013A pdb=" N LEU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG E 291 " --> pdb=" O PRO E 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 286 through 291' Processing helix chain 'E' and resid 305 through 317 Processing helix chain 'E' and resid 327 through 335 Processing helix chain 'E' and resid 339 through 357 removed outlier: 3.554A pdb=" N LEU E 343 " --> pdb=" O ASN E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 381 removed outlier: 3.533A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 83 removed outlier: 3.620A pdb=" N LYS F 56 " --> pdb=" O ILE F 52 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL F 59 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N LEU F 60 " --> pdb=" O LYS F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 175 Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 191 through 208 removed outlier: 4.341A pdb=" N LEU F 204 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Proline residue: F 205 - end of helix Processing helix chain 'F' and resid 209 through 214 Processing helix chain 'F' and resid 232 through 243 Processing helix chain 'F' and resid 253 through 258 removed outlier: 3.850A pdb=" N VAL F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLN F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 253 through 258' Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 303 through 316 Processing helix chain 'F' and resid 358 through 370 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 411 Processing helix chain 'F' and resid 416 through 428 Processing helix chain 'K' and resid 23 through 33 removed outlier: 3.560A pdb=" N ALA K 27 " --> pdb=" O GLN K 23 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 104 removed outlier: 4.070A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 121 Processing helix chain 'K' and resid 173 through 185 Processing helix chain 'K' and resid 190 through 206 Processing helix chain 'K' and resid 234 through 241 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 3.695A pdb=" N ILE A 151 " --> pdb=" O GLY A 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 152 current: chain 'C' and resid 85 through 89 removed outlier: 5.310A pdb=" N LYS C 94 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 122 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE B 115 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N HIS B 120 " --> pdb=" O ILE B 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 134 current: chain 'B' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 121 through 123 current: chain 'D' and resid 100 through 105 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 110 through 114 current: chain 'D' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 142 current: chain 'E' and resid 68 through 73 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 82 current: chain 'E' and resid 107 through 110 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 107 through 110 current: chain 'F' and resid 121 through 126 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 131 through 133 current: chain 'F' and resid 160 through 163 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 240 removed outlier: 6.145A pdb=" N CYS A 236 " --> pdb=" O LEU A 271 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE A 273 " --> pdb=" O CYS A 236 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE A 238 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ASP A 275 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N VAL A 240 " --> pdb=" O ASP A 275 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N CYS A 270 " --> pdb=" O LYS A 316 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N LEU A 318 " --> pdb=" O CYS A 270 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 272 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ALA A 320 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N PHE A 274 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY A 211 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ILE A 341 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU A 213 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 210 through 213 removed outlier: 6.048A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N SER C 244 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE C 292 " --> pdb=" O SER C 244 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE C 246 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ALA C 294 " --> pdb=" O ILE C 246 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N MET C 248 " --> pdb=" O ALA C 294 " (cutoff:3.500A) removed outlier: 8.359A pdb=" N ASN C 296 " --> pdb=" O MET C 248 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N VAL C 186 " --> pdb=" O MET C 293 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N THR C 295 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU C 188 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG C 313 " --> pdb=" O GLY C 185 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 165 through 167 removed outlier: 4.814A pdb=" N THR G 221 " --> pdb=" O LYS G 226 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS G 226 " --> pdb=" O THR G 221 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 69 through 70 Processing sheet with id=AA7, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AA8, first strand: chain 'H' and resid 66 through 69 removed outlier: 6.428A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER H 133 " --> pdb=" O SER H 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 34 through 36 Processing sheet with id=AB1, first strand: chain 'I' and resid 42 through 44 Processing sheet with id=AB2, first strand: chain 'I' and resid 47 through 48 Processing sheet with id=AB3, first strand: chain 'I' and resid 66 through 69 removed outlier: 6.217A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 72 through 74 current: chain 'I' and resid 132 through 138 Processing sheet with id=AB4, first strand: chain 'J' and resid 158 through 161 removed outlier: 4.671A pdb=" N VAL J 33 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY J 44 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL J 35 " --> pdb=" O VAL J 42 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL J 42 " --> pdb=" O VAL J 35 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU J 208 " --> pdb=" O LEU J 220 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 69 through 70 removed outlier: 3.887A pdb=" N CYS J 70 " --> pdb=" O VAL J 134 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL J 134 " --> pdb=" O CYS J 70 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY J 135 " --> pdb=" O ARG J 143 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG J 143 " --> pdb=" O GLY J 135 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 158 through 161 removed outlier: 5.521A pdb=" N GLY L 216 " --> pdb=" O GLU L 220 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU L 220 " --> pdb=" O GLY L 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 63 through 67 removed outlier: 3.743A pdb=" N VAL L 66 " --> pdb=" O ILE L 70 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 162 through 165 Processing sheet with id=AB9, first strand: chain 'M' and resid 66 through 70 removed outlier: 6.920A pdb=" N LEU M 66 " --> pdb=" O VAL M 77 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL M 77 " --> pdb=" O LEU M 66 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ASN M 68 " --> pdb=" O MET M 75 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N MET M 75 " --> pdb=" O ASN M 68 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'c' and resid 25 through 26 removed outlier: 6.984A pdb=" N VAL c 25 " --> pdb=" O GLN c 176 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'c' and resid 30 through 33 removed outlier: 6.239A pdb=" N GLN c 30 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N VAL c 69 " --> pdb=" O GLN c 30 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR c 32 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASP c 71 " --> pdb=" O TYR c 32 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N VAL c 67 " --> pdb=" O VAL c 62 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL c 62 " --> pdb=" O VAL c 67 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N VAL c 69 " --> pdb=" O GLU c 60 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N GLU c 60 " --> pdb=" O VAL c 69 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY c 55 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TRP c 111 " --> pdb=" O GLY c 55 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N MET c 57 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N VAL c 141 " --> pdb=" O MET c 107 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL c 109 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N VAL c 143 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N TRP c 111 " --> pdb=" O VAL c 143 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL c 145 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N HIS c 113 " --> pdb=" O VAL c 145 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N ILE c 157 " --> pdb=" O ILE c 205 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE c 205 " --> pdb=" O ILE c 157 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL c 31 " --> pdb=" O ASN c 206 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 246 through 251 removed outlier: 3.533A pdb=" N ASP B 285 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N SER B 280 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE B 328 " --> pdb=" O SER B 280 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL B 282 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ALA B 330 " --> pdb=" O VAL B 282 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE B 284 " --> pdb=" O ALA B 330 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 222 " --> pdb=" O MET B 329 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR B 331 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU B 224 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 227 through 231 removed outlier: 7.503A pdb=" N GLY D 201 " --> pdb=" O ARG D 329 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N ILE D 331 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N LEU D 203 " --> pdb=" O ILE D 331 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 194 through 199 removed outlier: 6.725A pdb=" N ASN E 194 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N PHE E 231 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU E 196 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ASP E 233 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL E 198 " --> pdb=" O ASP E 233 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY E 169 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ILE E 299 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU E 171 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 247 through 252 removed outlier: 6.538A pdb=" N THR F 247 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N PHE F 284 " --> pdb=" O THR F 247 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N LEU F 249 " --> pdb=" O PHE F 284 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP F 286 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU F 251 " --> pdb=" O ASP F 286 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER F 281 " --> pdb=" O LYS F 327 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N ILE F 329 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE F 283 " --> pdb=" O ILE F 329 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA F 331 " --> pdb=" O ILE F 283 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE F 285 " --> pdb=" O ALA F 331 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AC8, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.723A pdb=" N ILE K 67 " --> pdb=" O MET K 78 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N MET K 78 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N GLU K 69 " --> pdb=" O CYS K 76 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N CYS K 76 " --> pdb=" O GLU K 69 " (cutoff:3.500A) 1614 hydrogen bonds defined for protein. 