Starting phenix.real_space_refine on Tue Sep 15 09:57:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6qg2_4545/09_2026/6qg2_4545.cif Found real_map, /net/cci-nas-00/data/ceres_data/6qg2_4545/09_2026/6qg2_4545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6qg2_4545/09_2026/6qg2_4545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6qg2_4545/09_2026/6qg2_4545.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6qg2_4545/09_2026/6qg2_4545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6qg2_4545/09_2026/6qg2_4545.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6qg2_4545/09_2026/6qg2_4545.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6qg2_4545/09_2026/6qg2_4545.cif" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 177 5.16 5 C 24589 2.51 5 N 6619 2.21 5 O 7277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38664 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2351 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 289} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "D" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2665 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 16, 'TRANS': 328} Chain breaks: 2 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 1, 'PHE:plan': 1, 'ASN:plan1': 2, 'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 2164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2164 Classifications: {'peptide': 267} Link IDs: {'PTRANS': 16, 'TRANS': 250} Chain breaks: 6 Chain: "F" Number of atoms: 2967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2967 Classifications: {'peptide': 375} Link IDs: {'PTRANS': 20, 'TRANS': 354} Chain breaks: 8 Chain: "G" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 2744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2744 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 342} Chain breaks: 2 Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 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: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3406 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 15, 'TRANS': 415} Chain breaks: 1 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: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1967 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "L" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1967 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "O" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 143 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} Chain: "N" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3044 Classifications: {'peptide': 408} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 20, 'TRANS': 387} Chain breaks: 4 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 2, 'GLU:plan': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "P" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1036 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain breaks: 3 Residues with excluded nonbonded symmetry interactions: 108 residue: pdb=" N GLN F 414 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN F 414 " occ=0.00 residue: pdb=" N THR F 415 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR F 415 " occ=0.00 residue: pdb=" N MET F 416 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET F 416 " occ=0.00 residue: pdb=" N PHE F 417 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE F 417 " occ=0.00 residue: pdb=" N THR F 418 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR F 418 " occ=0.00 residue: pdb=" N LYS F 419 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS F 419 " occ=0.00 residue: pdb=" N ASN F 420 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN F 420 " occ=0.00 residue: pdb=" N ILE F 421 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE F 421 " occ=0.00 residue: pdb=" N GLN F 422 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN F 422 " occ=0.00 residue: pdb=" N ILE F 423 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE F 423 " occ=0.00 residue: pdb=" N GLN F 424 " occ=0.00 ... (7 atoms not shown) pdb=" NE2 GLN F 424 " occ=0.00 residue: pdb=" N ALA F 426 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA F 426 " occ=0.00 ... (remaining 96 not shown) Time building chain proxies: 7.91, per 1000 atoms: 0.20 Number of scatterers: 38664 At special positions: 0 Unit cell: (276.04, 164.82, 135.34, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 177 16.00 P 2 15.00 O 7277 8.00 N 6619 7.00 C 24589 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.80 Conformation dependent library (CDL) restraints added in 1.5 seconds 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9398 Finding SS restraints... Secondary structure from input PDB file: 129 helices and 48 sheets defined 32.4% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.853A pdb=" N THR A 9 " --> pdb=" O ASN A 5 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 13 " --> pdb=" O THR A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 35 removed outlier: 3.656A pdb=" N ALA A 26 " --> pdb=" O MET A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 60 Processing helix chain 'A' and resid 64 through 81 removed outlier: 4.475A pdb=" N ALA A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 removed outlier: 4.047A pdb=" N CYS A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 115 Processing helix chain 'A' and resid 132 through 146 Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.201A pdb=" N GLN A 164 " --> pdb=" O LYS A 160 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A 171 " --> pdb=" O THR A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 21 through 38 removed outlier: 3.771A pdb=" N ILE B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS B 37 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 38 " --> pdb=" O LEU B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 60 removed outlier: 4.386A pdb=" N ASN B 47 " --> pdb=" O ALA B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.777A pdb=" N LEU B 81 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 84 No H-bonds generated for 'chain 'B' and resid 82 through 84' Processing helix chain 'B' and resid 86 through 97 removed outlier: 4.291A pdb=" N CYS B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 91 " --> pdb=" O TRP B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 116 removed outlier: 3.530A pdb=" N VAL B 102 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LYS B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 161 through 173 removed outlier: 3.764A pdb=" N LYS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 173 " --> pdb=" O LEU B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.921A pdb=" N ALA B 186 " --> pdb=" O ALA B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 224 Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 36 through 55 Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 82 through 108 removed outlier: 3.633A pdb=" N GLU C 98 " --> pdb=" O VAL C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 166 Processing helix chain 'C' and resid 193 through 205 removed outlier: 3.786A pdb=" N LEU C 197 " --> pdb=" O SER C 193 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 236 removed outlier: 3.644A pdb=" N THR C 223 " --> pdb=" O PHE C 219 " (cutoff:3.500A) removed outlier: 8.362A pdb=" N LYS C 224 " --> pdb=" O PRO C 220 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN C 225 " --> pdb=" O ASN C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 255 removed outlier: 3.693A pdb=" N MET C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 289 Processing helix chain 'C' and resid 317 through 321 removed outlier: 3.767A pdb=" N ILE C 321 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 369 removed outlier: 4.078A pdb=" N ILE C 364 " --> pdb=" O PHE C 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 32 Processing helix chain 'D' and resid 36 through 55 removed outlier: 3.582A pdb=" N ALA D 54 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA D 55 " --> pdb=" O PHE D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 78 removed outlier: 4.065A pdb=" N LEU D 63 " --> pdb=" O HIS D 59 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 108 removed outlier: 3.730A pdb=" N GLU D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 167 Processing helix chain 'D' and resid 168 through 173 removed outlier: 3.719A pdb=" N GLN D 173 " --> pdb=" O ASP D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.569A pdb=" N ASP D 178 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU D 179 " --> pdb=" O ALA D 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 175 through 179' Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.907A pdb=" N ARG D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 237 removed outlier: 4.221A pdb=" N ASN D 225 " --> pdb=" O ASN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 289 Processing helix chain 'D' and resid 308 through 313 removed outlier: 3.814A pdb=" N VAL D 313 " --> pdb=" O VAL D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.752A pdb=" N LYS D 329 " --> pdb=" O ASP D 326 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG D 330 " --> pdb=" O PRO D 327 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 326 through 330' Processing helix chain 'D' and resid 357 through 359 No H-bonds generated for 'chain 'D' and resid 357 through 359' Processing helix chain 'D' and resid 360 through 367 removed outlier: 3.916A pdb=" N ILE D 364 " --> pdb=" O PHE D 360 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 87 removed outlier: 3.830A pdb=" N TYR E 79 " --> pdb=" O PRO E 75 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL E 80 " --> pdb=" O MET E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 152 through 159 Processing helix chain 'E' and resid 180 through 190 removed outlier: 3.910A pdb=" N VAL E 184 " --> pdb=" O PRO E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 291 removed outlier: 3.784A pdb=" N LEU E 290 " --> pdb=" O GLN E 286 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 286 through 291' Processing helix chain 'E' and resid 403 through 412 removed outlier: 4.274A pdb=" N LYS E 412 " --> pdb=" O VAL E 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 88 Processing helix chain 'F' and resid 102 through 110 Processing helix chain 'F' and resid 152 through 159 Processing helix chain 'F' and resid 181 through 191 Processing helix chain 'F' and resid 257 through 262 removed outlier: 4.241A pdb=" N ASN F 262 " --> pdb=" O HIS F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 405 through 412 Processing helix chain 'G' and resid 271 through 283 removed outlier: 4.473A pdb=" N LEU G 275 " --> pdb=" O HIS G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 307 removed outlier: 4.896A pdb=" N CYS G 293 " --> pdb=" O SER G 289 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE G 294 " --> pdb=" O ILE G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 318 through 334 Processing helix chain 'G' and resid 337 through 354 Processing helix chain 'G' and resid 362 through 379 removed outlier: 3.546A pdb=" N ASP G 366 " --> pdb=" O ALA G 362 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU G 369 " --> pdb=" O LYS G 365 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE G 379 " --> pdb=" O ALA G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 393 Processing helix chain 'G' and resid 406 through 418 Processing helix chain 'G' and resid 436 through 446 Processing helix chain 'G' and resid 459 through 