Starting phenix.real_space_refine on Tue Aug 26 20:42:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wod_37683/08_2025/8wod_37683.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wod_37683/08_2025/8wod_37683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wod_37683/08_2025/8wod_37683.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wod_37683/08_2025/8wod_37683.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wod_37683/08_2025/8wod_37683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wod_37683/08_2025/8wod_37683.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.051 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: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 26215 2.51 5 N 7074 2.21 5 O 7714 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41094 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 19, 'TRANS': 471} Chain breaks: 2 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "J" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2242 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 128} Link IDs: {'PTRANS': 16, 'TRANS': 320} Chain breaks: 2 Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 598 Unresolved non-hydrogen dihedrals: 395 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLN:plan1': 12, 'HIS:plan': 6, 'GLU:plan': 15, 'ASP:plan': 14, 'ARG:plan': 9, 'ASN:plan1': 10, 'TYR:plan': 2, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 290 Chain: "K" Number of atoms: 2048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2048 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 16, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 656 Unresolved non-hydrogen angles: 829 Unresolved non-hydrogen dihedrals: 526 Unresolved non-hydrogen chiralities: 59 Planarities with less than four sites: {'ASP:plan': 17, 'GLN:plan1': 15, 'HIS:plan': 6, 'GLU:plan': 16, 'PHE:plan': 3, 'ARG:plan': 8, 'ASN:plan1': 17, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 365 Chain: "L" Number of atoms: 4966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 4966 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 30, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 414 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASP:plan': 7, 'ASN:plan1': 8, 'GLU:plan': 13, 'TYR:plan': 5, 'HIS:plan': 5, 'GLN:plan1': 6, 'PHE:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 207 Chain: "M" Number of atoms: 4955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 4955 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 30, 'TRANS': 641} Chain breaks: 1 Unresolved non-hydrogen bonds: 333 Unresolved non-hydrogen angles: 416 Unresolved non-hydrogen dihedrals: 275 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 15, 'ASN:plan1': 8, 'ASP:plan': 7, 'TYR:plan': 5, 'ARG:plan': 5, 'HIS:plan': 4, 'GLN:plan1': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 215 Chain: "N" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 3632 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 327} Link IDs: {'PTRANS': 25, 'TRANS': 587} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1237 Unresolved non-hydrogen angles: 1572 Unresolved non-hydrogen dihedrals: 1023 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 14, 'ASN:plan1': 22, 'ASP:plan': 29, 'PHE:plan': 18, 'TYR:plan': 13, 'ARG:plan': 26, 'TRP:plan': 5, 'GLU:plan': 37, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 756 Chain: "O" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4144 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 25, 'TRANS': 534} Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 10, 'ASP:plan': 6, 'ASN:plan1': 7, 'TYR:plan': 4, 'HIS:plan': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 138 Chain: "P" Number of atoms: 2457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2457 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 3 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 405 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 9, 'GLU:plan': 10, 'ARG:plan': 3, 'HIS:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 173 Chain: "R" Number of atoms: 2619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2619 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 48} Link IDs: {'PTRANS': 17, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 177 Unresolved non-hydrogen angles: 213 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 5, 'ARG:plan': 3, 'GLN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 92 Chain: "S" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2334 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 16, 'TRANS': 323} Chain breaks: 2 Unresolved non-hydrogen bonds: 408 Unresolved non-hydrogen angles: 501 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'ASP:plan': 13, 'GLU:plan': 14, 'ARG:plan': 6, 'ASN:plan1': 10, 'HIS:plan': 3, 'GLN:plan1': 13, 'TYR:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 242 Chain: "T" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2654 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 18, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "F" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2654 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 18, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "Q" Number of atoms: 2654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2654 