4653 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: 6.51 Time building geometry restraints manager: 3.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11006 1.35 - 1.48: 7168 1.48 - 1.60: 14757 1.60 - 1.73: 12 1.73 - 1.86: 290 Bond restraints: 33233 Sorted by residual: bond pdb=" C ALA B 278 " pdb=" N PRO B 279 " ideal model delta sigma weight residual 1.334 1.383 -0.049 2.34e-02 1.83e+03 4.39e+00 bond pdb=" C SER M 15 " pdb=" N PRO M 16 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.30e-02 5.92e+03 3.69e+00 bond pdb=" CA ASN C 50 " pdb=" C ASN C 50 " ideal model delta sigma weight residual 1.522 1.498 0.025 1.40e-02 5.10e+03 3.14e+00 bond pdb=" C LEU E 151 " pdb=" N PRO E 152 " ideal model delta sigma weight residual 1.335 1.355 -0.021 1.19e-02 7.06e+03 3.00e+00 bond pdb=" CG1 ILE B 284 " pdb=" CD1 ILE B 284 " ideal model delta sigma weight residual 1.513 1.450 0.063 3.90e-02 6.57e+02 2.58e+00 ... (remaining 33228 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 43788 2.44 - 4.87: 980 4.87 - 7.31: 131 7.31 - 9.75: 37 9.75 - 12.18: 6 Bond angle restraints: 44942 Sorted by residual: angle pdb=" N PRO c 23 " pdb=" CA PRO c 23 " pdb=" CB PRO c 23 " ideal model delta sigma weight residual 103.00 110.37 -7.37 1.10e+00 8.26e-01 4.49e+01 angle pdb=" N GLN F 436 " pdb=" CA GLN F 436 " pdb=" C GLN F 436 " ideal model delta sigma weight residual 114.56 107.75 6.81 1.27e+00 6.20e-01 2.87e+01 angle pdb=" N GLN B 181 " pdb=" CA GLN B 181 " pdb=" C GLN B 181 " ideal model delta sigma weight residual 114.56 108.24 6.32 1.27e+00 6.20e-01 2.48e+01 angle pdb=" C ASP L 226 " pdb=" CA ASP L 226 " pdb=" CB ASP L 226 " ideal model delta sigma weight residual 117.23 110.87 6.36 1.36e+00 5.41e-01 2.19e+01 angle pdb=" N MET B 412 " pdb=" CA MET B 412 " pdb=" C MET B 412 " ideal model delta sigma weight residual 113.16 107.45 5.71 1.24e+00 6.50e-01 2.12e+01 ... (remaining 44937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.85: 19541 32.85 - 65.69: 840 65.69 - 98.54: 70 98.54 - 131.39: 1 131.39 - 164.23: 1 Dihedral angle restraints: 20453 sinusoidal: 8294 harmonic: 12159 Sorted by residual: dihedral pdb=" CA HIS C 90 " pdb=" C HIS C 90 " pdb=" N PRO C 91 " pdb=" CA PRO C 91 " ideal model delta harmonic sigma weight residual -180.00 -124.49 -55.51 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA LEU F 86 " pdb=" C LEU F 86 " pdb=" N PRO F 87 " pdb=" CA PRO F 87 " ideal model delta harmonic sigma weight residual 180.00 130.64 49.36 0 5.00e+00 4.00e-02 9.75e+01 dihedral pdb=" CA THR B 53 " pdb=" C THR B 53 " pdb=" N PRO B 54 " pdb=" CA PRO B 54 " ideal model delta harmonic sigma weight residual 180.00 133.73 46.27 0 5.00e+00 4.00e-02 8.56e+01 ... (remaining 20450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 4006 0.053 - 0.106: 942 0.106 - 0.158: 181 0.158 - 0.211: 13 0.211 - 0.264: 5 Chirality restraints: 5147 Sorted by residual: chirality pdb=" CG LEU I 92 " pdb=" CB LEU I 92 " pdb=" CD1 LEU I 92 " pdb=" CD2 LEU I 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CB ILE B 122 " pdb=" CA ILE B 122 " pdb=" CG1 ILE B 122 " pdb=" CG2 ILE B 122 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA ASP C 132 " pdb=" N ASP C 132 " pdb=" C ASP C 132 " pdb=" CB ASP C 132 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 5144 not shown) Planarity restraints: 5816 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 90 " 0.066 5.00e-02 4.00e+02 1.00e-01 1.60e+01 pdb=" N PRO C 91 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO C 91 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 91 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 24 " -0.020 2.00e-02 2.50e+03 2.55e-02 1.30e+01 pdb=" CG TYR H 24 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR H 24 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR H 24 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR H 24 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR H 24 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 24 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 24 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 80 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.37e+00 pdb=" C MET C 80 " 0.053 2.00e-02 2.50e+03 pdb=" O MET C 80 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP C 81 " -0.018 2.00e-02 2.50e+03 ... (remaining 5813 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 379 2.57 - 3.15: 28717 3.15 - 3.73: 53926 3.73 - 4.32: 71495 4.32 - 4.90: 116730 Nonbonded interactions: 271247 Sorted by model distance: nonbonded pdb=" OG1 THR F 234 " pdb="MG MG F 502 " model vdw 1.985 2.170 nonbonded pdb=" O3G ATP F 501 " pdb="MG MG F 502 " model vdw 1.990 2.170 nonbonded pdb=" OG1 THR E 181 " pdb="MG MG E 502 " model vdw 2.052 2.170 nonbonded pdb=" O ALA I 27 " pdb=" ND1 HIS I 30 " model vdw 2.061 3.120 nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 501 " model vdw 2.061 2.230 ... (remaining 271242 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 2.560 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: 0.020 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.500 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33237 Z= 0.188 Angle : 0.884 12.185 44946 Z= 0.486 Chirality : 0.047 0.264 5147 Planarity : 0.006 0.100 5816 Dihedral : 17.400 164.232 12589 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.36 % Allowed : 7.11 % Favored : 92.53 % Rotamer: Outliers : 3.57 % Allowed : 23.79 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.05 % 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: -0.44 (0.13), residues: 4134 helix: 0.64 (0.12), residues: 1776 sheet: -0.27 (0.18), residues: 718 loop : -1.28 (0.16), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 53 TYR 0.060 0.002 TYR H 24 PHE 0.030 0.002 PHE D 299 TRP 0.015 0.002 TRP A 78 HIS 0.014 0.001 HIS M 120 Details of bonding type rmsd covalent geometry : bond 0.00391 (33233) covalent geometry : angle 0.88362 (44942) SS BOND : bond 0.00523 ( 2) SS BOND : angle 3.32437 ( 4) hydrogen bonds : bond 0.12288 ( 1614) hydrogen bonds : angle 6.33245 ( 4653) metal coordination : bond 0.00368 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 600 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ARG cc_start: 0.8486 (OUTLIER) cc_final: 0.8085 (tmm-80) REVERT: A 299 MET cc_start: 0.8676 (tmm) cc_final: 0.8436 (tmm) REVERT: C 23 TYR cc_start: 0.3787 (OUTLIER) cc_final: 0.2115 (t80) REVERT: G 80 MET cc_start: 0.5479 (tpp) cc_final: 0.4485 (tpt) REVERT: H 42 ASN cc_start: 0.5175 (OUTLIER) cc_final: 0.4812 (p0) REVERT: I 61 PHE cc_start: 0.3886 (OUTLIER) cc_final: 0.3169 (m-80) REVERT: I 72 MET cc_start: 0.2973 (mmt) cc_final: 0.2545 (mmt) REVERT: I 174 MET cc_start: 0.6835 (ppp) cc_final: 0.5931 (ptp) REVERT: L 55 GLU cc_start: 0.4726 (pm20) cc_final: 0.4184 (pm20) REVERT: L 83 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7119 (pp) REVERT: L 140 MET cc_start: 0.6045 (mtp) cc_final: 0.5091 (mtm) REVERT: c 46 ARG cc_start: 0.5922 (mtm180) cc_final: 0.5220 (tpp80) REVERT: c 52 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8754 (mp0) REVERT: c 64 ASP cc_start: 0.8864 (m-30) cc_final: 0.8565 (t0) REVERT: c 67 VAL cc_start: 0.8609 (OUTLIER) cc_final: 0.8179 (m) REVERT: c 101 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8326 (pp30) REVERT: c 121 TRP cc_start: 0.8396 (p-90) cc_final: 0.8148 (p-90) REVERT: c 139 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7659 (mtp180) REVERT: c 154 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8433 (tptt) REVERT: c 164 ASN cc_start: 0.8940 (OUTLIER) cc_final: 0.8066 (t0) REVERT: c 167 MET cc_start: 0.7692 (mmm) cc_final: 0.7223 (mmm) REVERT: c 216 MET cc_start: 0.9102 (mtp) cc_final: 0.8796 (ttt) REVERT: c 223 LYS cc_start: 0.8698 (mtmt) cc_final: 0.8401 (ptmt) REVERT: c 234 TYR cc_start: 0.8953 (m-80) cc_final: 0.8055 (p90) REVERT: c 248 MET cc_start: 0.9323 (mmm) cc_final: 0.8943 (mmm) REVERT: B 74 MET cc_start: 0.6676 (mmm) cc_final: 0.6239 (mmm) REVERT: B 411 ARG cc_start: 0.6905 (mtm-85) cc_final: 0.5914 (mmp-170) REVERT: D 45 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8125 (tttt) REVERT: D 127 ASN cc_start: 0.8277 (OUTLIER) cc_final: 0.8017 (t0) REVERT: D 188 PHE cc_start: 0.6630 (OUTLIER) cc_final: 0.6299 (p90) REVERT: D 351 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7702 (tppt) REVERT: D 395 LEU cc_start: 0.8496 (mt) cc_final: 0.7888 (tp) REVERT: E 48 LYS cc_start: 0.9104 (tttm) cc_final: 0.8511 (tptt) REVERT: E 214 LEU cc_start: 0.9063 (tp) cc_final: 0.8833 (tp) REVERT: E 277 MET cc_start: 0.8547 (mmt) cc_final: 0.8220 (mmt) REVERT: F 81 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8895 (tppp) REVERT: F 83 ASN cc_start: 0.9068 (t0) cc_final: 0.8619 (t0) REVERT: F 86 LEU cc_start: 0.8769 (pt) cc_final: 0.8096 (pp) REVERT: F 182 THR cc_start: 0.9266 (p) cc_final: 0.8947 (t) REVERT: F 259 MET cc_start: 0.8270 (ttt) cc_final: 0.8062 (ttt) REVERT: F 263 ASP cc_start: 0.7323 (t0) cc_final: 0.6929 (t0) REVERT: F 310 MET cc_start: 0.9339 (tmm) cc_final: 0.8912 (tmm) REVERT: F 405 MET cc_start: 0.8962 (mmm) cc_final: 0.8403 (mmt) outliers start: 124 outliers final: 88 residues processed: 686 average time/residue: 0.2051 time to fit residues: 226.9715 Evaluate side-chains 627 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 525 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 266 ASP Chi-restraints excluded: chain C residue 394 ASP Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain c residue 52 GLU Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 67 VAL Chi-restraints excluded: chain c residue 101 GLN Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 128 ASN Chi-restraints excluded: chain c residue 139 ARG Chi-restraints excluded: chain c residue 154 LYS Chi-restraints excluded: chain c residue 164 ASN Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 176 GLN Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 188 SER Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 259 VAL Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain c residue 300 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 222 HIS Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain E residue 50 LEU Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 92 ASN Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 315 ASN Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 213 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 7.