463 removed outlier: 3.739A pdb=" N PHE G 463 " --> pdb=" O ASP G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 499 Processing helix chain 'G' and resid 528 through 532 Processing helix chain 'G' and resid 582 through 586 removed outlier: 3.503A pdb=" N GLU G 585 " --> pdb=" O SER G 582 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER G 586 " --> pdb=" O GLU G 583 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 582 through 586' Processing helix chain 'H' and resid 271 through 283 removed outlier: 3.861A pdb=" N LEU H 275 " --> pdb=" O HIS H 271 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N HIS H 283 " --> pdb=" O SER H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 289 through 307 removed outlier: 3.599A pdb=" N CYS H 293 " --> pdb=" O SER H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 318 through 334 Processing helix chain 'H' and resid 337 through 354 Processing helix chain 'H' and resid 359 through 379 removed outlier: 3.637A pdb=" N GLU H 369 " --> pdb=" O LYS H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 394 Processing helix chain 'H' and resid 406 through 419 Processing helix chain 'H' and resid 435 through 448 Processing helix chain 'H' and resid 459 through 464 removed outlier: 3.988A pdb=" N PHE H 463 " --> pdb=" O LEU H 459 " (cutoff:3.500A) Processing helix chain 'H' and resid 488 through 499 Processing helix chain 'I' and resid 48 through 52 removed outlier: 3.893A pdb=" N LEU I 52 " --> pdb=" O ARG I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 71 removed outlier: 4.461A pdb=" N TYR I 62 " --> pdb=" O PRO I 58 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 93 removed outlier: 3.966A pdb=" N ILE I 86 " --> pdb=" O HIS I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 126 Processing helix chain 'I' and resid 144 through 159 removed outlier: 4.448A pdb=" N MET I 148 " --> pdb=" O ASP I 144 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP I 159 " --> pdb=" O MET I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 214 through 216 No H-bonds generated for 'chain 'I' and resid 214 through 216' Processing helix chain 'I' and resid 217 through 222 removed outlier: 4.037A pdb=" N VAL I 221 " --> pdb=" O LEU I 217 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP I 222 " --> pdb=" O LEU I 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 217 through 222' Processing helix chain 'I' and resid 240 through 249 removed outlier: 4.298A pdb=" N LEU I 244 " --> pdb=" O SER I 240 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 266 Processing helix chain 'I' and resid 288 through 300 Processing helix chain 'J' and resid 59 through 71 removed outlier: 3.867A pdb=" N THR J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 93 removed outlier: 3.777A pdb=" N ILE J 86 " --> pdb=" O HIS J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 115 through 126 Processing helix chain 'J' and resid 145 through 159 Processing helix chain 'J' and resid 241 through 249 Processing helix chain 'J' and resid 258 through 265 Processing helix chain 'J' and resid 287 through 300 Processing helix chain 'K' and resid 94 through 112 Processing helix chain 'K' and resid 113 through 120 removed outlier: 3.598A pdb=" N PHE K 119 " --> pdb=" O CYS K 115 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 132 removed outlier: 3.736A pdb=" N LEU K 126 " --> pdb=" O PRO K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 138 removed outlier: 4.307A pdb=" N LYS K 137 " --> pdb=" O PRO K 133 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE K 138 " --> pdb=" O LEU K 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 133 through 138' Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.868A pdb=" N ALA K 144 " --> pdb=" O HIS K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 162 through 174 removed outlier: 3.530A pdb=" N LEU K 166 " --> pdb=" O SER K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 207 Processing helix chain 'K' and resid 240 through 256 removed outlier: 3.539A pdb=" N LEU K 244 " --> pdb=" O GLY K 240 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N SER K 246 " --> pdb=" O GLU K 242 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR K 256 " --> pdb=" O THR K 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 120 removed outlier: 4.206A pdb=" N ILE L 96 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS L 97 " --> pdb=" O GLU L 93 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS L 115 " --> pdb=" O ILE L 111 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 135 removed outlier: 4.026A pdb=" N LEU L 126 " --> pdb=" O PRO L 122 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N TRP L 132 " --> pdb=" O LYS L 128 " (cutoff:3.500A) Proline residue: L 133 - end of helix Processing helix chain 'L' and resid 141 through 151 Processing helix chain 'L' and resid 154 through 158 removed outlier: 3.668A pdb=" N GLY L 157 " --> pdb=" O VAL L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 163 through 174 Processing helix chain 'L' and resid 197 through 207 Processing helix chain 'L' and resid 240 through 257 removed outlier: 3.735A pdb=" N LEU L 244 " --> pdb=" O GLY L 240 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER L 246 " --> pdb=" O GLU L 242 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS L 257 " --> pdb=" O GLU L 253 " (cutoff:3.500A) Processing helix chain 'M' and resid 113 through 121 Processing helix chain 'M' and resid 201 through 211 removed outlier: 3.667A pdb=" N VAL M 210 " --> pdb=" O SER M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 239 removed outlier: 3.827A pdb=" N SER M 230 " --> pdb=" O GLN M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 270 Processing helix chain 'M' and resid 290 through 302 removed outlier: 4.085A pdb=" N VAL M 294 " --> pdb=" O ASN M 290 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE M 302 " --> pdb=" O ILE M 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 131 through 141 Processing helix chain 'N' and resid 113 through 121 Processing helix chain 'N' and resid 201 through 211 removed outlier: 3.557A pdb=" N VAL N 210 " --> pdb=" O SER N 206 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 239 removed outlier: 3.874A pdb=" N SER N 230 " --> pdb=" O GLN N 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 256 through 270 removed outlier: 4.326A pdb=" N LEU N 260 " --> pdb=" O GLU N 256 " (cutoff:3.500A) Processing helix chain 'N' and resid 291 through 302 removed outlier: 4.318A pdb=" N ILE N 302 " --> pdb=" O ILE N 298 " (cutoff:3.500A) Processing helix chain 'P' and resid 131 through 141 Processing helix chain 'P' and resid 176 through 184 Processing helix chain 'P' and resid 187 through 199 removed outlier: 3.811A pdb=" N LEU P 191 " --> pdb=" O SER P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 218 through 231 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 179 removed outlier: 4.245A pdb=" N THR A 177 " --> pdb=" O CYS A 151 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 153 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 154 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU A 127 " --> pdb=" O PHE A 195 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL A 194 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N VAL A 230 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 196 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE A 227 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 8.734A pdb=" N ILE A 284 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N VAL A 229 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 201 removed outlier: 3.764A pdb=" N ILE A 207 " --> pdb=" O THR A 275 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 275 " --> pdb=" O ILE A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.942A pdb=" N ARG B 150 " --> pdb=" O ASP B 124 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 128 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N THR B 154 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE B 125 " --> pdb=" O LYS B 193 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE B 195 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LEU B 127 " --> pdb=" O PHE B 195 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY B 197 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N HIS B 129 " --> pdb=" O GLY B 197 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N VAL B 194 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL B 230 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 196 " --> pdb=" O VAL B 230 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N PHE B 227 " --> pdb=" O ALA B 282 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N ILE B 284 " --> pdb=" O PHE B 227 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL B 229 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 240 through 243 removed outlier: 3.512A pdb=" N LYS C 257 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 259 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE C 272 " --> pdb=" O LYS C 263 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR C 271 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL C 341 " --> pdb=" O THR C 271 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 240 through 243 removed outlier: 3.512A pdb=" N LYS C 257 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE C 259 " --> pdb=" O LEU C 187 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL C 258 " --> pdb=" O PHE C 293 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N VAL C 295 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE C 260 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE C 348 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE C 350 " --> pdb=" O ALA C 294 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 331 through 333 removed outlier: 6.291A pdb=" N VAL G 451 " --> pdb=" O ASP C 332 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL G 426 " --> pdb=" O MET G 452 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ALA G 454 " --> pdb=" O VAL G 426 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N VAL G 428 " --> pdb=" O ALA G 454 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 292 through 294 removed outlier: 6.101A pdb=" N VAL D 258 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 185 " --> pdb=" O LYS D 257 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE D 259 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 187 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLU D 184 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU D 214 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU D 186 " --> pdb=" O LEU D 214 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N THR D 216 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LEU D 241 " --> pdb=" O PHE D 211 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL D 213 " --> pdb=" O LEU D 241 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL D 243 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL D 215 " --> pdb=" O VAL D 243 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU H 557 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 264 through 265 Processing sheet with id=AA9, first strand: chain 'D' and resid 314 through 315 removed outlier: 3.618A pdb=" N GLU D 314 " --> pdb=" O THR D 338 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR D 338 " --> pdb=" O GLU D 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 332 through 333 removed outlier: 7.511A pdb=" N THR H 398 " --> pdb=" O LYS H 425 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N ILE H 427 " --> pdb=" O THR H 398 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE H 400 " --> pdb=" O ILE H 427 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N VAL H 429 " --> pdb=" O ILE H 400 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N THR H 402 " --> pdb=" O VAL H 429 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N THR H 399 " --> pdb=" O TYR H 469 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 134 through 136 removed outlier: 8.347A pdb=" N SER E 93 " --> pdb=" O ILE E 3 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ALA E 5 " --> pdb=" O SER E 93 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL E 95 " --> pdb=" O ALA E 5 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL E 7 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN E 4 " --> pdb=" O ASP E 166 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL E 168 " --> pdb=" O GLN E 4 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 273 through 274 removed outlier: 3.638A pdb=" N PHE E 392 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.821A pdb=" N PHE E 223 " --> pdb=" O SER E 269 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 134 through 136 removed outlier: 3.668A pdb=" N HIS F 134 " --> pdb=" O ILE F 92 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA F 5 " --> pdb=" O SER F 93 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N VAL F 95 " --> pdb=" O ALA F 5 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N VAL F 7 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N TYR F 278 " --> pdb=" O ILE F 169 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR F 390 " --> pdb=" O ALA F 196 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR F 198 " --> pdb=" O THR F 390 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 239 through 240 removed outlier: 3.757A pdb=" N TYR F 226 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE F 223 " --> pdb=" O SER F 269 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N PHE I 224 " --> pdb=" O VAL F 268 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 444 through 447 removed outlier: 6.476A pdb=" N ASN F 445 " --> pdb=" O VAL F 463 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 464 " --> pdb=" O LEU F 480 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU F 497 " --> pdb=" O ILE F 479 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 466 through 467 removed outlier: 3.874A pdb=" N LEU F 467 " --> pdb=" O CYS F 483 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.549A pdb=" N LYS F 490 " --> pdb=" O TYR F 506 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 471 through 473 removed outlier: 3.779A pdb=" N CYS G 506 " --> pdb=" O LEU G 472 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN G 574 " --> pdb=" O GLY G 581 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY G 581 " --> pdb=" O ASN G 574 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE G 576 " --> pdb=" O LYS G 579 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 476 through 477 removed outlier: 3.664A pdb=" N SER G 476 " --> pdb=" O TYR G 484 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU G 483 " --> pdb=" O ALA G 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 476 through 477 Processing sheet with id=AC4, first strand: chain 'H' and resid 503 through 506 removed outlier: 7.206A pdb=" N VAL H 503 " --> pdb=" O PRO H 571 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLY H 573 " --> pdb=" O VAL H 503 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS H 575 " --> pdb=" O VAL H 505 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 75 through 77 Processing sheet with id=AC6, first strand: chain 'I' and resid 230 through 231 removed outlier: 4.051A pdb=" N SER I 169 " --> pdb=" O ILE I 231 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET I 166 " --> pdb=" O TYR I 276 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N THR I 278 " --> pdb=" O MET I 166 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LEU I 168 " --> pdb=" O THR I 278 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 319 through 321 removed outlier: 3.631A pdb=" N ILE I 325 " --> pdb=" O GLU I 321 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N TYR I 326 " --> pdb=" O ILE I 345 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ALA I 344 " --> pdb=" O ILE I 362 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 331 through 333 Processing sheet with id=AC9, first strand: chain 'I' and resid 356 through 358 removed outlier: 6.572A pdb=" N LYS I 356 " --> pdb=" O ILE I 374 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE I 391 " --> pdb=" O ARG I 373 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N THR I 401 " --> pdb=" O ILE I 420 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP I 422 " --> pdb=" O THR I 401 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N GLY I 403 " --> pdb=" O ASP I 422 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N MET I 424 " --> pdb=" O GLY I 403 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASN I 405 " --> pdb=" O MET I 424 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 378 through 379 removed outlier: 7.947A pdb=" N PHE I 378 " --> pdb=" O ILE I 396 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'J' and resid 104 through 108 removed outlier: 7.043A pdb=" N LEU J 27 " --> pdb=" O HIS J 73 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL J 75 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA J 29 " --> pdb=" O VAL J 75 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU J 77 " --> pdb=" O ALA J 29 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL J 31 " --> pdb=" O LEU J 77 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N CYS J 79 " --> pdb=" O VAL J 31 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE J 133 " --> pdb=" O GLN J 28 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE J 235 " --> pdb=" O CYS J 167 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N CYS J 167 " --> pdb=" O ILE J 235 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR J 274 " --> pdb=" O ILE J 163 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N THR J 165 " --> pdb=" O TYR J 274 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N TYR J 276 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N CYS J 167 " --> pdb=" O TYR J 276 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 185 through 187 Processing sheet with id=AD4, first strand: chain 'J' and resid 318 through 321 removed outlier: 3.667A pdb=" N LYS J 327 " --> pdb=" O SER J 319 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ILE J 325 " --> pdb=" O GLU J 321 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N TYR J 326 " --> pdb=" O ILE J 345 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 338 through 339 removed outlier: 7.872A pdb=" N LYS J 338 " --> pdb=" O ILE J 357 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'J' and resid 368 through 370 removed outlier: 7.043A pdb=" N ASN J 387 " --> pdb=" O GLY J 369 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 373 through 375 removed outlier: 3.928A pdb=" N LEU J 408 " --> pdb=" O ILE J 390 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ARG J 407 " --> pdb=" O LEU J 426 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 378 through 379 Processing sheet with id=AD9, first strand: chain 'K' and resid 19 through 23 removed outlier: 6.705A pdb=" N ASP K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N VAL K 76 " --> pdb=" O TYR K 82 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR K 82 " --> pdb=" O VAL K 76 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 31 through 35 Processing sheet with id=AE2, first strand: chain 'K' and resid 219 through 222 removed outlier: 3.914A pdb=" N LYS K 219 " --> pdb=" O THR K 231 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL K 229 " --> pdb=" O LYS K 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL K 188 " --> pdb=" O TYR K 228 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU K 230 " --> pdb=" O ALA K 186 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER K 191 " --> pdb=" O VAL K 261 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL K 261 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 19 through 23 removed outlier: 4.010A pdb=" N LYS L 35 " --> pdb=" O ASN L 23 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LEU L 47 " --> pdb=" O LEU L 85 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR L 82 " --> pdb=" O VAL L 76 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL L 76 " --> pdb=" O TYR L 82 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ASP L 84 " --> pdb=" O LEU L 74 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 227 through 233 removed outlier: 4.133A pdb=" N TYR L 228 " --> pdb=" O VAL L 188 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL L 188 " --> pdb=" O TYR L 228 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU L 230 " --> pdb=" O ALA L 186 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER L 191 " --> pdb=" O VAL L 261 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL L 261 " --> pdb=" O SER L 191 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 141 through 149 removed outlier: 3.837A pdb=" N ARG M 187 " --> pdb=" O ILE M 147 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LYS M 149 " --> pdb=" O LEU M 185 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU M 185 " --> pdb=" O LYS M 149 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ALA M 99 " --> pdb=" O HIS M 188 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER M 190 " --> pdb=" O ALA M 99 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE M 101 " --> pdb=" O SER M 190 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N VAL M 192 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE M 103 " --> pdb=" O VAL M 192 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA M 214 " --> pdb=" O ILE M 245 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU M 247 " --> pdb=" O ALA M 214 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N LEU M 216 " --> pdb=" O LEU M 247 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL M 281 " --> pdb=" O VAL M 244 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE M 246 " --> pdb=" O VAL M 281 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 314 through 321 removed outlier: 8.438A pdb=" N LEU M 315 " --> pdb=" O LEU M 343 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU M 343 " --> pdb=" O LEU M 315 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL M 317 " --> pdb=" O SER M 341 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER M 341 " --> pdb=" O VAL M 317 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY M 394 " --> pdb=" O ILE M 342 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY M 397 " --> pdb=" O LEU M 380 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU M 380 " --> pdb=" O GLY M 397 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N GLY M 399 " --> pdb=" O VAL M 378 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 425 through 441 removed outlier: 4.054A pdb=" N ASN M 425 " --> pdb=" O THR M 493 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA M 491 " --> pdb=" O TYR M 427 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N ASP M 429 " --> pdb=" O SER M 489 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N SER M 