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN J 15 HIS J 146 GLN L 53 GLN ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 176 GLN c 254 ASN B 81 ASN B 242 GLN D 294 ASN ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 63 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 HIS F 323 ASN F 428 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.111862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.085877 restraints weight = 106283.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088307 restraints weight = 50083.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089769 restraints weight = 29764.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090701 restraints weight = 20759.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.091283 restraints weight = 16206.900| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33237 Z= 0.190 Angle : 0.743 11.949 44946 Z= 0.383 Chirality : 0.046 0.295 5147 Planarity : 0.005 0.079 5816 Dihedral : 10.272 172.318 4855 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.89 % Favored : 92.74 % Rotamer: Outliers : 5.18 % Allowed : 21.23 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.05 % 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: -0.26 (0.13), residues: 4134 helix: 0.86 (0.12), residues: 1803 sheet: -0.29 (0.19), residues: 717 loop : -1.24 (0.16), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 346 TYR 0.024 0.002 TYR I 121 PHE 0.020 0.002 PHE C 283 TRP 0.010 0.001 TRP A 78 HIS 0.014 0.001 HIS E 323 Details of bonding type rmsd covalent geometry : bond 0.00424 (33233) covalent geometry : angle 0.74327 (44942) SS BOND : bond 0.00397 ( 2) SS BOND : angle 2.01161 ( 4) hydrogen bonds : bond 0.04960 ( 1614) hydrogen bonds : angle 5.55584 ( 4653) metal coordination : bond 0.00787 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 565 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: A 231 ASN cc_start: 0.8401 (OUTLIER) cc_final: 0.8050 (m110) REVERT: A 241 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8084 (mm) REVERT: A 255 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7872 (ttp-110) REVERT: A 256 MET cc_start: 0.8649 (mtt) cc_final: 0.8383 (mtp) REVERT: A 299 MET cc_start: 0.8999 (tmm) cc_final: 0.8581 (tmm) REVERT: A 390 THR cc_start: 0.9470 (m) cc_final: 0.9269 (m) REVERT: A 418 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8690 (pttt) REVERT: C 23 TYR cc_start: 0.3479 (OUTLIER) cc_final: 0.1945 (t80) REVERT: C 250 GLU cc_start: 0.8934 (pt0) cc_final: 0.8613 (pp20) REVERT: C 314 LYS cc_start: 0.8923 (mttp) cc_final: 0.8592 (ptpp) REVERT: C 391 MET cc_start: 0.8223 (mmt) cc_final: 0.7592 (tpp) REVERT: C 405 TRP cc_start: 0.5974 (OUTLIER) cc_final: 0.5202 (m100) REVERT: G 78 CYS cc_start: 0.7568 (t) cc_final: 0.7067 (t) REVERT: G 83 MET cc_start: 0.7532 (mmp) cc_final: 0.7031 (mmm) REVERT: H 42 ASN cc_start: 0.7232 (OUTLIER) cc_final: 0.6817 (p0) REVERT: H 112 GLN cc_start: 0.8752 (pt0) cc_final: 0.8512 (pt0) REVERT: I 53 HIS cc_start: 0.8345 (t70) cc_final: 0.8112 (t-170) REVERT: I 61 PHE cc_start: 0.3750 (OUTLIER) cc_final: 0.3381 (m-80) REVERT: L 128 TYR cc_start: 0.6770 (OUTLIER) cc_final: 0.5987 (t80) REVERT: L 140 MET cc_start: 0.6360 (mtp) cc_final: 0.5596 (mtm) REVERT: M 129 ARG cc_start: 0.8148 (ptt90) cc_final: 0.6856 (ptm-80) REVERT: M 183 GLU cc_start: 0.9060 (tt0) cc_final: 0.8371 (mp0) REVERT: c 46 ARG cc_start: 0.5680 (mtm180) cc_final: 0.5428 (tpp80) REVERT: c 134 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: c 164 ASN cc_start: 0.8593 (m-40) cc_final: 0.8041 (t0) REVERT: c 167 MET cc_start: 0.7323 (mmm) cc_final: 0.6967 (mmm) REVERT: c 234 TYR cc_start: 0.8910 (m-80) cc_final: 0.8041 (p90) REVERT: B 220 LYS cc_start: 0.6753 (OUTLIER) cc_final: 0.6440 (mtpt) REVERT: B 309 MET cc_start: 0.8007 (mmm) cc_final: 0.7768 (mmm) REVERT: B 364 ILE cc_start: 0.9484 (OUTLIER) cc_final: 0.9274 (mp) REVERT: B 394 ASP cc_start: 0.8637 (m-30) cc_final: 0.8384 (m-30) REVERT: B 411 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.6147 (tpt170) REVERT: B 412 MET cc_start: 0.9138 (tpt) cc_final: 0.8925 (tpt) REVERT: D 45 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8017 (tttt) REVERT: D 188 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7064 (p90) REVERT: D 291 GLU cc_start: 0.7947 (tp30) cc_final: 0.7601 (tp30) REVERT: D 296 MET cc_start: 0.8940 (mtp) cc_final: 0.8695 (mtp) REVERT: D 309 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8871 (mtp) REVERT: D 340 GLN cc_start: 0.8455 (tp40) cc_final: 0.7614 (tp-100) REVERT: D 395 LEU cc_start: 0.8696 (mt) cc_final: 0.7883 (tp) REVERT: E 48 LYS cc_start: 0.9096 (tttm) cc_final: 0.8370 (tptt) REVERT: E 59 GLU cc_start: 0.7827 (tp30) cc_final: 0.7508 (tp30) REVERT: E 214 LEU cc_start: 0.9121 (tp) cc_final: 0.8918 (tp) REVERT: E 264 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7866 (ttm) REVERT: E 277 MET cc_start: 0.8698 (mmt) cc_final: 0.8456 (mmt) REVERT: F 81 LYS cc_start: 0.9258 (mmmt) cc_final: 0.9048 (tppp) REVERT: F 83 ASN cc_start: 0.9201 (t0) cc_final: 0.8112 (t0) REVERT: F 182 THR cc_start: 0.9226 (p) cc_final: 0.8873 (t) REVERT: F 373 MET cc_start: 0.8034 (OUTLIER) cc_final: 0.7820 (ttm) REVERT: F 405 MET cc_start: 0.9403 (mmm) cc_final: 0.8737 (mmt) outliers start: 180 outliers final: 105 residues processed: 692 average time/residue: 0.2120 time to fit residues: 234.5301 Evaluate side-chains 628 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 506 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 231 ASN Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 128 TYR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain c residue 27 THR Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 101 GLN Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 128 ASN Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 139 ARG Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 188 SER Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 259 VAL Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 334 ILE Chi-restraints excluded: chain B residue 364 ILE Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 222 HIS Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 41 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 177 optimal weight: 30.0000 chunk 320 optimal weight: 0.7980 chunk 404 optimal weight: 0.9980 chunk 8 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 379 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 231 ASN A 296 GLN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 100 ASN ** H 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN I 123 GLN J 15 HIS L 60 GLN M 170 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.111819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085726 restraints weight = 105749.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088125 restraints weight = 49963.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.089588 restraints weight = 29896.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090510 restraints weight = 20962.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.091088 restraints weight = 16433.918| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33237 Z= 0.173 Angle : 0.712 11.207 44946 Z= 0.364 Chirality : 0.045 0.215 5147 Planarity : 0.005 0.090 5816 Dihedral : 9.744 176.488 4793 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.09 % Favored : 92.57 % Rotamer: Outliers : 5.61 % Allowed : 21.29 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.05 % 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: -0.22 (0.13), residues: 4134 helix: 0.91 (0.12), residues: 1812 sheet: -0.48 (0.18), residues: 737 loop : -1.15 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 346 TYR 0.022 0.002 TYR I 121 PHE 0.020 0.002 PHE C 283 TRP 0.012 0.001 TRP c 121 HIS 0.010 0.001 HIS M 120 Details of bonding type rmsd covalent geometry : bond 0.00388 (33233) covalent geometry : angle 0.71228 (44942) SS BOND : bond 0.00319 ( 2) SS BOND : angle 1.55024 ( 4) hydrogen bonds : bond 0.04419 ( 1614) hydrogen bonds : angle 5.31230 ( 4653) metal coordination : bond 0.00745 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 756 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 561 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7852 (tm-30) REVERT: A 241 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8140 (mm) REVERT: A 299 MET cc_start: 0.8806 (tmm) cc_final: 0.8209 (tmm) REVERT: A 303 ILE cc_start: 0.9427 (mt) cc_final: 0.9014 (mt) REVERT: A 418 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8656 (pttt) REVERT: C 23 TYR cc_start: 0.3391 (OUTLIER) cc_final: 0.1751 (t80) REVERT: C 161 ILE cc_start: 0.9296 (tp) cc_final: 0.9072 (tp) REVERT: C 162 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8859 (mtpp) REVERT: C 250 GLU cc_start: 0.8878 (pt0) cc_final: 0.8591 (pp20) REVERT: C 405 TRP cc_start: 0.6047 (OUTLIER) cc_final: 0.5279 (m100) REVERT: G 80 MET cc_start: 0.6549 (tpt) cc_final: 0.6081 (tpt) REVERT: G 83 MET cc_start: 0.7573 (mmp) cc_final: 0.6952 (mmm) REVERT: H 42 ASN cc_start: 0.7250 (OUTLIER) cc_final: 0.6800 (p0) REVERT: H 112 GLN cc_start: 0.8760 (pt0) cc_final: 0.8482 (pt0) REVERT: H 118 MET cc_start: 0.8393 (ttm) cc_final: 0.8026 (tpp) REVERT: I 61 PHE cc_start: 0.3659 (OUTLIER) cc_final: 0.3326 (m-80) REVERT: I 174 MET cc_start: 0.8236 (ptp) cc_final: 0.7252 (ppp) REVERT: J 118 TYR cc_start: 0.7346 (t80) cc_final: 0.7133 (t80) REVERT: L 128 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.6280 (t80) REVERT: L 140 MET cc_start: 0.6441 (mtp) cc_final: 0.5641 (mtm) REVERT: M 50 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7046 (pm20) REVERT: M 62 SER cc_start: 0.4844 (OUTLIER) cc_final: 0.4575 (t) REVERT: M 129 ARG cc_start: 0.8444 (ptt90) cc_final: 0.8081 (ptt90) REVERT: c 101 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8620 (pp30) REVERT: c 134 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7622 (tm-30) REVERT: c 164 ASN cc_start: 0.8499 (m-40) cc_final: 0.8134 (t0) REVERT: c 167 MET cc_start: 0.7114 (mmm) cc_final: 0.6849 (mmm) REVERT: c 234 TYR cc_start: 0.8902 (m-80) cc_final: 0.8075 (p90) REVERT: B 74 MET cc_start: 0.6560 (mmm) cc_final: 0.6159 (mmm) REVERT: B 101 ASP cc_start: 0.8793 (t0) cc_final: 0.8487 (t0) REVERT: B 220 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6148 (mtpt) REVERT: B 309 MET cc_start: 0.7987 (mmm) cc_final: 0.7678 (mmm) REVERT: B 401 GLU cc_start: 0.8303 (tp30) cc_final: 0.7514 (tp30) REVERT: B 412 MET cc_start: 0.9030 (tpt) cc_final: 0.8623 (tpt) REVERT: D 45 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8031 (tttt) REVERT: D 188 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.6814 (p90) REVERT: D 309 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8810 (mtp) REVERT: D 340 GLN cc_start: 0.8368 (tp40) cc_final: 0.7813 (tp-100) REVERT: D 351 LYS cc_start: 0.8414 (mtmm) cc_final: 0.7923 (tppt) REVERT: D 395 LEU cc_start: 0.8633 (mt) cc_final: 0.7929 (tp) REVERT: E 48 LYS cc_start: 0.9039 (tttm) cc_final: 0.8354 (tptt) REVERT: E 59 GLU cc_start: 0.7824 (tp30) cc_final: 0.7588 (tp30) REVERT: E 106 THR cc_start: 0.8970 (OUTLIER) cc_final: 0.8564 (t) REVERT: E 264 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7814 (ttm) REVERT: E 349 GLU cc_start: 0.8269 (mm-30) cc_final: 0.8029 (mm-30) REVERT: F 86 LEU cc_start: 0.8838 (pt) cc_final: 0.8224 (pp) REVERT: F 150 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8640 (mp) REVERT: F 182 THR cc_start: 0.9089 (p) cc_final: 0.8746 (t) REVERT: F 310 MET cc_start: 0.9350 (tmm) cc_final: 0.9133 (tmm) REVERT: F 405 MET cc_start: 0.9323 (mmm) cc_final: 0.8691 (mmt) outliers start: 195 outliers final: 122 residues processed: 704 average time/residue: 0.2055 time to fit residues: 235.1067 Evaluate side-chains 637 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 497 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 27 TYR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 128 TYR Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 188 ASP Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 101 GLN Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 126 ASP Chi-restraints excluded: chain c residue 128 ASN Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 170 LEU Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 188 SER Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain B residue 220 LYS Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 309 MET Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 233 ASP Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 335 VAL Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 117 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 296 optimal weight: 7.9990 chunk 260 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 250 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 342 optimal weight: 3.9990 chunk 225 optimal weight: 0.0670 chunk 76 optimal weight: 0.7980 chunk 133 optimal weight: 20.0000 chunk 87 optimal weight: 0.4980 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN H 119 GLN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 254 ASN D 127 ASN D 295 GLN E 63 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN F 323 ASN F 325 GLN F 428 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.113661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.087882 restraints weight = 105310.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.090322 restraints weight = 49326.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.091803 restraints weight = 29392.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.092737 restraints weight = 20494.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.093314 restraints weight = 16017.838| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33237 Z= 0.134 Angle : 0.689 10.364 44946 Z= 0.350 Chirality : 0.045 0.232 5147 Planarity : 0.005 0.084 5816 Dihedral : 9.357 178.305 4779 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.58 % Favored : 93.11 % Rotamer: Outliers : 5.15 % Allowed : 22.21 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.03 % 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: -0.08 (0.13), residues: 4134 helix: 1.07 (0.12), residues: 1797 sheet: -0.50 (0.19), residues: 730 loop : -1.07 (0.16), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG M 169 TYR 0.022 0.001 TYR H 24 PHE 0.025 0.002 PHE I 124 TRP 0.013 0.001 TRP c 121 HIS 0.010 0.001 HIS M 120 Details of bonding type rmsd covalent geometry : bond 0.00295 (33233) covalent geometry : angle 0.68915 (44942) SS BOND : bond 0.00429 ( 2) SS BOND : angle 1.38161 ( 4) hydrogen bonds : bond 0.04053 ( 1614) hydrogen bonds : angle 5.07102 ( 4653) metal coordination : bond 0.00174 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 583 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: A 299 MET cc_start: 0.8826 (tmm) cc_final: 0.8381 (tmm) REVERT: A 362 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8070 (mtp) REVERT: A 418 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8705 (pttt) REVERT: C 23 TYR cc_start: 0.3382 (OUTLIER) cc_final: 0.1747 (t80) REVERT: C 104 ASP cc_start: 0.8049 (t0) cc_final: 0.7662 (p0) REVERT: C 112 CYS cc_start: 0.7567 (p) cc_final: 0.7073 (p) REVERT: C 161 ILE cc_start: 0.9273 (tp) cc_final: 0.9062 (tp) REVERT: C 196 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8744 (mttt) REVERT: C 218 GLU cc_start: 0.7597 (mt-10) cc_final: 0.7392 (mt-10) REVERT: C 250 GLU cc_start: 0.8863 (pt0) cc_final: 0.8523 (pp20) REVERT: C 270 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7693 (mp10) REVERT: C 391 MET cc_start: 0.7900 (mmt) cc_final: 0.7249 (tpp) REVERT: C 405 TRP cc_start: 0.6171 (OUTLIER) cc_final: 0.5604 (t60) REVERT: G 78 CYS cc_start: 0.7602 (t) cc_final: 0.6144 (t) REVERT: G 80 MET cc_start: 0.6369 (tpt) cc_final: 0.5991 (tpt) REVERT: G 83 MET cc_start: 0.7499 (mmp) cc_final: 0.6798 (mmm) REVERT: G 138 MET cc_start: 0.8049 (tpt) cc_final: 0.7479 (tpt) REVERT: G 236 ASP cc_start: 0.7026 (t0) cc_final: 0.6769 (m-30) REVERT: H 95 GLN cc_start: 0.6759 (mt0) cc_final: 0.6539 (mt0) REVERT: H 112 GLN cc_start: 0.8757 (pt0) cc_final: 0.8481 (pt0) REVERT: H 118 MET cc_start: 0.8457 (ttm) cc_final: 0.8106 (tpp) REVERT: I 53 HIS cc_start: 0.8215 (t-170) cc_final: 0.7960 (t-170) REVERT: I 61 PHE cc_start: 0.3726 (OUTLIER) cc_final: 0.3417 (m-80) REVERT: I 116 ASP cc_start: 0.8748 (m-30) cc_final: 0.8507 (m-30) REVERT: I 174 MET cc_start: 0.8171 (ptp) cc_final: 0.7170 (ppp) REVERT: I 223 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7342 (p) REVERT: J 122 ASN cc_start: 0.8799 (t0) cc_final: 0.8503 (m-40) REVERT: J 127 PHE cc_start: 0.7737 (m-80) cc_final: 0.7440 (m-80) REVERT: L 140 MET cc_start: 0.6463 (mtp) cc_final: 0.5804 (mtm) REVERT: M 62 SER cc_start: 0.4658 (OUTLIER) cc_final: 0.4417 (t) REVERT: M 124 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6242 (mm) REVERT: c 101 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8532 (pp30) REVERT: c 118 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7845 (p90) REVERT: c 134 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: c 164 ASN cc_start: 0.8457 (m-40) cc_final: 0.8038 (t0) REVERT: c 167 MET cc_start: 0.7138 (mmm) cc_final: 0.6921 (mmm) REVERT: c 175 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.5521 (ptm-80) REVERT: c 234 TYR cc_start: 0.8832 (m-80) cc_final: 0.8008 (p90) REVERT: B 74 MET cc_start: 0.6577 (mmm) cc_final: 0.6214 (mmm) REVERT: B 101 ASP cc_start: 0.8771 (t0) cc_final: 0.8475 (t0) REVERT: B 200 SER cc_start: 0.9171 (m) cc_final: 0.8619 (p) REVERT: B 401 GLU cc_start: 0.8179 (tp30) cc_final: 0.7273 (tp30) REVERT: B 412 MET cc_start: 0.8884 (tpt) cc_final: 0.8587 (tpt) REVERT: D 45 LYS cc_start: 0.9045 (OUTLIER) cc_final: 0.8075 (tttt) REVERT: D 188 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.7049 (p90) REVERT: D 340 GLN cc_start: 0.8271 (tp40) cc_final: 0.8010 (tp-100) REVERT: D 351 LYS cc_start: 0.8352 (mtmm) cc_final: 0.7763 (tppt) REVERT: D 392 TYR cc_start: 0.7079 (m-80) cc_final: 0.5428 (m-80) REVERT: D 395 LEU cc_start: 0.8539 (mt) cc_final: 0.7847 (tp) REVERT: D 400 GLU cc_start: 0.8424 (tp30) cc_final: 0.7685 (tp30) REVERT: E 48 LYS cc_start: 0.8988 (tttm) cc_final: 0.8301 (tptt) REVERT: E 264 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7734 (ttt) REVERT: E 352 MET cc_start: 0.8370 (mmm) cc_final: 0.8120 (mmm) REVERT: F 86 LEU cc_start: 0.8859 (pt) cc_final: 0.8213 (pp) REVERT: F 150 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8599 (mp) REVERT: F 182 THR cc_start: 0.9060 (p) cc_final: 0.8714 (t) REVERT: F 405 MET cc_start: 0.9320 (mmm) cc_final: 0.8711 (mmt) outliers start: 179 outliers final: 101 residues processed: 714 average time/residue: 0.2132 time to fit residues: 246.2623 Evaluate side-chains 615 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 496 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 362 MET Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 119 GLN Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 33 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 101 GLN Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 188 SER Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 264 MET Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 324 THR Chi-restraints excluded: chain F residue 349 ASP Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 166 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 125 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 372 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 309 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 262 optimal weight: 0.2980 chunk 142 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN H 119 GLN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 GLN ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 92 GLN D 295 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN F 417 HIS K 155 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.112467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087343 restraints weight = 105508.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.089301 restraints weight = 52343.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090272 restraints weight = 29011.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090591 restraints weight = 25712.