489 " --> pdb=" O ASP M 429 " (cutoff:3.500A) removed outlier: 11.724A pdb=" N GLU M 431 " --> pdb=" O LEU M 487 " (cutoff:3.500A) removed outlier: 11.518A pdb=" N LEU M 487 " --> pdb=" O GLU M 431 " (cutoff:3.500A) removed outlier: 11.099A pdb=" N ASN M 433 " --> pdb=" O LEU M 485 " (cutoff:3.500A) removed outlier: 11.218A pdb=" N LEU M 485 " --> pdb=" O ASN M 433 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N PHE M 435 " --> pdb=" O ALA M 483 " (cutoff:3.500A) removed outlier: 11.537A pdb=" N ALA M 483 " --> pdb=" O PHE M 435 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N MET M 482 " --> pdb=" O VAL M 478 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL M 478 " --> pdb=" O MET M 482 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ARG M 484 " --> pdb=" O VAL M 476 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR M 488 " --> pdb=" O GLY M 472 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N GLY M 472 " --> pdb=" O THR M 488 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ALA M 470 " --> pdb=" O PRO M 490 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR M 469 " --> pdb=" O ILE M 466 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE M 466 " --> pdb=" O THR M 469 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR M 471 " --> pdb=" O VAL M 464 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL M 461 " --> pdb=" O ARG M 504 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ARG M 504 " --> pdb=" O VAL M 461 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE M 499 " --> pdb=" O TRP M 514 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N TRP M 514 " --> pdb=" O ILE M 499 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LEU M 501 " --> pdb=" O ILE M 512 " (cutoff:3.500A) removed outlier: 11.616A pdb=" N ARG M 510 " --> pdb=" O ARG M 439 " (cutoff:3.500A) removed outlier: 11.848A pdb=" N ARG M 439 " --> pdb=" O ARG M 510 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE M 512 " --> pdb=" O LEU M 437 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 141 through 149 removed outlier: 3.851A pdb=" N ALA N 143 " --> pdb=" O PHE N 191 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS N 149 " --> pdb=" O LEU N 185 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU N 185 " --> pdb=" O LYS N 149 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE N 103 " --> pdb=" O VAL N 192 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 314 through 320 removed outlier: 7.132A pdb=" N ARG N 314 " --> pdb=" O LEU N 343 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU N 343 " --> pdb=" O ARG N 314 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLY N 339 " --> pdb=" O ILE N 318 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N SER N 320 " --> pdb=" O VAL N 337 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL N 337 " --> pdb=" O SER N 320 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N GLY N 397 " --> pdb=" O LEU N 380 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LEU N 380 " --> pdb=" O GLY N 397 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N GLY N 399 " --> pdb=" O VAL N 378 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 510 through 511 removed outlier: 4.357A pdb=" N LEU N 501 " --> pdb=" O GLY N 513 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY N 513 " --> pdb=" O LEU N 501 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP N 514 " --> pdb=" O PHE N 435 " (cutoff:3.500A) removed outlier: 12.176A pdb=" N ILE N 426 " --> pdb=" O SER N 489 " (cutoff:3.500A) removed outlier: 12.960A pdb=" N SER N 489 " --> pdb=" O ILE N 426 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR N 428 " --> pdb=" O LEU N 487 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR N 488 " --> pdb=" O GLY N 472 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N GLY N 472 " --> pdb=" O THR N 488 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA N 470 " --> pdb=" O PRO N 490 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE N 466 " --> pdb=" O THR N 469 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR N 471 " --> pdb=" O VAL N 464 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN N 465 " --> pdb=" O ALA N 500 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 171 through 172 removed outlier: 4.212A pdb=" N VAL P 212 " --> pdb=" O SER P 204 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER P 204 " --> pdb=" O VAL P 212 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 244 through 245 1290 hydrogen bonds defined for protein. 3738 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: 8.44 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 12514 1.34 - 1.48: 8591 1.48 - 1.61: 17936 1.61 - 1.75: 1 1.75 - 1.88: 262 Bond restraints: 39304 Sorted by residual: bond pdb=" CA VAL J 242 " pdb=" CB VAL J 242 " ideal model delta sigma weight residual 1.537 1.564 -0.028 5.00e-03 4.00e+04 3.03e+01 bond pdb=" CA GLY M 141 " pdb=" C GLY M 141 " ideal model delta sigma weight residual 1.518 1.557 -0.038 7.30e-03 1.88e+04 2.75e+01 bond pdb=" O1P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.509 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" O2P SEP L 52 " pdb=" P SEP L 52 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" O3P SEP K 52 " pdb=" P SEP K 52 " ideal model delta sigma weight residual 1.610 1.511 0.099 2.00e-02 2.50e+03 2.46e+01 ... (remaining 39299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 49809 2.70 - 5.41: 3015 5.41 - 8.11: 315 8.11 - 10.81: 34 10.81 - 13.51: 4 Bond angle restraints: 53177 Sorted by residual: angle pdb=" C SER N 489 " pdb=" N PRO N 490 " pdb=" CA PRO N 490 " ideal model delta sigma weight residual 119.84 129.20 -9.36 1.25e+00 6.40e-01 5.61e+01 angle pdb=" N PHE B 149 " pdb=" CA PHE B 149 " pdb=" C PHE B 149 " ideal model delta sigma weight residual 108.45 117.78 -9.33 1.26e+00 6.30e-01 5.48e+01 angle pdb=" C LEU I 97 " pdb=" N PRO I 98 " pdb=" CA PRO I 98 " ideal model delta sigma weight residual 119.84 128.84 -9.00 1.25e+00 6.40e-01 5.18e+01 angle pdb=" N LYS M 300 " pdb=" CA LYS M 300 " pdb=" C LYS M 300 " ideal model delta sigma weight residual 110.97 118.75 -7.78 1.09e+00 8.42e-01 5.09e+01 angle pdb=" N VAL A 211 " pdb=" CA VAL A 211 " pdb=" C VAL A 211 " ideal model delta sigma weight residual 110.62 117.78 -7.16 1.02e+00 9.61e-01 4.92e+01 ... (remaining 53172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 20199 17.67 - 35.34: 2824 35.34 - 53.01: 631 53.01 - 70.68: 338 70.68 - 88.35: 42 Dihedral angle restraints: 24034 sinusoidal: 9591 harmonic: 14443 Sorted by residual: dihedral pdb=" C ILE K 150 " pdb=" N ILE K 150 " pdb=" CA ILE K 150 " pdb=" CB ILE K 150 " ideal model delta harmonic sigma weight residual -122.00 -136.70 14.70 0 2.50e+00 1.60e-01 3.46e+01 dihedral pdb=" C ILE L 150 " pdb=" N ILE L 150 " pdb=" CA ILE L 150 " pdb=" CB ILE L 150 " ideal model delta harmonic sigma weight residual -122.00 -136.25 14.25 0 2.50e+00 1.60e-01 3.25e+01 dihedral pdb=" N ILE K 150 " pdb=" C ILE K 150 " pdb=" CA ILE K 150 " pdb=" CB ILE K 150 " ideal model delta harmonic sigma weight residual 123.40 137.37 -13.97 0 2.50e+00 1.60e-01 3.12e+01 ... (remaining 24031 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 4908 0.099 - 0.198: 1028 0.198 - 0.297: 242 0.297 - 0.396: 42 0.396 - 0.495: 17 Chirality restraints: 6237 Sorted by residual: chirality pdb=" CA LEU J 202 " pdb=" N LEU J 202 " pdb=" C LEU J 202 " pdb=" CB LEU J 202 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.12e+00 chirality pdb=" CA ARG M 356 " pdb=" N ARG M 356 " pdb=" C ARG M 356 " pdb=" CB ARG M 356 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ASN C 275 " pdb=" N ASN C 275 " pdb=" C ASN C 275 " pdb=" CB ASN C 275 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 ... (remaining 6234 not shown) Planarity restraints: 6785 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS M 139 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C LYS M 139 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS M 139 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU M 140 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR I 304 " -0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO I 305 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO I 305 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I 305 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 157 " -0.045 5.00e-02 4.00e+02 6.76e-02 7.32e+00 pdb=" N PRO A 158 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " -0.038 5.00e-02 4.00e+02 ... (remaining 6782 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 5 1.97 - 2.70: 249 2.70 - 3.43: 51014 3.43 - 4.17: 80197 4.17 - 4.90: 137678 Nonbonded interactions: 269143 Sorted by model distance: nonbonded pdb=" OG SER F 413 " pdb=" OE1 GLN F 414 " model vdw 1.236 3.040 nonbonded pdb=" OG SER F 413 " pdb=" CD GLN F 414 " model vdw 1.543 3.270 nonbonded pdb=" OD2 ASP B 17 " pdb=" NH1 ARG B 133 " model vdw 1.700 3.120 nonbonded pdb=" OG SER F 413 " pdb=" NE2 GLN F 414 " model vdw 1.775 3.120 nonbonded pdb=" ND2 ASN M 144 " pdb=" OE2 GLU M 383 " model vdw 1.777 3.120 ... (remaining 269138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' } 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=0.00 max=1.00 mean=0.98 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: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 33.350 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.150 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3744 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 : 0.009 0.101 39304 Z= 0.603 Angle : 1.437 13.515 53177 Z= 0.943 Chirality : 0.090 0.495 6237 Planarity : 0.005 0.077 6785 Dihedral : 18.646 88.352 14636 Min Nonbonded Distance : 1.236 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 3.41 % Allowed : 13.22 % Favored : 83.37 % Rotamer: Outliers : 7.64 % Allowed : 13.89 % Favored : 78.47 % Cbeta Deviations : 0.74 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.11), residues: 4841 helix: 1.61 (0.12), residues: 1454 sheet: -0.47 (0.23), residues: 519 loop : -3.19 (0.10), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 301 TYR 0.021 0.002 TYR G 322 PHE 0.018 0.002 PHE C 51 TRP 0.011 0.001 TRP I 99 HIS 0.007 0.001 HIS H 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00851 / 0.60 (39304) covalent geometry : angle 1.43656 / 0.94 (53177) hydrogen bonds : bond 0.18413 / 12.42 ( 1282) hydrogen bonds : angle 7.30151 / 5.18 ( 3738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 326 poor density : 582 time to evaluate : 1.567 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: 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 224 ARG cc_start: 0.3206 (OUTLIER) cc_final: 0.2443 (tpt170) REVERT: A 236 PHE cc_start: 0.1595 (OUTLIER) cc_final: 0.1277 (m-80) REVERT: C 238 ILE cc_start: 0.0582 (OUTLIER) cc_final: -0.0330 (mm) REVERT: C 260 ILE cc_start: 0.7678 (mt) cc_final: 0.7407 (mt) REVERT: C 310 GLU cc_start: 0.4119 (OUTLIER) cc_final: 0.2972 (mm-30) REVERT: C 312 PHE cc_start: 0.7941 (m-80) cc_final: 0.7282 (m-80) REVERT: D 31 ARG cc_start: 0.4375 (mtm180) cc_final: 0.3181 (mmt180) REVERT: D 104 MET cc_start: 0.0714 (mmt) cc_final: -0.0820 (mtt) REVERT: D 162 ILE cc_start: 0.7520 (mt) cc_final: 0.7246 (mm) REVERT: D 280 SER cc_start: 0.8889 (p) cc_final: 0.8654 (t) REVERT: E 144 ILE cc_start: 0.5066 (OUTLIER) cc_final: 0.4590 (tt) REVERT: F 141 ILE cc_start: -0.2074 (OUTLIER) cc_final: -0.2452 (pt) REVERT: F 222 PHE cc_start: -0.1778 (OUTLIER) cc_final: -0.2594 (m-80) REVERT: F 237 ILE cc_start: 0.6092 (mt) cc_final: 0.5794 (tp) REVERT: F 258 HIS cc_start: 0.6681 (OUTLIER) cc_final: 0.6325 (m-70) REVERT: F 274 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.5652 (m-40) REVERT: F 428 ILE cc_start: 0.2709 (mp) cc_final: 0.1801 (mm) REVERT: F 447 LYS cc_start: -0.3379 (mttt) cc_final: -0.4295 (tptp) REVERT: F 448 MET cc_start: 0.2392 (ttm) cc_final: 0.1461 (tpt) REVERT: F 457 ILE cc_start: 0.1217 (mt) cc_final: -0.0091 (tt) REVERT: F 467 LEU cc_start: -0.3009 (mp) cc_final: -0.3353 (mp) REVERT: F 512 ASN cc_start: 0.2544 (m-40) cc_final: 0.2061 (m-40) REVERT: F 521 ASN cc_start: 0.1230 (m-40) cc_final: 0.0255 (t0) REVERT: F 522 VAL cc_start: -0.4198 (t) cc_final: -0.4505 (p) REVERT: G 284 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.5474 (t80) REVERT: G 424 ILE cc_start: -0.0322 (OUTLIER) cc_final: -0.0906 (tt) REVERT: G 486 ARG cc_start: 0.5513 (mtm180) cc_final: 0.5005 (mpp80) REVERT: G 565 LEU cc_start: 0.4759 (OUTLIER) cc_final: 0.4185 (mp) REVERT: H 324 SER cc_start: 0.8608 (m) cc_final: 0.8173 (t) REVERT: H 386 ILE cc_start: 0.6061 (mt) cc_final: 0.5794 (mt) REVERT: H 427 ILE cc_start: 0.8261 (mt) cc_final: 0.7465 (mp) REVERT: H 428 VAL cc_start: 0.8370 (t) cc_final: 0.8089 (p) REVERT: H 477 ILE cc_start: 0.2892 (OUTLIER) cc_final: 0.1770 (mt) REVERT: H 501 ILE cc_start: 0.6165 (OUTLIER) cc_final: 0.5093 (pp) REVERT: H 530 ASN cc_start: 0.6456 (m-40) cc_final: 0.5692 (m-40) REVERT: J 65 GLU cc_start: 0.7843 (tt0) cc_final: 0.7599 (tt0) REVERT: J 163 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.5922 (mp) REVERT: J 173 THR cc_start: 0.7150 (OUTLIER) cc_final: 0.6897 (m) REVERT: J 274 TYR cc_start: 0.2934 (OUTLIER) cc_final: -0.1516 (m-80) REVERT: J 357 ILE cc_start: 0.8333 (OUTLIER) cc_final: 0.8083 (tt) REVERT: K 64 ARG cc_start: -0.1833 (OUTLIER) cc_final: -0.2428 (mmt180) REVERT: L 33 TYR cc_start: 0.3215 (p90) cc_final: 0.1970 (p90) REVERT: L 54 ARG cc_start: 0.4070 (OUTLIER) cc_final: 0.2648 (mmt180) REVERT: M 204 MET cc_start: 0.2424 (tpt) cc_final: 0.1655 (tpp) REVERT: N 201 MET cc_start: -0.0432 (mmm) cc_final: -0.1273 (mmm) REVERT: N 211 MET cc_start: 0.1129 (mtp) cc_final: 0.0631 (mtm) REVERT: N 310 MET cc_start: 0.5960 (mmm) cc_final: 0.5375 (mmt) REVERT: N 489 SER cc_start: 0.4581 (OUTLIER) cc_final: 0.3675 (p) outliers start: 326 outliers final: 48 residues processed: 853 average time/residue: 0.2379 time to fit residues: 330.4433 Evaluate side-chains 397 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 328 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 9.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 4.9990 chunk 470 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 50.4249 > 50:) overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 ASN C 66 GLN C 72 ASN C 156 GLN C 222 ASN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 10 HIS D 19 ASN D 33 GLN D 58 ASN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 HIS D 86 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN D 375 HIS E 133 HIS ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN F 156 GLN F 189 ASN F 193 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 271 HIS G 446 ASN G 475 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 500 ASN H 271 HIS ** H 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 517 GLN H 574 ASN I 371 ASN I 417 ASN I 460 GLN J 28 GLN J 56 ASN J 73 HIS ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 92 ASN J 212 GLN J 241 HIS ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 388 ASN J 393 HIS J 423 ASN K 41 ASN K 140 HIS ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 ASN M 324 ASN M 465 ASN N 98 GLN ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 243 HIS N 286 GLN ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.118669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.097390 restraints weight = 214341.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.099052 restraints weight = 164000.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.100032 restraints weight = 130075.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.100983 restraints weight = 109693.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.101428 restraints weight = 96893.323| |-----------------------------------------------------------------------------| r_work (final): 0.4648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4648 r_free = 0.4648 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 803 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4648 r_free = 0.4648 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 803 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5578 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 39304 Z= 0.226 Angle : 0.856 11.258 53177 Z= 0.445 Chirality : 0.052 0.256 6237 Planarity : 0.006 0.067 6785 Dihedral : 6.517 45.033 5276 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 1.09 % Allowed : 11.24 % Favored : 87.67 % Rotamer: Outliers : 0.26 % Allowed : 5.58 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.12), residues: 4841 helix: 1.85 (0.14), residues: 1461 sheet: -0.82 (0.20), residues: 639 loop : -3.19 (0.10), residues: 2741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 254 TYR 0.030 0.003 TYR G 322 PHE 0.037 0.002 PHE I 145 TRP 0.037 0.003 TRP C 366 HIS 0.026 0.002 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 (39304) covalent geometry : angle 0.85630 / 0.44 (53177) hydrogen bonds : bond 0.04625 / 3.17 ( 1282) hydrogen bonds : angle 5.80410 / 4.15 ( 3738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 391 time to evaluate : 1.680 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: symmetry clash revert: symmetry clash REVERT: B 249 MET cc_start: 0.3215 (mtt) cc_final: 0.2943 (mtp) REVERT: C 160 ASP cc_start: 0.6401 (m-30) cc_final: 0.6199 (m-30) REVERT: C 181 HIS cc_start: 0.8239 (m-70) cc_final: 0.7442 (m-70) REVERT: C 217 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6633 (mt-10) REVERT: C 312 PHE cc_start: 0.8864 (m-80) cc_final: 0.8304 (m-80) REVERT: C 357 ASN cc_start: 0.9237 (t0) cc_final: 0.9014 (t0) REVERT: D 162 ILE cc_start: 0.8446 (mt) cc_final: 0.8101 (mm) REVERT: D 212 THR cc_start: 0.7014 (p) cc_final: 0.6801 (t) REVERT: D 336 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.5528 (pp30) REVERT: F 76 MET cc_start: 0.6219 (ppp) cc_final: 0.5983 (tmm) REVERT: F 447 LYS cc_start: -0.5183 (mttt) cc_final: -0.5604 (tptp) REVERT: F 448 MET cc_start: 0.0977 (ttm) cc_final: 0.0556 (tpt) REVERT: F 512 ASN cc_start: -0.1124 (m-40) cc_final: -0.1834 (m-40) REVERT: F 522 VAL cc_start: -0.1421 (t) cc_final: -0.1879 (p) REVERT: G 409 LEU cc_start: 0.9226 (mt) cc_final: 0.9002 (mt) REVERT: H 298 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8806 (mm-30) REVERT: H 427 ILE cc_start: 0.8985 (mt) cc_final: 0.7856 (mp) REVERT: H 428 VAL cc_start: 0.9105 (t) cc_final: 0.8838 (p) REVERT: H 440 MET cc_start: 0.8501 (tpt) cc_final: 0.8131 (tpt) REVERT: H 456 ILE cc_start: 0.8250 (tp) cc_final: 0.8026 (tp) REVERT: H 530 ASN cc_start: 0.7831 (m-40) cc_final: 0.7625 (m110) REVERT: H 559 LYS cc_start: 0.8313 (tppt) cc_final: 0.7988 (tppt) REVERT: I 259 PHE cc_start: 0.7166 (t80) cc_final: 0.6835 (t80) REVERT: I 455 GLN cc_start: 0.0975 (tp40) cc_final: 0.0735 (tp40) REVERT: K 30 MET cc_start: -0.1952 (mtt) cc_final: -0.2299 (mtt) REVERT: K 45 MET cc_start: 0.5379 (tpt) cc_final: 0.5044 (tpt) REVERT: K 206 LYS cc_start: 0.6935 (mttt) cc_final: 0.6512 (tttm) REVERT: N 211 MET cc_start: 0.1096 (mtp) cc_final: 0.0787 (ttm) REVERT: N 310 MET cc_start: 0.4608 (mmm) cc_final: 0.4326 (mmt) outliers start: 11 outliers final: 1 residues processed: 399 average time/residue: 0.2320 time to fit residues: 154.7528 Evaluate side-chains 271 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 269 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 354 optimal weight: 20.0000 chunk 266 optimal weight: 0.0370 chunk 422 optimal weight: 30.0000 chunk 50 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 252 optimal weight: 7.9990 chunk 339 optimal weight: 7.9990 chunk 406 optimal weight: 30.0000 chunk 89 optimal weight: 5.9990 chunk 148 optimal weight: 30.0000 chunk 239 optimal weight: 8.9990 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 HIS ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN C 33 GLN C 222 ASN C 225 ASN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 236 HIS D 352 ASN ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 186 GLN F 219 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 534 ASN H 384 GLN H 389 ASN ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 365 ASN I 417 ASN J 82 HIS J 228 ASN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 GLN L 109 HIS M 98 GLN ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 ASN ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.115024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4616 r_free = 0.4616 target = 0.096227 restraints weight = 204632.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.097661 restraints weight = 164286.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.098759 restraints weight = 134687.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.099301 restraints weight = 118266.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.099996 restraints weight = 105056.816| |-----------------------------------------------------------------------------| r_work (final): 0.4653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5563 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 39304 Z= 0.202 Angle : 0.781 11.142 53177 Z= 0.405 Chirality : 0.050 0.356 6237 Planarity : 0.006 0.073 6785 Dihedral : 6.332 42.663 5276 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.91 % Allowed : 12.89 % Favored : 86.20 % Rotamer: Outliers : 0.21 % Allowed : 5.32 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.12), residues: 4841 helix: 1.07 (0.13), residues: 1481 sheet: -0.98 (0.20), residues: 599 loop : -3.14 (0.10), residues: 2761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 406 TYR 0.025 0.002 TYR B 228 PHE 0.038 0.002 PHE C 288 TRP 0.043 0.003 TRP F 83 HIS 0.014 0.002 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (39304) covalent geometry : angle 0.78098 / 0.41 (53177) hydrogen bonds : bond 0.04264 / 2.88 ( 1282) hydrogen bonds : angle 5.52772 / 3.90 ( 3738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 344 time to evaluate : 1.532 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 283 LEU cc_start: 0.5282 (mt) cc_final: 0.4978 (mt) REVERT: B 192 ASP cc_start: 0.7261 (t0) cc_final: 0.6292 (t0) REVERT: B 193 LYS cc_start: 0.7448 (pttm) cc_final: 0.7240 (pttm) REVERT: B 239 MET cc_start: 0.4310 (ttt) cc_final: 0.4105 (ttt) REVERT: B 249 MET cc_start: 0.2786 (mtt) cc_final: 0.2495 (mtp) REVERT: C 50 ARG cc_start: 0.7535 (mtt180) cc_final: 0.6927 (ttt180) REVERT: C 259 ILE cc_start: 0.7131 (mm) cc_final: 0.6911 (mm) REVERT: C 312 PHE cc_start: 0.8891 (m-80) cc_final: 0.8373 (m-80) REVERT: C 357 ASN cc_start: 0.9210 (t0) cc_final: 0.8944 (t0) REVERT: D 162 ILE cc_start: 0.8562 (mt) cc_final: 0.8187 (mm) REVERT: D 293 PHE cc_start: 0.5810 (m-80) cc_final: 0.5580 (m-80) REVERT: D 341 VAL cc_start: 0.8978 (t) cc_final: 0.8756 (t) REVERT: E 58 MET cc_start: -0.3997 (tpt) cc_final: -0.4218 (tpt) REVERT: E 391 LEU cc_start: 0.8463 (pt) cc_final: 0.8213 (pp) REVERT: E 402 MET cc_start: 0.6804 (tmm) cc_final: 0.6562 (ppp) REVERT: F 76 MET cc_start: 0.6330 (ppp) cc_final: 0.5835 (tmm) REVERT: F 447 LYS cc_start: -0.5542 (mttt) cc_final: -0.5973 (tptp) REVERT: F 496 LYS cc_start: 0.0301 (mptt) cc_final: 0.0086 (mmtt) REVERT: F 512 ASN cc_start: -0.2091 (m-40) cc_final: -0.2516 (m-40) REVERT: F 522 VAL cc_start: -0.1647 (t) cc_final: -0.1994 (p) REVERT: G 293 CYS cc_start: 0.8551 (p) cc_final: 0.8028 (t) REVERT: G 296 MET cc_start: 0.6893 (tmm) cc_final: 0.6303 (tmm) REVERT: G 304 ILE cc_start: 0.8412 (mm) cc_final: 0.8007 (pt) REVERT: G 384 GLN cc_start: 0.9401 (mt0) cc_final: 0.8625 (tp-100) REVERT: G 409 LEU cc_start: 0.9428 (mt) cc_final: 0.9168 (mt) REVERT: H 298 GLU cc_start: 0.9059 (mt-10) cc_final: 0.8804 (mm-30) REVERT: H 427 ILE cc_start: 0.9041 (mt) cc_final: 0.8136 (mp) REVERT: H 428 VAL cc_start: 0.9165 (t) cc_final: 0.8936 (p) REVERT: H 440 MET cc_start: 0.8433 (tpt) cc_final: 0.8195 (tpt) REVERT: I 230 LEU cc_start: 0.9094 (mt) cc_final: 0.8599 (mp) REVERT: I 259 PHE cc_start: 0.7150 (t80) cc_final: 0.6849 (t80) REVERT: I 455 GLN cc_start: 0.0673 (tp40) cc_final: 0.0417 (tp40) REVERT: K 21 MET cc_start: 0.4426 (tpt) cc_final: 0.4064 (tpp) REVERT: K 45 MET cc_start: 0.5455 (tpt) cc_final: 0.5207 (tpt) REVERT: K 206 LYS cc_start: 0.7468 (mttt) cc_final: 0.7155 (mmmt) REVERT: M 204 MET cc_start: 0.2241 (ttt) cc_final: 0.2019 (tmm) REVERT: N 310 MET cc_start: 0.4871 (mmm) cc_final: 0.4490 (mmt) REVERT: P 222 MET cc_start: 0.0580 (ptp) cc_final: -0.0839 (mmt) outliers start: 9 outliers final: 3 residues processed: 352 average time/residue: 0.2249 time to fit residues: 135.0851 Evaluate side-chains 264 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 261 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 445 optimal weight: 50.0000 chunk 217 optimal weight: 9.9990 chunk 452 optimal weight: 0.0070 chunk 479 optimal weight: 30.0000 chunk 432 optimal weight: 40.0000 chunk 332 optimal weight: 5.9990 chunk 414 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 312 optimal weight: 5.9990 chunk 118 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 352 ASN ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 384 GLN H 539 ASN H 546 ASN ** I 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 365 ASN J 212 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 111 HIS M 197 HIS M 450 GLN ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4972 r_free = 0.4972 target = 0.115821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4632 r_free = 0.4632 target = 0.096558 restraints weight = 202929.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4653 r_free = 0.4653 target = 0.097544 restraints weight = 161545.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.098470 restraints weight = 134557.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.098470 restraints weight = 119554.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.098470 restraints weight = 119554.319| |-----------------------------------------------------------------------------| r_work (final): 0.4615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 39304 Z= 0.145 Angle : 0.692 11.886 53177 Z= 0.354 Chirality : 0.047 0.256 6237 Planarity : 0.005 0.060 6785 Dihedral : 6.043 35.168 5276 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.89 % Allowed : 10.64 % Favored : 88.47 % Rotamer: Outliers : 0.14 % Allowed : 3.77 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.12), residues: 4841 helix: 1.10 (0.13), residues: 1486 sheet: -1.12 (0.20), residues: 615 loop : -3.01 (0.10), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 334 TYR 0.022 0.002 TYR K 33 PHE 0.039 0.002 PHE C 51 TRP 0.036 0.002 TRP E 83 HIS 0.019 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (39304) covalent geometry : angle 0.69248 / 0.35 (53177) hydrogen bonds : bond 0.03621 / 2.46 ( 1282) hydrogen bonds : angle 5.21410 / 3.68 ( 3738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 359 time to evaluate : 1.513 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: symmetry clash revert: symmetry clash REVERT: A 239 MET cc_start: 0.3175 (mtp) cc_final: 0.2927 (ttm) REVERT: C 50 ARG cc_start: 0.7443 (mtt180) cc_final: 0.6772 (ttt180) REVERT: C 312 PHE cc_start: 0.8915 (m-80) cc_final: 0.8400 (m-80) REVERT: C 315 PHE cc_start: 0.8117 (m-80) cc_final: 0.7088 (m-10) REVERT: C 357 ASN cc_start: 0.9173 (t0) cc_final: 0.8864 (t0) REVERT: D 162 ILE cc_start: 0.8596 (mt) cc_final: 0.8237 (mm) REVERT: D 227 HIS cc_start: 0.8420 (t-90) cc_final: 0.8177 (t-90) REVERT: D 252 MET cc_start: 0.5346 (ttt) cc_final: 0.5058 (ttt) REVERT: E 391 LEU cc_start: 0.8461 (pt) cc_final: 0.8208 (pp) REVERT: F 76 MET cc_start: 0.6377 (ppp) cc_final: 0.5950 (tmm) REVERT: F 447 LYS cc_start: -0.5354 (mttt) cc_final: -0.5624 (tptp) REVERT: F 462 ARG cc_start: -0.0070 (mmt90) cc_final: -0.0307 (tpp-160) REVERT: F 512 ASN cc_start: -0.3353 (m-40) cc_final: -0.3694 (m-40) REVERT: F 522 VAL cc_start: -0.2319 (t) cc_final: -0.2584 (p) REVERT: G 304 ILE cc_start: 0.8451 (mm) cc_final: 0.8056 (pt) REVERT: G 384 GLN cc_start: 0.9236 (mt0) cc_final: 0.8584 (tp-100) REVERT: G 409 LEU cc_start: 0.9333 (mt) cc_final: 0.9039 (mt) REVERT: G 469 TYR cc_start: 0.7789 (m-10) cc_final: 0.7412 (m-10) REVERT: H 298 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8685 (mm-30) REVERT: H 427 ILE cc_start: 0.8851 (mt) cc_final: 0.8092 (mp) REVERT: H 428 VAL cc_start: 0.9018 (t) cc_final: 0.8814 (p) REVERT: I 259 PHE cc_start: 0.7326 (t80) cc_final: 0.7064 (t80) REVERT: I 455 GLN cc_start: 0.0860 (tp40) cc_final: 0.0583 (tp40) REVERT: J 166 MET cc_start: 0.7963 (mpp) cc_final: 0.7664 (mpp) REVERT: J 421 ASP cc_start: 0.8820 (m-30) cc_final: 0.8545 (m-30) REVERT: K 21 MET cc_start: 0.5158 (tpt) cc_final: 0.4755 (tpp) REVERT: K 45 MET cc_start: 0.5830 (tpt) cc_final: 0.5574 (tpt) REVERT: K 206 LYS cc_start: 0.7523 (mttt) cc_final: 0.7250 (mmmt) REVERT: M 211 MET cc_start: -0.1685 (mtm) cc_final: -0.2220 (mtp) REVERT: N 310 MET cc_start: 0.4727 (mmm) cc_final: 0.4453 (mmt) REVERT: P 222 MET cc_start: 0.0318 (ptp) cc_final: -0.1206 (mmt) outliers start: 6 outliers final: 2 residues processed: 364 average time/residue: 0.2085 time to fit residues: 128.3461 Evaluate side-chains 267 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 265 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 51 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 224 optimal weight: 0.9980 chunk 376 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 256 optimal weight: 0.0770 chunk 388 optimal weight: 30.0000 chunk 356 optimal weight: 6.9990 chunk 380 optimal weight: 20.0000 overall best weight: 4.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN D 19 ASN D 183 HIS ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 517 GLN G 553 GLN G 574 ASN H 280 HIS ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 GLN M 249 ASN ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.113753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.094281 restraints weight = 208112.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.095744 restraints weight = 166665.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.097046 restraints weight = 134221.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.097046 restraints weight = 109973.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4660 r_free = 0.4660 target = 0.097046 restraints weight = 109973.909| |-----------------------------------------------------------------------------| r_work (final): 0.4592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 39304 Z= 0.162 Angle : 0.711 11.958 53177 Z= 0.364 Chirality : 0.048 0.235 6237 Planarity : 0.005 0.077 6785 Dihedral : 6.028 36.076 5276 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.87 % Allowed : 12.04 % Favored : 87.09 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.12), residues: 4841 helix: 0.85 (0.13), residues: 1498 sheet: -1.31 (0.20), residues: 617 loop : -3.01 (0.11), residues: 2726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 89 TYR 0.030 0.002 TYR J 274 PHE 0.029 0.002 PHE C 51 TRP 0.043 0.002 TRP E 83 HIS 0.016 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (39304) covalent geometry : angle 0.71108 / 0.36 (53177) hydrogen bonds : bond 0.03728 / 2.54 ( 1282) hydrogen bonds : angle 5.22408 / 3.68 ( 3738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 1.366 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 58 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7470 (pptt) REVERT: A 239 MET cc_start: 0.3340 (mtp) cc_final: 0.2984 (ttm) REVERT: C 50 ARG cc_start: 0.7478 (mtt180) cc_final: 0.6824 (ttt180) REVERT: C 104 MET cc_start: 0.5971 (ptt) cc_final: 0.5007 (tpt) REVERT: C 259 ILE cc_start: 0.7047 (mm) cc_final: 0.6808 (mm) REVERT: C 312 PHE cc_start: 0.8921 (m-80) cc_final: 0.8401 (m-80) REVERT: C 315 PHE cc_start: 0.8167 (m-80) cc_final: 0.6775 (m-80) REVERT: C 357 ASN cc_start: 0.9166 (t0) cc_final: 0.8877 (t0) REVERT: D 162 ILE cc_start: 0.8612 (mt) cc_final: 0.8239 (mm) REVERT: D 341 VAL cc_start: 0.8959 (t) cc_final: 0.8665 (t) REVERT: E 391 LEU cc_start: 0.8500 (pt) cc_final: 0.8289 (pp) REVERT: E 406 ARG cc_start: 0.8094 (ptp90) cc_final: 0.7208 (mmt180) REVERT: F 76 MET cc_start: 0.6491 (ppp) cc_final: 0.5960 (tmm) REVERT: F 447 LYS cc_start: -0.4818 (mttt) cc_final: -0.5162 (tptp) REVERT: G 384 GLN cc_start: 0.9315 (mt0) cc_final: 0.8559 (tp-100) REVERT: G 409 LEU cc_start: 0.9441 (mt) cc_final: 0.9195 (mt) REVERT: G 440 MET cc_start: 0.8111 (ppp) cc_final: 0.7840 (ppp) REVERT: G 469 TYR cc_start: 0.7978 (m-10) cc_final: 0.7561 (m-10) REVERT: H 298 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8588 (mm-30) REVERT: H 427 ILE cc_start: 0.8993 (mt) cc_final: 0.8251 (mp) REVERT: I 108 MET cc_start: 0.0762 (mpp) cc_final: -0.0235 (mmt) REVERT: I 227 ARG cc_start: 0.8707 (ttt-90) cc_final: 0.8347 (mtp85) REVERT: I 259 PHE cc_start: 0.7553 (t80) cc_final: 0.7240 (t80) REVERT: I 306 LEU cc_start: 0.9334 (mm) cc_final: 0.9123 (mm) REVERT: I 424 MET cc_start: 0.4220 (mtt) cc_final: 0.2550 (mtm) REVERT: J 307 VAL cc_start: 0.6947 (t) cc_final: 0.6710 (t) REVERT: J 421 ASP cc_start: 0.8888 (m-30) cc_final: 0.8592 (m-30) REVERT: K 45 MET cc_start: 0.5801 (tpt) cc_final: 0.5349 (tpt) REVERT: K 206 LYS cc_start: 0.7549 (mttt) cc_final: 0.7313 (pptt) REVERT: N 310 MET cc_start: 0.4874 (mmm) cc_final: 0.4529 (mmt) REVERT: P 222 MET cc_start: 0.0390 (ptp) cc_final: -0.1054 (mmt) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.2159 time to fit residues: 122.8814 Evaluate side-chains 257 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 292 optimal weight: 1.9990 chunk 201 optimal weight: 8.9990 chunk 277 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 148 optimal weight: 0.9990 chunk 360 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 395 optimal weight: 30.0000 chunk 385 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 97 ASN A 161 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 ASN D 183 HIS ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 HIS ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 59 GLN F 265 ASN G 280 HIS ** G 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 73 HIS ** I 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5001 r_free = 0.5001 target = 0.116902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.096769 restraints weight = 199960.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.097728 restraints weight = 161637.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.098929 restraints weight = 136104.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.099995 restraints weight = 115638.