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090622 restraints weight = 21728.272| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 33237 Z= 0.161 Angle : 0.699 13.043 44946 Z= 0.352 Chirality : 0.045 0.250 5147 Planarity : 0.005 0.101 5816 Dihedral : 9.078 176.034 4753 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.63 % Favored : 93.03 % Rotamer: Outliers : 5.24 % Allowed : 22.41 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.03 % 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: -0.06 (0.13), residues: 4134 helix: 1.12 (0.12), residues: 1801 sheet: -0.65 (0.18), residues: 748 loop : -1.01 (0.17), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 169 TYR 0.036 0.002 TYR L 24 PHE 0.019 0.002 PHE A 274 TRP 0.011 0.001 TRP c 111 HIS 0.028 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00367 (33233) covalent geometry : angle 0.69864 (44942) SS BOND : bond 0.00251 ( 2) SS BOND : angle 1.38785 ( 4) hydrogen bonds : bond 0.04011 ( 1614) hydrogen bonds : angle 5.04264 ( 4653) metal coordination : bond 0.00882 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 530 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: A 241 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8169 (mm) REVERT: A 299 MET cc_start: 0.8819 (tmm) cc_final: 0.8276 (tmm) REVERT: A 303 ILE cc_start: 0.9444 (mt) cc_final: 0.9037 (mt) REVERT: A 418 LYS cc_start: 0.8978 (mmmt) cc_final: 0.8748 (pttt) REVERT: C 23 TYR cc_start: 0.2674 (OUTLIER) cc_final: 0.1151 (t80) REVERT: C 112 CYS cc_start: 0.7632 (p) cc_final: 0.7125 (p) REVERT: C 162 LYS cc_start: 0.9090 (mtpp) cc_final: 0.8803 (mtpp) REVERT: C 270 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7643 (mp10) REVERT: C 385 MET cc_start: 0.8296 (ptp) cc_final: 0.7996 (ptp) REVERT: G 78 CYS cc_start: 0.7684 (t) cc_final: 0.7051 (t) REVERT: G 83 MET cc_start: 0.7574 (mmp) cc_final: 0.6847 (mmm) REVERT: H 112 GLN cc_start: 0.8776 (pt0) cc_final: 0.8510 (pt0) REVERT: I 61 PHE cc_start: 0.3646 (OUTLIER) cc_final: 0.3325 (m-80) REVERT: I 174 MET cc_start: 0.8220 (ptp) cc_final: 0.7203 (ppp) REVERT: J 122 ASN cc_start: 0.8776 (t0) cc_final: 0.8483 (m-40) REVERT: J 127 PHE cc_start: 0.7733 (m-80) cc_final: 0.7501 (m-80) REVERT: L 140 MET cc_start: 0.6411 (mtp) cc_final: 0.5596 (mtm) REVERT: L 166 GLN cc_start: 0.7951 (tp40) cc_final: 0.7499 (mt0) REVERT: M 62 SER cc_start: 0.4654 (OUTLIER) cc_final: 0.4400 (t) REVERT: M 124 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.6440 (mm) REVERT: c 92 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: c 164 ASN cc_start: 0.8893 (m-40) cc_final: 0.8227 (t0) REVERT: c 167 MET cc_start: 0.7522 (mmm) cc_final: 0.7135 (mmm) REVERT: c 175 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.5524 (ptm-80) REVERT: c 234 TYR cc_start: 0.8969 (m-80) cc_final: 0.8056 (p90) REVERT: B 74 MET cc_start: 0.6619 (mmm) cc_final: 0.6218 (mmm) REVERT: B 101 ASP cc_start: 0.9040 (t0) cc_final: 0.8795 (t0) REVERT: B 401 GLU cc_start: 0.8172 (tp30) cc_final: 0.7501 (tp30) REVERT: B 412 MET cc_start: 0.8798 (tpt) cc_final: 0.8540 (tpt) REVERT: D 45 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8008 (tttt) REVERT: D 188 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.7096 (p90) REVERT: D 291 GLU cc_start: 0.8054 (tp30) cc_final: 0.7476 (tp30) REVERT: D 340 GLN cc_start: 0.8357 (tp40) cc_final: 0.8098 (tp-100) REVERT: D 351 LYS cc_start: 0.8440 (mtmm) cc_final: 0.7859 (tppt) REVERT: D 392 TYR cc_start: 0.7258 (m-80) cc_final: 0.6948 (m-80) REVERT: E 48 LYS cc_start: 0.9055 (tttm) cc_final: 0.8323 (tptt) REVERT: E 161 ARG cc_start: 0.8490 (mtm180) cc_final: 0.7966 (mtp85) REVERT: E 267 PHE cc_start: 0.7170 (OUTLIER) cc_final: 0.6192 (m-80) REVERT: E 349 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7757 (mm-30) REVERT: F 86 LEU cc_start: 0.8851 (pt) cc_final: 0.8227 (pp) REVERT: F 182 THR cc_start: 0.9069 (p) cc_final: 0.8713 (t) REVERT: F 258 GLN cc_start: 0.7502 (tt0) cc_final: 0.6864 (tt0) REVERT: F 263 ASP cc_start: 0.6885 (OUTLIER) cc_final: 0.6408 (t0) REVERT: F 310 MET cc_start: 0.9288 (tmm) cc_final: 0.9053 (tmm) REVERT: F 405 MET cc_start: 0.9333 (mmm) cc_final: 0.8713 (mmt) REVERT: K 59 MET cc_start: 0.7733 (mmm) cc_final: 0.7511 (tmm) outliers start: 182 outliers final: 125 residues processed: 659 average time/residue: 0.2056 time to fit residues: 220.6332 Evaluate side-chains 628 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 490 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain H residue 42 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 19 ARG Chi-restraints excluded: chain M residue 62 SER Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 92 GLN Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 188 SER Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 189 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 384 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 chunk 225 optimal weight: 0.9990 chunk 136 optimal weight: 30.0000 chunk 29 optimal weight: 1.9990 chunk 213 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 388 optimal weight: 0.9990 chunk 382 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 224 ASN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 128 ASN c 221 HIS B 154 HIS B 242 GLN D 127 ASN D 295 GLN E 32 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 307 GLN F 323 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.113193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.087529 restraints weight = 105440.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.089944 restraints weight = 49451.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.091411 restraints weight = 29480.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.092337 restraints weight = 20533.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.092920 restraints weight = 16043.678| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33237 Z= 0.144 Angle : 0.701 15.684 44946 Z= 0.351 Chirality : 0.045 0.237 5147 Planarity : 0.005 0.102 5816 Dihedral : 8.863 172.044 4748 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.46 % Favored : 93.20 % Rotamer: Outliers : 4.86 % Allowed : 23.50 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.03 % 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: -0.01 (0.13), residues: 4134 helix: 1.19 (0.12), residues: 1793 sheet: -0.63 (0.18), residues: 740 loop : -1.00 (0.17), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 346 TYR 0.026 0.001 TYR L 24 PHE 0.027 0.002 PHE I 130 TRP 0.013 0.001 TRP c 121 HIS 0.016 0.001 HIS C 90 Details of bonding type rmsd covalent geometry : bond 0.00323 (33233) covalent geometry : angle 0.70118 (44942) SS BOND : bond 0.00252 ( 2) SS BOND : angle 1.73911 ( 4) hydrogen bonds : bond 0.03886 ( 1614) hydrogen bonds : angle 4.98373 ( 4653) metal coordination : bond 0.00437 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 543 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7922 (tm-30) REVERT: A 143 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8263 (p0) REVERT: A 299 MET cc_start: 0.8826 (tmm) cc_final: 0.8273 (tmm) REVERT: A 303 ILE cc_start: 0.9412 (mt) cc_final: 0.8980 (mt) REVERT: A 418 LYS cc_start: 0.8907 (mmmt) cc_final: 0.8702 (pttt) REVERT: C 23 TYR cc_start: 0.3228 (OUTLIER) cc_final: 0.1594 (t80) REVERT: C 112 CYS cc_start: 0.7385 (p) cc_final: 0.6916 (p) REVERT: C 162 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8710 (mtpp) REVERT: C 211 PHE cc_start: 0.8940 (t80) cc_final: 0.8591 (t80) REVERT: C 250 GLU cc_start: 0.8927 (pt0) cc_final: 0.8497 (pp20) REVERT: C 270 GLN cc_start: 0.7901 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: C 327 ASP cc_start: 0.7711 (m-30) cc_final: 0.7218 (m-30) REVERT: C 385 MET cc_start: 0.8208 (ptp) cc_final: 0.7988 (ptp) REVERT: C 391 MET cc_start: 0.8010 (mmt) cc_final: 0.7171 (tpp) REVERT: G 80 MET cc_start: 0.6758 (tpt) cc_final: 0.6419 (tpt) REVERT: G 83 MET cc_start: 0.7487 (mmp) cc_final: 0.6775 (mmm) REVERT: G 236 ASP cc_start: 0.7037 (t0) cc_final: 0.6755 (m-30) REVERT: H 112 GLN cc_start: 0.8740 (pt0) cc_final: 0.8454 (pt0) REVERT: H 118 MET cc_start: 0.8705 (tpp) cc_final: 0.8358 (tpp) REVERT: I 61 PHE cc_start: 0.3577 (OUTLIER) cc_final: 0.3253 (m-80) REVERT: I 100 GLN cc_start: 0.8354 (tt0) cc_final: 0.7997 (tt0) REVERT: I 115 CYS cc_start: 0.8472 (m) cc_final: 0.8182 (m) REVERT: I 174 MET cc_start: 0.8290 (ptp) cc_final: 0.7270 (ppp) REVERT: J 122 ASN cc_start: 0.8776 (t0) cc_final: 0.8152 (m-40) REVERT: J 127 PHE cc_start: 0.7671 (m-80) cc_final: 0.7378 (m-80) REVERT: J 224 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8588 (tp30) REVERT: L 24 TYR cc_start: 0.7994 (m-80) cc_final: 0.7442 (m-80) REVERT: L 140 MET cc_start: 0.6282 (mtp) cc_final: 0.5507 (mtm) REVERT: L 166 GLN cc_start: 0.7946 (tp40) cc_final: 0.7534 (mt0) REVERT: M 50 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7520 (pm20) REVERT: M 124 LEU cc_start: 0.6507 (OUTLIER) cc_final: 0.6244 (mm) REVERT: M 135 PHE cc_start: 0.7990 (p90) cc_final: 0.7538 (p90) REVERT: c 95 MET cc_start: 0.9209 (tpp) cc_final: 0.8841 (tpp) REVERT: c 164 ASN cc_start: 0.8472 (m-40) cc_final: 0.8021 (t0) REVERT: c 175 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.5571 (ptm-80) REVERT: c 234 TYR cc_start: 0.8816 (m-80) cc_final: 0.8022 (p90) REVERT: B 74 MET cc_start: 0.6580 (mmm) cc_final: 0.6196 (mmm) REVERT: B 101 ASP cc_start: 0.8766 (t0) cc_final: 0.8488 (t0) REVERT: B 309 MET cc_start: 0.7873 (mmm) cc_final: 0.7416 (mmm) REVERT: B 401 GLU cc_start: 0.8188 (tp30) cc_final: 0.7473 (tp30) REVERT: B 411 ARG cc_start: 0.7327 (mtm-85) cc_final: 0.6120 (mmp-170) REVERT: B 412 MET cc_start: 0.8771 (tpt) cc_final: 0.8553 (tpt) REVERT: D 45 LYS cc_start: 0.9098 (OUTLIER) cc_final: 0.8085 (tttt) REVERT: D 188 PHE cc_start: 0.7258 (OUTLIER) cc_final: 0.6983 (p90) REVERT: D 291 GLU cc_start: 0.7927 (tp30) cc_final: 0.7554 (tp30) REVERT: D 340 GLN cc_start: 0.8350 (tp40) cc_final: 0.8108 (tp-100) REVERT: D 351 LYS cc_start: 0.8457 (mtmm) cc_final: 0.7907 (tppt) REVERT: D 392 TYR cc_start: 0.7259 (m-80) cc_final: 0.6890 (m-80) REVERT: E 48 LYS cc_start: 0.9021 (tttm) cc_final: 0.8353 (tptt) REVERT: E 161 ARG cc_start: 0.8540 (mtm180) cc_final: 0.8139 (mtp85) REVERT: E 267 PHE cc_start: 0.6992 (OUTLIER) cc_final: 0.6133 (m-80) REVERT: E 349 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7910 (mm-30) REVERT: F 86 LEU cc_start: 0.8912 (pt) cc_final: 0.8295 (pp) REVERT: F 182 THR cc_start: 0.9017 (p) cc_final: 0.8670 (t) REVERT: F 258 GLN cc_start: 0.7416 (tt0) cc_final: 0.6667 (tt0) REVERT: F 263 ASP cc_start: 0.6841 (t0) cc_final: 0.6275 (t0) REVERT: F 405 MET cc_start: 0.9320 (mmm) cc_final: 0.8718 (mmt) REVERT: K 59 MET cc_start: 0.7731 (mmm) cc_final: 0.7531 (tmm) REVERT: K 214 ASN cc_start: 0.7967 (p0) cc_final: 0.7750 (p0) outliers start: 169 outliers final: 127 residues processed: 657 average time/residue: 0.2032 time to fit residues: 217.7230 Evaluate side-chains 645 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 507 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 50 GLU Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 188 SER Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 221 HIS Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 259 VAL Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 189 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 219 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 273 optimal weight: 5.9990 chunk 373 optimal weight: 2.9990 chunk 320 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 120 optimal weight: 30.0000 chunk 378 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 224 ASN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 65 HIS c 92 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.111738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.085647 restraints weight = 106077.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088024 restraints weight = 50594.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089487 restraints weight = 30393.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.090403 restraints weight = 21288.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.090978 restraints weight = 16709.856| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33237 Z= 0.184 Angle : 0.714 14.558 44946 Z= 0.360 Chirality : 0.045 0.222 5147 Planarity : 0.005 0.100 5816 Dihedral : 8.839 170.329 4744 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.75 % Favored : 92.94 % Rotamer: Outliers : 5.24 % Allowed : 23.45 % Favored : 71.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.03 % 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: -0.03 (0.13), residues: 4134 helix: 1.20 (0.12), residues: 1790 sheet: -0.70 (0.18), residues: 745 loop : -1.00 (0.17), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG M 169 TYR 0.034 0.002 TYR F 132 PHE 0.026 0.002 PHE I 124 TRP 0.014 0.001 TRP c 121 HIS 0.020 0.001 HIS c 221 Details of bonding type rmsd covalent geometry : bond 0.00414 (33233) covalent geometry : angle 0.71402 (44942) SS BOND : bond 0.00128 ( 2) SS BOND : angle 1.60680 ( 4) hydrogen bonds : bond 0.03941 ( 1614) hydrogen bonds : angle 5.02293 ( 4653) metal coordination : bond 0.00945 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 518 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8047 (tm-30) REVERT: A 241 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8495 (mt) REVERT: A 299 MET cc_start: 0.8928 (tmm) cc_final: 0.8262 (tmm) REVERT: A 303 ILE cc_start: 0.9424 (mt) cc_final: 0.8972 (mt) REVERT: A 418 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8737 (pttt) REVERT: C 23 TYR cc_start: 0.2930 (OUTLIER) cc_final: 0.1429 (t80) REVERT: C 112 CYS cc_start: 0.7569 (p) cc_final: 0.7133 (p) REVERT: C 162 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8814 (mtpp) REVERT: C 250 GLU cc_start: 0.9012 (pt0) cc_final: 0.8523 (pp20) REVERT: C 270 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7650 (mp10) REVERT: C 327 ASP cc_start: 0.7660 (m-30) cc_final: 0.7371 (m-30) REVERT: C 391 MET cc_start: 0.8113 (mmt) cc_final: 0.7207 (tpp) REVERT: G 83 MET cc_start: 0.7392 (mmp) cc_final: 0.6699 (mmm) REVERT: G 138 MET cc_start: 0.8700 (mmm) cc_final: 0.8152 (mmm) REVERT: H 112 GLN cc_start: 0.8751 (pt0) cc_final: 0.8456 (pt0) REVERT: H 118 MET cc_start: 0.8760 (tpp) cc_final: 0.8348 (tpp) REVERT: H 177 ARG cc_start: 0.6995 (ttt180) cc_final: 0.5549 (mmt-90) REVERT: I 61 PHE cc_start: 0.3654 (OUTLIER) cc_final: 0.3319 (m-80) REVERT: I 100 GLN cc_start: 0.8296 (tt0) cc_final: 0.7951 (tt0) REVERT: I 115 CYS cc_start: 0.8412 (m) cc_final: 0.8135 (m) REVERT: I 174 MET cc_start: 0.8266 (ptp) cc_final: 0.7242 (ppp) REVERT: J 52 LYS cc_start: 0.9020 (mtmt) cc_final: 0.8564 (ptmt) REVERT: J 122 ASN cc_start: 0.8775 (t0) cc_final: 0.8154 (m-40) REVERT: J 127 PHE cc_start: 0.7729 (m-80) cc_final: 0.7382 (m-80) REVERT: J 224 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8642 (tp30) REVERT: L 140 MET cc_start: 0.6289 (mtp) cc_final: 0.5443 (mtm) REVERT: M 135 PHE cc_start: 0.7811 (p90) cc_final: 0.7540 (p90) REVERT: c 92 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.8220 (pp30) REVERT: c 164 ASN cc_start: 0.8659 (m-40) cc_final: 0.8084 (t0) REVERT: c 167 MET cc_start: 0.6867 (mmm) cc_final: 0.6620 (mmm) REVERT: c 175 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.5513 (ptm-80) REVERT: c 234 TYR cc_start: 0.8922 (m-80) cc_final: 0.8028 (p90) REVERT: B 74 MET cc_start: 0.6590 (mmm) cc_final: 0.6180 (mmm) REVERT: B 101 ASP cc_start: 0.8844 (t0) cc_final: 0.8584 (t0) REVERT: B 202 GLU cc_start: 0.7723 (tt0) cc_final: 0.6223 (tt0) REVERT: B 242 GLN cc_start: 0.8968 (tp-100) cc_final: 0.8221 (tm-30) REVERT: B 309 MET cc_start: 0.7986 (mmm) cc_final: 0.7765 (mmm) REVERT: B 401 GLU cc_start: 0.8305 (tp30) cc_final: 0.7568 (tp30) REVERT: B 411 ARG cc_start: 0.7376 (mtm-85) cc_final: 0.6024 (mmp-170) REVERT: D 45 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8050 (tttt) REVERT: D 188 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.7062 (p90) REVERT: D 291 GLU cc_start: 0.7857 (tp30) cc_final: 0.7489 (tp30) REVERT: D 340 GLN cc_start: 0.8526 (tp40) cc_final: 0.8231 (tp-100) REVERT: D 392 TYR cc_start: 0.7382 (m-80) cc_final: 0.6536 (m-80) REVERT: E 122 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8229 (mtp) REVERT: E 161 ARG cc_start: 0.8611 (mtm180) cc_final: 0.7703 (mtm180) REVERT: E 267 PHE cc_start: 0.7020 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: E 349 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8033 (mm-30) REVERT: E 383 LYS cc_start: 0.8586 (tmtt) cc_final: 0.8371 (tptt) REVERT: F 182 THR cc_start: 0.9079 (p) cc_final: 0.8717 (t) REVERT: F 258 GLN cc_start: 0.7413 (tt0) cc_final: 0.6570 (tt0) REVERT: F 263 ASP cc_start: 0.7022 (OUTLIER) cc_final: 0.6452 (t0) REVERT: F 373 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7704 (ttm) REVERT: F 405 MET cc_start: 0.9362 (mmm) cc_final: 0.8730 (mmt) REVERT: K 214 ASN cc_start: 0.7987 (p0) cc_final: 0.7775 (p0) outliers start: 182 outliers final: 139 residues processed: 642 average time/residue: 0.1880 time to fit residues: 196.5762 Evaluate side-chains 650 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 498 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 256 MET Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 62 ILE Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 92 GLN Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 231 LEU Chi-restraints excluded: chain c residue 259 VAL Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain E residue 53 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 122 MET Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 166 ASP Chi-restraints excluded: chain K residue 189 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 220 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 265 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 198 optimal weight: 7.9990 chunk 339 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 126 optimal weight: 50.0000 chunk 24 optimal weight: 3.9990 chunk 266 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 118 ASN ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 224 ASN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 92 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 GLN D 295 GLN ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 323 ASN ** F 417 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.111854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.087042 restraints weight = 106299.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.089019 restraints weight = 52947.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.089817 restraints weight = 28250.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.090106 restraints weight = 24833.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.090141 restraints weight = 21085.494| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 33237 Z= 0.175 Angle : 0.714 13.552 44946 Z= 0.360 Chirality : 0.045 0.258 5147 Planarity : 0.005 0.098 5816 Dihedral : 8.831 167.241 4743 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.82 % Favored : 92.86 % Rotamer: Outliers : 4.98 % Allowed : 23.96 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.03 % 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: -0.03 (0.13), residues: 4134 helix: 1.22 (0.12), residues: 1791 sheet: -0.73 (0.18), residues: 739 loop : -1.03 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 169 TYR 0.040 0.002 TYR F 132 PHE 0.019 0.002 PHE C 283 TRP 0.016 0.002 TRP c 121 HIS 0.012 0.001 HIS M 120 Details of bonding type rmsd covalent geometry : bond 0.00397 (33233) covalent geometry : angle 0.71360 (44942) SS BOND : bond 0.00125 ( 2) SS BOND : angle 1.42832 ( 4) hydrogen bonds : bond 0.03915 ( 1614) hydrogen bonds : angle 5.01074 ( 4653) metal coordination : bond 0.00816 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 519 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8144 (tm-30) REVERT: A 241 ILE cc_start: 0.8831 (OUTLIER) cc_final: 0.8552 (mt) REVERT: A 299 MET cc_start: 0.8843 (tmm) cc_final: 0.8166 (tmm) REVERT: A 303 ILE cc_start: 0.9397 (mt) cc_final: 0.8928 (mt) REVERT: A 418 LYS cc_start: 0.8993 (mmmt) cc_final: 0.8763 (pttt) REVERT: C 23 TYR cc_start: 0.2653 (OUTLIER) cc_final: 0.1236 (t80) REVERT: C 112 CYS cc_start: 0.7679 (p) cc_final: 0.7236 (p) REVERT: C 162 LYS cc_start: 0.8989 (mtpp) cc_final: 0.8697 (mtpp) REVERT: C 270 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7692 (mp10) REVERT: C 327 ASP cc_start: 0.7642 (m-30) cc_final: 0.7397 (m-30) REVERT: C 385 MET cc_start: 0.8445 (ptp) cc_final: 0.8136 (ptp) REVERT: C 391 MET cc_start: 0.8224 (mmt) cc_final: 0.7245 (tpp) REVERT: G 80 MET cc_start: 0.6827 (tpt) cc_final: 0.6444 (tpt) REVERT: G 83 MET cc_start: 0.7390 (mmp) cc_final: 0.6816 (mmm) REVERT: G 236 ASP cc_start: 0.6815 (t0) cc_final: 0.6553 (m-30) REVERT: H 112 GLN cc_start: 0.8747 (pt0) cc_final: 0.8423 (pt0) REVERT: H 177 ARG cc_start: 0.7043 (ttt180) cc_final: 0.5597 (tpt170) REVERT: I 53 HIS cc_start: 0.8485 (t70) cc_final: 0.8164 (t-170) REVERT: I 61 PHE cc_start: 0.3620 (OUTLIER) cc_final: 0.3294 (m-80) REVERT: I 100 GLN cc_start: 0.8281 (tt0) cc_final: 0.7925 (tt0) REVERT: I 115 CYS cc_start: 0.8261 (m) cc_final: 0.7985 (m) REVERT: I 156 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.8006 (p90) REVERT: I 174 MET cc_start: 0.8265 (ptp) cc_final: 0.7282 (ppp) REVERT: J 52 LYS cc_start: 0.9018 (mtmt) cc_final: 0.8490 (ptmm) REVERT: J 122 ASN cc_start: 0.8757 (t0) cc_final: 0.8147 (m-40) REVERT: J 224 GLU cc_start: 0.9077 (mm-30) cc_final: 0.8642 (tp30) REVERT: L 24 TYR cc_start: 0.8104 (m-80) cc_final: 0.7513 (m-80) REVERT: L 140 MET cc_start: 0.6500 (mtp) cc_final: 0.5540 (mtm) REVERT: M 135 PHE cc_start: 0.7848 (p90) cc_final: 0.7563 (p90) REVERT: c 92 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8196 (pp30) REVERT: c 164 ASN cc_start: 0.9010 (m-40) cc_final: 0.8189 (t0) REVERT: c 167 MET cc_start: 0.7261 (mmm) cc_final: 0.6943 (mmm) REVERT: c 175 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.5512 (ptm-80) REVERT: c 234 TYR cc_start: 0.8999 (m-80) cc_final: 0.8071 (p90) REVERT: B 74 MET cc_start: 0.6627 (mmm) cc_final: 0.6210 (mmm) REVERT: B 101 ASP cc_start: 0.9054 (t0) cc_final: 0.8832 (t0) REVERT: B 242 GLN cc_start: 0.8914 (tp-100) cc_final: 0.8232 (tm-30) REVERT: B 309 MET cc_start: 0.7964 (mmm) cc_final: 0.7759 (mmm) REVERT: B 401 GLU cc_start: 0.8256 (tp30) cc_final: 0.7548 (tp30) REVERT: B 411 ARG cc_start: 0.7297 (mtm-85) cc_final: 0.6055 (mmp-170) REVERT: B 412 MET cc_start: 0.9155 (tpt) cc_final: 0.8663 (tpt) REVERT: D 45 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8012 (tttt) REVERT: D 188 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.7030 (p90) REVERT: D 291 GLU cc_start: 0.7961 (tp30) cc_final: 0.7533 (tp30) REVERT: D 340 GLN cc_start: 0.8456 (tp40) cc_final: 0.8196 (tp-100) REVERT: D 351 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8039 (tppt) REVERT: D 392 TYR cc_start: 0.7319 (m-80) cc_final: 0.6493 (m-80) REVERT: E 161 ARG cc_start: 0.8559 (mtm180) cc_final: 0.7655 (mtm180) REVERT: E 264 MET cc_start: 0.8289 (ttt) cc_final: 0.7907 (ttp) REVERT: E 267 PHE cc_start: 0.7160 (OUTLIER) cc_final: 0.6270 (m-80) REVERT: E 349 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8003 (mm-30) REVERT: E 383 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8392 (tptt) REVERT: F 182 THR cc_start: 0.9061 (p) cc_final: 0.8698 (t) REVERT: F 258 GLN cc_start: 0.7352 (tt0) cc_final: 0.6584 (tt0) REVERT: F 263 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6397 (t0) REVERT: F 356 MET cc_start: 0.8314 (mmm) cc_final: 0.7791 (mmm) REVERT: F 405 MET cc_start: 0.9334 (mmm) cc_final: 0.8716 (mmt) REVERT: K 214 ASN cc_start: 0.7864 (p0) cc_final: 0.7661 (p0) outliers start: 173 outliers final: 140 residues processed: 639 average time/residue: 0.1868 time to fit residues: 194.5652 Evaluate side-chains 640 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 488 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 196 LYS Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 293 MET Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 156 TYR Chi-restraints excluded: chain I residue 164 ILE Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 185 THR Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 92 GLN Chi-restraints excluded: chain c residue 113 HIS Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 259 VAL Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain c residue 284 LEU Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 105 THR Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 329 MET Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 288 ILE Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 394 VAL Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 189 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 403 optimal weight: 0.0370 chunk 157 optimal weight: 10.0000 chunk 278 optimal weight: 10.0000 chunk 238 optimal weight: 3.9990 chunk 162 optimal weight: 30.0000 chunk 216 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 354 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 224 ASN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 GLN ** M 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 92 GLN ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.113369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.087573 restraints weight = 105511.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089995 restraints weight = 50075.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.091477 restraints weight = 29953.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092392 restraints weight = 20899.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.092974 restraints weight = 16366.309| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33237 Z= 0.135 Angle : 0.713 13.733 44946 Z= 0.357 Chirality : 0.045 0.274 5147 Planarity : 0.005 0.095 5816 Dihedral : 8.631 162.107 4741 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.46 % Favored : 93.23 % Rotamer: Outliers : 4.09 % Allowed : 24.91 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.03 % 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: 0.03 (0.13), residues: 4134 helix: 1.24 (0.12), residues: 1798 sheet: -0.72 (0.19), residues: 742 loop : -0.95 (0.17), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 346 TYR 0.032 0.001 TYR I 121 PHE 0.017 0.001 PHE C 283 TRP 0.020 0.001 TRP c 121 HIS 0.019 0.001 HIS M 120 Details of bonding type rmsd covalent geometry : bond 0.00303 (33233) covalent geometry : angle 0.71262 (44942) SS BOND : bond 0.00152 ( 2) SS BOND : angle 1.39031 ( 4) hydrogen bonds : bond 0.03812 ( 1614) hydrogen bonds : angle 4.91815 ( 4653) metal coordination : bond 0.00233 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 540 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8398 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: A 143 ASP cc_start: 0.8616 (OUTLIER) cc_final: 0.8286 (p0) REVERT: A 299 MET cc_start: 0.8905 (tmm) cc_final: 0.8269 (tmm) REVERT: A 303 ILE cc_start: 0.9415 (mt) cc_final: 0.8945 (mt) REVERT: A 418 LYS cc_start: 0.8940 (mmmt) cc_final: 0.8738 (pttt) REVERT: C 23 TYR cc_start: 0.3068 (OUTLIER) cc_final: 0.1566 (t80) REVERT: C 112 CYS cc_start: 0.7563 (p) cc_final: 0.7118 (p) REVERT: C 162 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8659 (mtpp) REVERT: C 211 PHE cc_start: 0.8877 (t80) cc_final: 0.8639 (t80) REVERT: C 270 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7636 (mp10) REVERT: C 327 ASP cc_start: 0.7719 (m-30) cc_final: 0.7344 (m-30) REVERT: C 391 MET cc_start: 0.8032 (mmt) cc_final: 0.7325 (tpp) REVERT: G 78 CYS cc_start: 0.8050 (t) cc_final: 0.7000 (t) REVERT: G 80 MET cc_start: 0.6847 (tpt) cc_final: 0.6471 (tpt) REVERT: G 83 MET cc_start: 0.7420 (mmp) cc_final: 0.6687 (mmm) REVERT: G 236 ASP cc_start: 0.6940 (t0) cc_final: 0.6677 (m-30) REVERT: H 112 GLN cc_start: 0.8810 (pt0) cc_final: 0.8484 (pt0) REVERT: H 118 MET cc_start: 0.8861 (tpp) cc_final: 0.8614 (tpp) REVERT: H 177 ARG cc_start: 0.6977 (ttt180) cc_final: 0.5732 (ttt90) REVERT: I 53 HIS cc_start: 0.8473 (t70) cc_final: 0.8158 (t-170) REVERT: I 61 PHE cc_start: 0.3851 (OUTLIER) cc_final: 0.3500 (m-80) REVERT: I 100 GLN cc_start: 0.8291 (tt0) cc_final: 0.7963 (tt0) REVERT: I 156 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7659 (p90) REVERT: I 174 MET cc_start: 0.8244 (ptp) cc_final: 0.7247 (ppp) REVERT: J 52 LYS cc_start: 0.8961 (mtmt) cc_final: 0.8474 (ptmm) REVERT: J 122 ASN cc_start: 0.8731 (t0) cc_final: 0.8150 (m-40) REVERT: J 224 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8685 (tp30) REVERT: L 140 MET cc_start: 0.6364 (mtp) cc_final: 0.5487 (mtm) REVERT: c 164 ASN cc_start: 0.8613 (m-40) cc_final: 0.8039 (t0) REVERT: c 234 TYR cc_start: 0.8863 (m-80) cc_final: 0.8031 (p90) REVERT: B 74 MET cc_start: 0.6609 (mmm) cc_final: 0.6204 (mmm) REVERT: B 101 ASP cc_start: 0.8818 (t0) cc_final: 0.8574 (t0) REVERT: B 242 GLN cc_start: 0.8860 (tp-100) cc_final: 0.8260 (tm-30) REVERT: B 309 MET cc_start: 0.7989 (mmm) cc_final: 0.7761 (mmm) REVERT: B 401 GLU cc_start: 0.8290 (tp30) cc_final: 0.7574 (tp30) REVERT: B 411 ARG cc_start: 0.7121 (mtm-85) cc_final: 0.5996 (mmp-170) REVERT: B 412 MET cc_start: 0.9168 (tpt) cc_final: 0.8664 (tpt) REVERT: D 45 LYS cc_start: 0.9067 (OUTLIER) cc_final: 0.8040 (tttt) REVERT: D 291 GLU cc_start: 0.7837 (tp30) cc_final: 0.7400 (tp30) REVERT: D 296 MET cc_start: 0.8904 (mtp) cc_final: 0.8605 (mtp) REVERT: D 340 GLN cc_start: 0.8473 (tp40) cc_final: 0.8213 (tp-100) REVERT: D 351 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8004 (tppt) REVERT: D 392 TYR cc_start: 0.7259 (m-80) cc_final: 0.6398 (m-80) REVERT: E 161 ARG cc_start: 0.8548 (mtm180) cc_final: 0.7688 (mtm180) REVERT: E 264 MET cc_start: 0.7901 (ttt) cc_final: 0.7259 (ttp) REVERT: E 267 PHE cc_start: 0.7079 (OUTLIER) cc_final: 0.6255 (m-80) REVERT: E 349 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7972 (mm-30) REVERT: E 383 LYS cc_start: 0.8589 (tmtt) cc_final: 0.8380 (tptt) REVERT: F 182 THR cc_start: 0.8988 (p) cc_final: 0.8635 (t) REVERT: F 258 GLN cc_start: 0.7278 (tt0) cc_final: 0.6519 (tt0) REVERT: F 263 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6370 (t0) REVERT: F 356 MET cc_start: 0.8278 (mmm) cc_final: 0.7820 (mmm) REVERT: F 373 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7634 (ttm) REVERT: F 405 MET cc_start: 0.9361 (mmm) cc_final: 0.8714 (mmt) REVERT: K 214 ASN cc_start: 0.7851 (p0) cc_final: 0.7650 (p0) outliers start: 142 outliers final: 114 residues processed: 639 average time/residue: 0.1902 time to fit residues: 197.9288 Evaluate side-chains 622 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 498 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 156 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 90 ASP Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 142 LEU Chi-restraints excluded: chain K residue 189 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 257 optimal weight: 0.0020 chunk 49 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 398 optimal weight: 20.0000 chunk 293 optimal weight: 0.3980 chunk 203 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 185 optimal weight: 9.9990 chunk 197 optimal weight: 7.9990 chunk 370 optimal weight: 1.9990 chunk 280 optimal weight: 0.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN G 224 ASN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.113310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087673 restraints weight = 106176.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.090093 restraints weight = 50139.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.091575 restraints weight = 29855.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092493 restraints weight = 20803.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.093070 restraints weight = 16282.380| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.3046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.135 33237 Z= 0.145 Angle : 0.728 13.393 44946 Z= 0.363 Chirality : 0.046 0.433 5147 Planarity : 0.005 0.094 5816 Dihedral : 8.512 158.838 4739 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.29 % Allowed : 6.48 % Favored : 93.23 % Rotamer: Outliers : 3.94 % Allowed : 25.63 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.03 % 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: -0.00 (0.13), residues: 4134 helix: 1.21 (0.12), residues: 1804 sheet: -0.75 (0.18), residues: 743 loop : -0.96 (0.17), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 346 TYR 0.031 0.001 TYR I 121 PHE 0.020 0.001 PHE J 127 TRP 0.024 0.002 TRP c 121 HIS 0.014 0.001 HIS M 120 Details of bonding type rmsd covalent geometry : bond 0.00333 (33233) covalent geometry : angle 0.72735 (44942) SS BOND : bond 0.00564 ( 2) SS BOND : angle 2.02090 ( 4) hydrogen bonds : bond 0.03815 ( 1614) hydrogen bonds : angle 4.93567 ( 4653) metal coordination : bond 0.00429 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8268 Ramachandran restraints generated. 