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.100486 restraints weight = 104628.780| |-----------------------------------------------------------------------------| r_work (final): 0.4671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5500 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 39304 Z= 0.116 Angle : 0.652 12.748 53177 Z= 0.328 Chirality : 0.046 0.235 6237 Planarity : 0.004 0.062 6785 Dihedral : 5.621 32.840 5276 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.56 % Favored : 89.71 % Rotamer: Outliers : 0.05 % Allowed : 1.69 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.12), residues: 4841 helix: 1.19 (0.14), residues: 1496 sheet: -1.05 (0.20), residues: 629 loop : -2.86 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 90 TYR 0.023 0.001 TYR H 453 PHE 0.019 0.001 PHE M 297 TRP 0.040 0.002 TRP C 366 HIS 0.013 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (39304) covalent geometry : angle 0.65208 / 0.33 (53177) hydrogen bonds : bond 0.03142 / 2.14 ( 1282) hydrogen bonds : angle 4.86056 / 3.42 ( 3738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 359 time to evaluate : 1.553 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: A 58 LYS cc_start: 0.7810 (mtmm) cc_final: 0.7563 (pptt) REVERT: A 239 MET cc_start: 0.3317 (mtp) cc_final: 0.2599 (ttm) REVERT: B 119 PHE cc_start: 0.6429 (p90) cc_final: 0.6178 (p90) REVERT: B 295 VAL cc_start: 0.6935 (t) cc_final: 0.6664 (t) REVERT: C 50 ARG cc_start: 0.7430 (mtt180) cc_final: 0.6807 (ttt180) REVERT: C 104 MET cc_start: 0.5811 (ptt) cc_final: 0.4751 (tpt) REVERT: C 181 HIS cc_start: 0.8336 (m-70) cc_final: 0.7970 (m90) REVERT: C 312 PHE cc_start: 0.8868 (m-80) cc_final: 0.8349 (m-80) REVERT: C 315 PHE cc_start: 0.7980 (m-80) cc_final: 0.6701 (m-80) REVERT: C 357 ASN cc_start: 0.9109 (t0) cc_final: 0.8810 (t0) REVERT: E 406 ARG cc_start: 0.7961 (ptp90) cc_final: 0.6928 (mmt180) REVERT: F 76 MET cc_start: 0.6458 (ppp) cc_final: 0.5962 (tmm) REVERT: F 265 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6416 (t0) REVERT: F 447 LYS cc_start: -0.5118 (mttt) cc_final: -0.5438 (tptp) REVERT: F 448 MET cc_start: -0.0294 (tpt) cc_final: -0.1030 (tpt) REVERT: F 462 ARG cc_start: 0.0038 (mmt180) cc_final: -0.0518 (tpp-160) REVERT: G 304 ILE cc_start: 0.8453 (mm) cc_final: 0.8079 (pt) REVERT: G 384 GLN cc_start: 0.9299 (mt0) cc_final: 0.8665 (tp-100) REVERT: G 388 ASP cc_start: 0.8081 (m-30) cc_final: 0.6822 (p0) REVERT: G 469 TYR cc_start: 0.7702 (m-10) cc_final: 0.7411 (m-10) REVERT: H 298 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8730 (mm-30) REVERT: H 427 ILE cc_start: 0.8871 (mt) cc_final: 0.8297 (mp) REVERT: I 108 MET cc_start: 0.0678 (mpp) cc_final: -0.0602 (mmt) REVERT: I 259 PHE cc_start: 0.7260 (t80) cc_final: 0.6975 (t80) REVERT: I 424 MET cc_start: 0.2624 (mtt) cc_final: 0.1426 (mtm) REVERT: J 307 VAL cc_start: 0.6763 (t) cc_final: 0.6532 (t) REVERT: K 45 MET cc_start: 0.5914 (tpt) cc_final: 0.5384 (tpt) REVERT: K 206 LYS cc_start: 0.7620 (mttt) cc_final: 0.7266 (tttm) REVERT: M 204 MET cc_start: 0.2723 (tmm) cc_final: 0.2436 (tmm) REVERT: N 310 MET cc_start: 0.4828 (mmm) cc_final: 0.4307 (mpp) REVERT: P 222 MET cc_start: 0.0836 (ptp) cc_final: -0.0528 (mmt) outliers start: 2 outliers final: 0 residues processed: 360 average time/residue: 0.2129 time to fit residues: 130.8857 Evaluate side-chains 274 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 273 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 169 optimal weight: 10.0000 chunk 432 optimal weight: 0.5980 chunk 249 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 462 optimal weight: 40.0000 chunk 278 optimal weight: 7.9990 chunk 435 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 325 optimal weight: 0.0770 chunk 96 optimal weight: 3.9990 chunk 217 optimal weight: 0.6980 overall best weight: 1.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 275 ASN C 375 HIS D 183 HIS ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 GLN F 298 GLN G 480 ASN ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5000 r_free = 0.5000 target = 0.116636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.097224 restraints weight = 202184.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4688 r_free = 0.4688 target = 0.098655 restraints weight = 160953.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4717 r_free = 0.4717 target = 0.099791 restraints weight = 127075.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.100257 restraints weight = 113163.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4726 r_free = 0.4726 target = 0.100263 restraints weight = 101838.926| |-----------------------------------------------------------------------------| r_work (final): 0.4667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5498 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39304 Z= 0.113 Angle : 0.637 14.782 53177 Z= 0.320 Chirality : 0.046 0.312 6237 Planarity : 0.004 0.088 6785 Dihedral : 5.446 32.856 5276 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.68 % Allowed : 10.47 % Favored : 88.85 % Rotamer: Outliers : 0.02 % Allowed : 1.19 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.12), residues: 4841 helix: 1.24 (0.14), residues: 1501 sheet: -1.10 (0.19), residues: 664 loop : -2.80 (0.11), residues: 2676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 75 TYR 0.022 0.001 TYR G 284 PHE 0.028 0.001 PHE C 229 TRP 0.035 0.001 TRP E 83 HIS 0.011 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (39304) covalent geometry : angle 0.63702 / 0.32 (53177) hydrogen bonds : bond 0.03093 / 2.10 ( 1282) hydrogen bonds : angle 4.76671 / 3.36 ( 3738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 341 time to evaluate : 1.704 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: A 58 LYS cc_start: 0.7823 (mtmm) cc_final: 0.7613 (pptt) REVERT: A 239 MET cc_start: 0.3504 (mtp) cc_final: 0.2917 (ttt) REVERT: C 50 ARG cc_start: 0.7452 (mtt180) cc_final: 0.6862 (ttt180) REVERT: C 104 MET cc_start: 0.6022 (ptt) cc_final: 0.5023 (tpt) REVERT: C 181 HIS cc_start: 0.8297 (m-70) cc_final: 0.7903 (m90) REVERT: C 259 ILE cc_start: 0.6994 (mm) cc_final: 0.6774 (mm) REVERT: C 315 PHE cc_start: 0.8126 (m-80) cc_final: 0.6764 (m-80) REVERT: C 357 ASN cc_start: 0.9176 (t0) cc_final: 0.8969 (t0) REVERT: D 339 ASP cc_start: 0.5970 (p0) cc_final: 0.5607 (p0) REVERT: E 58 MET cc_start: -0.2145 (tpp) cc_final: -0.2380 (tpt) REVERT: E 406 ARG cc_start: 0.8024 (ptp90) cc_final: 0.7058 (mmt180) REVERT: F 76 MET cc_start: 0.6526 (ppp) cc_final: 0.6023 (tmm) REVERT: F 447 LYS cc_start: -0.5118 (mttt) cc_final: -0.5322 (tptp) REVERT: F 448 MET cc_start: 0.0733 (tpt) cc_final: -0.0557 (tpt) REVERT: F 462 ARG cc_start: 0.0062 (mmt180) cc_final: -0.0279 (tpp-160) REVERT: G 304 ILE cc_start: 0.8485 (mm) cc_final: 0.8128 (pt) REVERT: G 384 GLN cc_start: 0.9288 (mt0) cc_final: 0.8604 (tp-100) REVERT: G 388 ASP cc_start: 0.8045 (m-30) cc_final: 0.6667 (p0) REVERT: G 440 MET cc_start: 0.8013 (ppp) cc_final: 0.7735 (ppp) REVERT: G 469 TYR cc_start: 0.7992 (m-10) cc_final: 0.7634 (m-10) REVERT: H 298 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8798 (mm-30) REVERT: H 427 ILE cc_start: 0.8909 (mt) cc_final: 0.8147 (mp) REVERT: I 108 MET cc_start: 0.0916 (mpp) cc_final: -0.0482 (mmt) REVERT: I 227 ARG cc_start: 0.8863 (ttt180) cc_final: 0.8621 (ttp80) REVERT: I 259 PHE cc_start: 0.7413 (t80) cc_final: 0.7110 (t80) REVERT: I 424 MET cc_start: 0.3762 (mtt) cc_final: 0.2576 (mtm) REVERT: J 307 VAL cc_start: 0.6802 (t) cc_final: 0.6500 (t) REVERT: J 421 ASP cc_start: 0.8952 (m-30) cc_final: 0.8658 (m-30) REVERT: K 206 LYS cc_start: 0.7666 (mttt) cc_final: 0.7444 (pptt) REVERT: M 204 MET cc_start: 0.2733 (tmm) cc_final: 0.2438 (tmm) REVERT: N 310 MET cc_start: 0.4527 (mmm) cc_final: 0.4228 (mmt) REVERT: P 222 MET cc_start: 0.0859 (ptp) cc_final: -0.0563 (mmt) outliers start: 1 outliers final: 0 residues processed: 341 average time/residue: 0.2201 time to fit residues: 128.5915 Evaluate side-chains 268 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 273 optimal weight: 20.0000 chunk 402 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 280 optimal weight: 7.9990 chunk 399 optimal weight: 50.0000 chunk 6 optimal weight: 20.0000 chunk 462 optimal weight: 50.0000 chunk 349 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 457 optimal weight: 50.0000 chunk 413 optimal weight: 50.0000 overall best weight: 12.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 80 ASN ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 HIS ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 10 HIS ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 268 ASN D 183 HIS ** D 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 ASN E 298 GLN ** E 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 405 ASN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 325 HIS ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN ** J 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 GLN J 220 ASN J 335 GLN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 GLN ** M 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 248 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.104816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.084839 restraints weight = 244365.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.086282 restraints weight = 188921.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.087742 restraints weight = 153650.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.087889 restraints weight = 124227.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.088348 restraints weight = 112335.371| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.7256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.113 39304 Z= 0.363 Angle : 1.056 17.049 53177 Z= 0.548 Chirality : 0.060 0.473 6237 Planarity : 0.008 0.116 6785 Dihedral : 7.430 44.717 5276 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 32.58 Ramachandran Plot: Outliers : 0.72 % Allowed : 14.25 % Favored : 85.02 % Rotamer: Outliers : 0.02 % Allowed : 2.11 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.09 (0.11), residues: 4841 helix: -0.58 (0.13), residues: 1506 sheet: -1.82 (0.20), residues: 613 loop : -3.12 (0.11), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 90 TYR 0.045 0.004 TYR B 166 PHE 0.068 0.004 PHE C 288 TRP 0.049 0.005 TRP C 366 HIS 0.016 0.003 HIS D 236 Details of bonding type rmsd/Z covalent geometry : bond 0.00788 / 0.36 (39304) covalent geometry : angle 1.05622 / 0.55 (53177) hydrogen bonds : bond 0.05814 / 3.94 ( 1282) hydrogen bonds : angle 6.33837 / 4.45 ( 3738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 1.507 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: B 20 MET cc_start: 0.4156 (tmm) cc_final: 0.3697 (tmm) REVERT: C 50 ARG cc_start: 0.7812 (mtt180) cc_final: 0.7350 (ttt180) REVERT: C 335 ASN cc_start: 0.5671 (t0) cc_final: 0.4664 (m-40) REVERT: C 357 ASN cc_start: 0.8895 (t0) cc_final: 0.8409 (t0) REVERT: D 272 ILE cc_start: 0.9041 (mt) cc_final: 0.8743 (mt) REVERT: D 341 VAL cc_start: 0.8938 (t) cc_final: 0.8621 (t) REVERT: F 448 MET cc_start: -0.1599 (tpt) cc_final: -0.2290 (tpt) REVERT: F 460 ARG cc_start: -0.1524 (tpm170) cc_final: -0.1907 (mmp-170) REVERT: G 384 GLN cc_start: 0.9111 (mt0) cc_final: 0.8791 (mp10) REVERT: H 409 LEU cc_start: 0.9506 (mt) cc_final: 0.9302 (mt) REVERT: H 427 ILE cc_start: 0.9175 (mt) cc_final: 0.8583 (mp) REVERT: H 482 PHE cc_start: 0.4811 (m-80) cc_final: 0.4426 (m-10) REVERT: I 65 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7982 (mt-10) REVERT: I 259 PHE cc_start: 0.8006 (t80) cc_final: 0.7497 (t80) REVERT: I 261 LYS cc_start: 0.8396 (tttt) cc_final: 0.8000 (pptt) REVERT: I 306 LEU cc_start: 0.9296 (mm) cc_final: 0.8754 (mt) REVERT: I 424 MET cc_start: 0.5082 (mtt) cc_final: 0.2209 (mtt) REVERT: J 166 MET cc_start: 0.8078 (mpp) cc_final: 0.7642 (mpp) REVERT: J 421 ASP cc_start: 0.8995 (m-30) cc_final: 0.8507 (m-30) REVERT: J 424 MET cc_start: 0.0616 (ptp) cc_final: 0.0405 (ptp) REVERT: K 45 MET cc_start: 0.5956 (tpt) cc_final: 0.5657 (tpt) REVERT: L 21 MET cc_start: 0.6136 (mpp) cc_final: 0.5830 (mpp) REVERT: M 204 MET cc_start: 0.3161 (tmm) cc_final: 0.2957 (tmm) REVERT: M 211 MET cc_start: -0.0654 (mtp) cc_final: -0.0881 (mtp) REVERT: N 239 MET cc_start: -0.4267 (ttm) cc_final: -0.5218 (tpp) REVERT: N 310 MET cc_start: 0.4435 (mmm) cc_final: 0.4033 (mpp) REVERT: N 367 LYS cc_start: 0.7844 (mppt) cc_final: 0.7588 (pptt) REVERT: P 222 MET cc_start: 0.1022 (ptp) cc_final: -0.0313 (mmm) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.2233 time to fit residues: 110.5649 Evaluate side-chains 219 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 82 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 255 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 388 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 380 optimal weight: 8.9990 chunk 89 optimal weight: 0.0020 chunk 406 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 141 HIS ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 254 GLN ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 HIS J 124 ASN J 156 HIS ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 ASN ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.115173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.091080 restraints weight = 266253.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.093260 restraints weight = 185329.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.094202 restraints weight = 131855.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.095162 restraints weight = 110808.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.096152 restraints weight = 82791.570| |-----------------------------------------------------------------------------| r_work (final): 0.4450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5865 moved from start: 0.7034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 39304 Z= 0.141 Angle : 0.723 14.002 53177 Z= 0.367 Chirality : 0.048 0.275 6237 Planarity : 0.005 0.099 6785 Dihedral : 6.294 46.290 5276 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.64 % Allowed : 10.39 % Favored : 88.97 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.11), residues: 4841 helix: 0.17 (0.13), residues: 1511 sheet: -1.68 (0.18), residues: 686 loop : -2.97 (0.11), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 438 TYR 0.026 0.002 TYR C 362 PHE 0.039 0.002 PHE C 288 TRP 0.046 0.002 TRP C 366 HIS 0.029 0.001 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (39304) covalent geometry : angle 0.72283 / 0.37 (53177) hydrogen bonds : bond 0.03768 / 2.54 ( 1282) hydrogen bonds : angle 5.42316 / 3.81 ( 3738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 1.678 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: A 22 MET cc_start: -0.3891 (mtt) cc_final: -0.4118 (mtt) REVERT: A 58 LYS cc_start: 0.7762 (mtmm) cc_final: 0.7558 (pptt) REVERT: A 239 MET cc_start: 0.4519 (mtp) cc_final: 0.3762 (ttm) REVERT: C 50 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7248 (ttt180) REVERT: C 315 PHE cc_start: 0.7325 (m-80) cc_final: 0.6447 (m-80) REVERT: C 357 ASN cc_start: 0.8743 (t0) cc_final: 0.8315 (t0) REVERT: D 174 GLN cc_start: 0.8481 (mp10) cc_final: 0.8113 (tp40) REVERT: D 280 SER cc_start: 0.9366 (m) cc_final: 0.9153 (t) REVERT: E 245 ARG cc_start: 0.6560 (mtt180) cc_final: 0.6021 (mpt180) REVERT: F 76 MET cc_start: 0.6095 (ppp) cc_final: 0.5679 (tmm) REVERT: F 448 MET cc_start: -0.1884 (tpt) cc_final: -0.3178 (tpt) REVERT: F 467 LEU cc_start: -0.2045 (pp) cc_final: -0.2291 (pp) REVERT: G 384 GLN cc_start: 0.9257 (mt0) cc_final: 0.8689 (tp-100) REVERT: G 388 ASP cc_start: 0.8217 (m-30) cc_final: 0.7090 (p0) REVERT: G 440 MET cc_start: 0.7340 (ppp) cc_final: 0.6991 (ppp) REVERT: H 298 GLU cc_start: 0.8334 (pt0) cc_final: 0.8129 (pp20) REVERT: H 302 ILE cc_start: 0.8624 (mm) cc_final: 0.8366 (mm) REVERT: I 69 LYS cc_start: 0.6671 (pptt) cc_final: 0.6374 (pptt) REVERT: I 108 MET cc_start: 0.0955 (mpp) cc_final: 0.0432 (mmt) REVERT: I 259 PHE cc_start: 0.7973 (t80) cc_final: 0.7661 (t80) REVERT: I 261 LYS cc_start: 0.8161 (tttt) cc_final: 0.7777 (pptt) REVERT: I 306 LEU cc_start: 0.9295 (mm) cc_final: 0.8754 (mt) REVERT: I 424 MET cc_start: 0.4512 (mtt) cc_final: 0.4090 (mtt) REVERT: J 307 VAL cc_start: 0.7308 (t) cc_final: 0.7087 (t) REVERT: J 421 ASP cc_start: 0.8928 (m-30) cc_final: 0.8390 (m-30) REVERT: M 201 MET cc_start: -0.0364 (mmt) cc_final: -0.0780 (mmt) REVERT: M 211 MET cc_start: 0.0184 (mtp) cc_final: -0.0027 (mtp) REVERT: N 367 LYS cc_start: 0.7775 (mppt) cc_final: 0.7315 (pptt) REVERT: P 222 MET cc_start: 0.0830 (ptp) cc_final: 0.0303 (tmm) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.2183 time to fit residues: 119.0476 Evaluate side-chains 251 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 177 optimal weight: 9.9990 chunk 53 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 480 optimal weight: 7.9990 chunk 455 optimal weight: 40.0000 chunk 81 optimal weight: 0.6980 chunk 264 optimal weight: 9.9990 chunk 448 optimal weight: 50.0000 chunk 330 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 415 HIS ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.114224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.089676 restraints weight = 266963.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.091692 restraints weight = 176739.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.092920 restraints weight = 128403.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4588 r_free = 0.4588 target = 0.094058 restraints weight = 100633.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4602 r_free = 0.4602 target = 0.094710 restraints weight = 83466.500| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.7156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 39304 Z= 0.147 Angle : 0.704 12.454 53177 Z= 0.358 Chirality : 0.047 0.281 6237 Planarity : 0.005 0.098 6785 Dihedral : 6.105 40.222 5276 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.60 % Allowed : 11.51 % Favored : 87.90 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.43 (0.12), residues: 4841 helix: 0.35 (0.13), residues: 1509 sheet: -1.71 (0.18), residues: 700 loop : -2.92 (0.11), residues: 2632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 432 TYR 0.027 0.002 TYR A 214 PHE 0.034 0.002 PHE C 288 TRP 0.047 0.002 TRP D 366 HIS 0.011 0.001 HIS K 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (39304) covalent geometry : angle 0.70445 / 0.36 (53177) hydrogen bonds : bond 0.03665 / 2.46 ( 1282) hydrogen bonds : angle 5.29194 / 3.72 ( 3738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9682 Ramachandran restraints generated. 4841 Oldfield, 0 Emsley, 4841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 317 time to evaluate : 1.613 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: A 58 LYS cc_start: 0.7679 (mtmm) cc_final: 0.7441 (pptt) REVERT: A 239 MET cc_start: 0.4167 (mtp) cc_final: 0.3222 (ttm) REVERT: B 13 PHE cc_start: 0.3864 (p90) cc_final: 0.3345 (p90) REVERT: C 50 ARG cc_start: 0.7451 (mtt180) cc_final: 0.7246 (ttt180) REVERT: C 315 PHE cc_start: 0.7459 (m-80) cc_final: 0.6666 (m-80) REVERT: C 357 ASN cc_start: 0.8880 (t0) cc_final: 0.8453 (t0) REVERT: D 174 GLN cc_start: 0.8452 (mp10) cc_final: 0.8137 (tp40) REVERT: D 227 HIS cc_start: 0.8183 (t-90) cc_final: 0.7979 (t-90) REVERT: D 254 ARG cc_start: 0.8585 (mtt180) cc_final: 0.8339 (mtt90) REVERT: E 245 ARG cc_start: 0.6530 (mtt180) cc_final: 0.6080 (mpt180) REVERT: F 76 MET cc_start: 0.6013 (ppp) cc_final: 0.5606 (tmm) REVERT: F 448 MET cc_start: -0.2017 (tpt) cc_final: -0.3138 (tpt) REVERT: G 384 GLN cc_start: 0.9330 (mt0) cc_final: 0.8691 (tp-100) REVERT: G 388 ASP cc_start: 0.8214 (m-30) cc_final: 0.6879 (p0) REVERT: G 440 MET cc_start: 0.7322 (ppp) cc_final: 0.7050 (ppp) REVERT: H 298 GLU cc_start: 0.8114 (pt0) cc_final: 0.7785 (pp20) REVERT: I 108 MET cc_start: 0.1098 (mpp) cc_final: 0.0427 (mmt) REVERT: I 259 PHE cc_start: 0.8124 (t80) cc_final: 0.7844 (t80) REVERT: I 261 LYS cc_start: 0.8339 (tttt) cc_final: 0.7958 (pptt) REVERT: I 424 MET cc_start: 0.3861 (mtt) cc_final: 0.2360 (mtm) REVERT: J 421 ASP cc_start: 0.8885 (m-30) cc_final: 0.8424 (m-30) REVERT: M 201 MET cc_start: 0.1183 (mmt) cc_final: 0.0883 (mmp) REVERT: N 367 LYS cc_start: 0.7505 (mppt) cc_final: 0.7045 (pptt) REVERT: P 222 MET cc_start: 0.1068 (ptp) cc_final: 0.0511 (tmm) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2114 time to fit residues: 116.7215 Evaluate side-chains 249 residues out of total 4398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 488 random chunks: chunk 434 optimal weight: 0.7980 chunk 363 optimal weight: 3.9990 chunk 302 optimal weight: 6.9990 chunk 482 optimal weight: 0.2980 chunk 307 optimal weight: 0.9990 chunk 167 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 472 optimal weight: 0.4980 chunk 285 optimal weight: 0.9980 chunk 368 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 GLN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** C 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** E 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 326 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 56 ASN ** J 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 HIS M 496 ASN ** N 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4994 r_free = 0.4994 target = 0.114460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.094530 restraints weight = 204313.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.095940 restraints weight = 160937.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4698 r_free = 0.4698 target = 0.097230 restraints weight = 126015.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.097540 restraints weight = 108226.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.097546 restraints weight = 98246.917| |-----------------------------------------------------------------------------| r_work (final): 0.4632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5558 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 39304 Z= 0.119 Angle : 0.661 12.167 53177 Z= 0.333 Chirality : 0.046 0.245 6237 Planarity : 0.005 0.107 6785 Dihedral : 5.573 34.748 5276 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.05 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.49 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.12), residues: 4841 helix: 0.80 (0.13), residues: 1504 sheet: -1.52 (0.18), residues: 726 loop : -2.84 (0.11), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 254 TYR 0.027 0.002 TYR B 274 PHE 0.020 0.002 PHE H 374 TRP 0.038 0.002 TRP J 99 HIS 0.027 0.001 HIS J 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (39304) covalent geometry : angle 0.66057 / 0.33 (53177) hydrogen bonds : bond 0.03232 / 2.17 ( 1282) hydrogen bonds : angle 4.94264 / 3.46 ( 3738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7607.88 seconds wall clock time: 132 minutes 24.58 seconds (7944.58 seconds total)