4134 Oldfield, 0 Emsley, 4134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 519 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.8052 (tm-30) REVERT: A 143 ASP cc_start: 0.8625 (OUTLIER) cc_final: 0.8279 (p0) REVERT: A 299 MET cc_start: 0.8921 (tmm) cc_final: 0.8248 (tmm) REVERT: A 303 ILE cc_start: 0.9419 (mt) cc_final: 0.8923 (mt) REVERT: C 23 TYR cc_start: 0.3100 (OUTLIER) cc_final: 0.1566 (t80) REVERT: C 112 CYS cc_start: 0.7584 (p) cc_final: 0.7138 (p) REVERT: C 162 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8591 (mtpp) REVERT: C 211 PHE cc_start: 0.8849 (t80) cc_final: 0.8631 (t80) REVERT: C 270 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7647 (mp10) REVERT: C 327 ASP cc_start: 0.7671 (m-30) cc_final: 0.7420 (m-30) REVERT: C 385 MET cc_start: 0.8356 (ptp) cc_final: 0.8060 (ptp) REVERT: C 391 MET cc_start: 0.8066 (mmt) cc_final: 0.7279 (tpp) REVERT: G 80 MET cc_start: 0.7371 (tpt) cc_final: 0.6874 (tpt) REVERT: G 236 ASP cc_start: 0.6935 (t0) cc_final: 0.6682 (m-30) REVERT: H 112 GLN cc_start: 0.8810 (pt0) cc_final: 0.8484 (pt0) REVERT: H 118 MET cc_start: 0.8871 (tpp) cc_final: 0.8633 (tpp) REVERT: H 177 ARG cc_start: 0.6900 (ttt180) cc_final: 0.5687 (ttt90) REVERT: I 53 HIS cc_start: 0.8497 (t70) cc_final: 0.8186 (t-170) REVERT: I 61 PHE cc_start: 0.3860 (OUTLIER) cc_final: 0.3508 (m-80) REVERT: I 100 GLN cc_start: 0.8304 (tt0) cc_final: 0.7980 (tt0) REVERT: I 156 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7686 (p90) REVERT: I 174 MET cc_start: 0.8231 (ptp) cc_final: 0.7281 (ppp) REVERT: J 15 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6369 (t70) REVERT: J 52 LYS cc_start: 0.8943 (mtmt) cc_final: 0.8472 (ptmm) REVERT: J 122 ASN cc_start: 0.8740 (t0) cc_final: 0.8190 (m-40) REVERT: J 224 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8697 (tp30) REVERT: L 140 MET cc_start: 0.6370 (mtp) cc_final: 0.5502 (mtm) REVERT: L 145 PHE cc_start: 0.6634 (m-80) cc_final: 0.6433 (m-80) REVERT: L 176 MET cc_start: 0.3377 (tpp) cc_final: 0.2966 (tpp) REVERT: c 164 ASN cc_start: 0.8685 (m-40) cc_final: 0.8030 (t0) REVERT: c 234 TYR cc_start: 0.8888 (m-80) cc_final: 0.8085 (p90) REVERT: B 74 MET cc_start: 0.6616 (mmm) cc_final: 0.6209 (mmm) REVERT: B 101 ASP cc_start: 0.8782 (t0) cc_final: 0.8551 (t0) REVERT: B 242 GLN cc_start: 0.8832 (tp-100) cc_final: 0.8269 (tm-30) REVERT: B 309 MET cc_start: 0.7998 (mmm) cc_final: 0.7757 (mmm) REVERT: B 401 GLU cc_start: 0.8292 (tp30) cc_final: 0.7563 (tp30) REVERT: B 411 ARG cc_start: 0.7112 (mtm-85) cc_final: 0.6043 (mmp-170) REVERT: D 45 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8045 (tttt) REVERT: D 291 GLU cc_start: 0.7823 (tp30) cc_final: 0.7382 (tp30) REVERT: D 296 MET cc_start: 0.8919 (mtp) cc_final: 0.8626 (mtp) REVERT: D 340 GLN cc_start: 0.8499 (tp40) cc_final: 0.8243 (tp-100) REVERT: D 351 LYS cc_start: 0.8536 (mtmm) cc_final: 0.7995 (tppt) REVERT: D 392 TYR cc_start: 0.7274 (m-80) cc_final: 0.6359 (m-80) REVERT: E 161 ARG cc_start: 0.8532 (mtm180) cc_final: 0.7685 (mtm180) REVERT: E 264 MET cc_start: 0.7817 (ttt) cc_final: 0.7182 (ttp) REVERT: E 267 PHE cc_start: 0.7051 (OUTLIER) cc_final: 0.6206 (m-80) REVERT: E 277 MET cc_start: 0.8626 (mmt) cc_final: 0.8377 (mmt) REVERT: E 383 LYS cc_start: 0.8605 (tmtt) cc_final: 0.8393 (tptt) REVERT: F 182 THR cc_start: 0.8952 (p) cc_final: 0.8598 (t) REVERT: F 258 GLN cc_start: 0.7279 (tt0) cc_final: 0.6503 (tt0) REVERT: F 263 ASP cc_start: 0.7043 (OUTLIER) cc_final: 0.6520 (t0) REVERT: F 356 MET cc_start: 0.8336 (mmm) cc_final: 0.7868 (mmm) REVERT: F 373 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7617 (ttm) REVERT: F 405 MET cc_start: 0.9366 (mmm) cc_final: 0.8726 (mmt) REVERT: K 214 ASN cc_start: 0.7845 (p0) cc_final: 0.7639 (p0) outliers start: 137 outliers final: 118 residues processed: 615 average time/residue: 0.2103 time to fit residues: 210.1548 Evaluate side-chains 625 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 496 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LYS Chi-restraints excluded: chain A residue 88 GLN Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain C residue 23 TYR Chi-restraints excluded: chain C residue 37 ASP Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 80 MET Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 109 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 215 SER Chi-restraints excluded: chain C residue 223 PHE Chi-restraints excluded: chain C residue 234 LEU Chi-restraints excluded: chain C residue 270 GLN Chi-restraints excluded: chain C residue 378 VAL Chi-restraints excluded: chain C residue 404 LEU Chi-restraints excluded: chain C residue 405 TRP Chi-restraints excluded: chain G residue 72 ILE Chi-restraints excluded: chain G residue 78 CYS Chi-restraints excluded: chain G residue 201 CYS Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain H residue 13 PHE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 165 LYS Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain H residue 210 VAL Chi-restraints excluded: chain I residue 56 LEU Chi-restraints excluded: chain I residue 61 PHE Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 103 GLU Chi-restraints excluded: chain I residue 117 ILE Chi-restraints excluded: chain I residue 156 TYR Chi-restraints excluded: chain I residue 175 LEU Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 15 HIS Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 36 ARG Chi-restraints excluded: chain J residue 69 VAL Chi-restraints excluded: chain J residue 129 ILE Chi-restraints excluded: chain J residue 132 LEU Chi-restraints excluded: chain J residue 167 SER Chi-restraints excluded: chain J residue 219 ILE Chi-restraints excluded: chain L residue 64 LEU Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain L residue 132 LEU Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain L residue 180 MET Chi-restraints excluded: chain M residue 69 VAL Chi-restraints excluded: chain M residue 77 VAL Chi-restraints excluded: chain M residue 216 VAL Chi-restraints excluded: chain M residue 230 ASP Chi-restraints excluded: chain c residue 42 LEU Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 69 VAL Chi-restraints excluded: chain c residue 87 VAL Chi-restraints excluded: chain c residue 118 PHE Chi-restraints excluded: chain c residue 134 GLU Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 156 VAL Chi-restraints excluded: chain c residue 175 ARG Chi-restraints excluded: chain c residue 178 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain c residue 192 LEU Chi-restraints excluded: chain c residue 279 ASP Chi-restraints excluded: chain c residue 281 LYS Chi-restraints excluded: chain B residue 71 TYR Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 138 PHE Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 LYS Chi-restraints excluded: chain B residue 292 THR Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 385 MET Chi-restraints excluded: chain B residue 387 LYS Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 60 TYR Chi-restraints excluded: chain D residue 78 GLU Chi-restraints excluded: chain D residue 98 GLN Chi-restraints excluded: chain D residue 115 ILE Chi-restraints excluded: chain D residue 132 LEU Chi-restraints excluded: chain D residue 200 ARG Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 289 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 407 ILE Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 110 TYR Chi-restraints excluded: chain E residue 115 VAL Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 181 THR Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 228 CYS Chi-restraints excluded: chain E residue 267 PHE Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 378 LYS Chi-restraints excluded: chain F residue 124 ILE Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 163 THR Chi-restraints excluded: chain F residue 244 THR Chi-restraints excluded: chain F residue 247 THR Chi-restraints excluded: chain F residue 250 LYS Chi-restraints excluded: chain F residue 261 ILE Chi-restraints excluded: chain F residue 263 ASP Chi-restraints excluded: chain F residue 296 PHE Chi-restraints excluded: chain F residue 373 MET Chi-restraints excluded: chain F residue 389 ASP Chi-restraints excluded: chain F residue 438 TYR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain K residue 142 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 242 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 0.1980 chunk 165 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 chunk 278 optimal weight: 2.9990 chunk 103 optimal weight: 30.0000 chunk 277 optimal weight: 8.9990 chunk 147 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 157 optimal weight: 3.9990 overall best weight: 2.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 206 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 ASN H 119 GLN ** H 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 ASN ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.112149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.086876 restraints weight = 106803.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088551 restraints weight = 51608.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.089764 restraints weight = 35953.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.091799 restraints weight = 22477.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.091462 restraints weight = 16369.877| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 33237 Z= 0.173 Angle : 0.737 12.800 44946 Z= 0.369 Chirality : 0.046 0.389 5147 Planarity : 0.005 0.094 5816 Dihedral : 8.480 156.174 4735 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.58 % Favored : 93.11 % Rotamer: Outliers : 4.06 % Allowed : 25.75 % Favored : 70.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.37 % Cis-general : 0.00 % Twisted Proline : 1.78 % Twisted General : 0.03 % 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: -0.05 (0.13), residues: 4134 helix: 1.19 (0.12), residues: 1802 sheet: -0.90 (0.18), residues: 750 loop : -0.94 (0.17), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 169 TYR 0.026 0.002 TYR F 132 PHE 0.018 0.002 PHE C 283 TRP 0.029 0.002 TRP c 121 HIS 0.015 0.001 HIS H 163 Details of bonding type rmsd covalent geometry : bond 0.00399 (33233) covalent geometry : angle 0.73683 (44942) SS BOND : bond 0.00109 ( 2) SS BOND : angle 2.04183 ( 4) hydrogen bonds : bond 0.03881 ( 1614) hydrogen bonds : angle 4.97775 ( 4653) metal coordination : bond 0.00829 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7484.21 seconds wall clock time: 129 minutes 42.13 seconds (7782.13 seconds total)