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 18, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 149 Unresolved non-hydrogen angles: 182 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 4, 'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 8.78, per 1000 atoms: 0.21 Number of scatterers: 41094 At special positions: 0 Unit cell: (152.32, 187.927, 222.545, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 7714 8.00 N 7074 7.00 C 26215 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: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10740 Finding SS restraints... Secondary structure from input PDB file: 233 helices and 38 sheets defined 42.3% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'D' and resid 76 through 83 Processing helix chain 'D' and resid 122 through 131 Processing helix chain 'D' and resid 155 through 161 Processing helix chain 'D' and resid 168 through 171 Processing helix chain 'D' and resid 172 through 185 removed outlier: 3.556A pdb=" N THR D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 234 through 242 Processing helix chain 'D' and resid 248 through 269 removed outlier: 4.077A pdb=" N ASN D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 299 removed outlier: 3.989A pdb=" N LEU D 292 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'D' and resid 376 through 381 Processing helix chain 'D' and resid 396 through 406 removed outlier: 3.807A pdb=" N LEU D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 442 removed outlier: 3.871A pdb=" N SER D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 464 Processing helix chain 'D' and resid 472 through 488 removed outlier: 5.459A pdb=" N ARG D 485 " --> pdb=" O VAL D 481 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS D 486 " --> pdb=" O LYS D 482 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'D' and resid 502 through 507 Processing helix chain 'D' and resid 519 through 529 removed outlier: 3.963A pdb=" N ARG D 523 " --> pdb=" O ASN D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 539 removed outlier: 3.716A pdb=" N GLY D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 544 removed outlier: 3.609A pdb=" N LEU D 544 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 25 removed outlier: 3.587A pdb=" N LEU J 18 " --> pdb=" O GLN J 14 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N HIS J 21 " --> pdb=" O SER J 17 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL J 22 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 41 removed outlier: 3.678A pdb=" N VAL J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 36 through 41' Processing helix chain 'J' and resid 52 through 63 removed outlier: 3.512A pdb=" N SER J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 83 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.510A pdb=" N ILE J 101 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 113 through 131 Processing helix chain 'J' and resid 139 through 151 removed outlier: 3.747A pdb=" N LYS J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 175 removed outlier: 3.512A pdb=" N LEU J 175 " --> pdb=" O ALA J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 199 removed outlier: 3.839A pdb=" N GLU J 197 " --> pdb=" O ILE J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 266 removed outlier: 3.748A pdb=" N VAL J 255 " --> pdb=" O MET J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 294 Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 310 through 320 Processing helix chain 'J' and resid 360 through 373 Processing helix chain 'K' and resid 12 through 25 Processing helix chain 'K' and resid 36 through 42 Processing helix chain 'K' and resid 52 through 63 removed outlier: 3.510A pdb=" N SER K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 83 removed outlier: 4.384A pdb=" N THR K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.552A pdb=" N ILE K 101 " --> pdb=" O LEU K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 131 removed outlier: 3.559A pdb=" N ALA K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 150 removed outlier: 3.738A pdb=" N LYS K 143 " --> pdb=" O THR K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 174 Processing helix chain 'K' and resid 193 through 199 removed outlier: 3.967A pdb=" N GLU K 197 " --> pdb=" O ILE K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 266 Processing helix chain 'K' and resid 280 through 294 Processing helix chain 'K' and resid 306 through 309 Processing helix chain 'K' and resid 310 through 320 Processing helix chain 'K' and resid 360 through 373 Processing helix chain 'L' and resid 78 through 83 Processing helix chain 'L' and resid 122 through 130 Processing helix chain 'L' and resid 155 through 161 Processing helix chain 'L' and resid 168 through 171 Processing helix chain 'L' and resid 172 through 185 Processing helix chain 'L' and resid 229 through 233 Processing helix chain 'L' and resid 234 through 243 Processing helix chain 'L' and resid 248 through 269 removed outlier: 3.939A pdb=" N ASN L 252 " --> pdb=" O GLY L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 302 removed outlier: 3.559A pdb=" N LEU L 292 " --> pdb=" O SER L 288 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU L 300 " --> pdb=" O LEU L 296 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER L 302 " --> pdb=" O ARG L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 311 through 315 removed outlier: 3.854A pdb=" N GLU L 315 " --> pdb=" O GLU L 312 " (cutoff:3.500A) Processing helix chain 'L' and resid 360 through 372 Processing helix chain 'L' and resid 373 through 375 No H-bonds generated for 'chain 'L' and resid 373 through 375' Processing helix chain 'L' and resid 376 through 381 Processing helix chain 'L' and resid 396 through 406 removed outlier: 3.933A pdb=" N LEU L 400 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 423 through 442 removed outlier: 3.853A pdb=" N SER L 442 " --> pdb=" O SER L 438 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 464 Processing helix chain 'L' and resid 472 through 488 removed outlier: 5.444A pdb=" N ARG L 485 " --> pdb=" O VAL L 481 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LYS L 486 " --> pdb=" O LYS L 482 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR L 487 " --> pdb=" O GLU L 483 " (cutoff:3.500A) Processing helix chain 'L' and resid 502 through 507 Processing helix chain 'L' and resid 519 through 529 removed outlier: 3.679A pdb=" N ARG L 523 " --> pdb=" O ASN L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 534 through 539 removed outlier: 4.026A pdb=" N GLY L 539 " --> pdb=" O GLU L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 544 removed outlier: 3.639A pdb=" N LEU L 544 " --> pdb=" O LEU L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 579 through 586 removed outlier: 3.590A pdb=" N ASN L 586 " --> pdb=" O ALA L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 592 through 603 removed outlier: 4.144A pdb=" N VAL L 596 " --> pdb=" O ASP L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 676 removed outlier: 3.654A pdb=" N HIS L 670 " --> pdb=" O PRO L 666 " (cutoff:3.500A) Processing helix chain 'L' and resid 680 through 687 Processing helix chain 'M' and resid 76 through 83 removed outlier: 3.954A pdb=" N LEU M 80 " --> pdb=" O PRO M 76 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU M 81 " --> pdb=" O ASP M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 131 Processing helix chain 'M' and resid 155 through 161 Processing helix chain 'M' and resid 168 through 171 Processing helix chain 'M' and resid 172 through 185 Processing helix chain 'M' and resid 229 through 233 removed outlier: 3.542A pdb=" N ALA M 232 " --> pdb=" O PRO M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 243 Processing helix chain 'M' and resid 248 through 269 removed outlier: 4.137A pdb=" N ASN M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 302 removed outlier: 3.617A pdb=" N LEU M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU M 300 " --> pdb=" O LEU M 296 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE M 301 " --> pdb=" O TYR M 297 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 302 " --> pdb=" O ARG M 298 " (cutoff:3.500A) Processing helix chain 'M' and resid 311 through 315 Processing helix chain 'M' and resid 360 through 372 removed outlier: 3.508A pdb=" N LYS M 372 " --> pdb=" O ALA M 368 " (cutoff:3.500A) Processing helix chain 'M' and resid 373 through 375 No H-bonds generated for 'chain 'M' and resid 373 through 375' Processing helix chain 'M' and resid 376 through 381 Processing helix chain 'M' and resid 396 through 406 removed outlier: 3.902A pdb=" N LEU M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 422 No H-bonds generated for 'chain 'M' and resid 420 through 422' Processing helix chain 'M' and resid 423 through 442 removed outlier: 3.798A pdb=" N SER M 442 " --> pdb=" O SER M 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 464 removed outlier: 3.527A pdb=" N TYR M 464 " --> pdb=" O ALA M 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 461 through 464' Processing helix chain 'M' and resid 472 through 484 Processing helix chain 'M' and resid 502 through 508 removed outlier: 3.565A pdb=" N GLN M 508 " --> pdb=" O THR M 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 529 removed outlier: 3.822A pdb=" N ARG M 523 " --> pdb=" O ASN M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 539 Processing helix chain 'M' and resid 540 through 544 removed outlier: 3.619A pdb=" N LEU M 544 " --> pdb=" O LEU M 541 " (cutoff:3.500A) Processing helix chain 'M' and resid 579 through 586 removed outlier: 3.556A pdb=" N ASN M 586 " --> pdb=" O ALA M 582 " (cutoff:3.500A) Processing helix chain 'M' and resid 592 through 603 removed outlier: 4.288A pdb=" N VAL M 596 " --> pdb=" O ASP M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 666 through 675 removed outlier: 3.646A pdb=" N HIS M 670 " --> pdb=" O PRO M 666 " (cutoff:3.500A) Processing helix chain 'M' and resid 681 through 687 Processing helix chain 'N' and resid 122 through 130 Processing helix chain 'N' and resid 155 through 161 Processing helix chain 'N' and resid 168 through 171 Processing helix chain 'N' and resid 172 through 185 Processing helix chain 'N' and resid 229 through 233 removed outlier: 3.528A pdb=" N ALA N 232 " --> pdb=" O PRO N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 242 Processing helix chain 'N' and resid 248 through 269 Processing helix chain 'N' and resid 289 through 299 Processing helix chain 'N' and resid 360 through 373 Processing helix chain 'N' and resid 376 through 381 Processing helix chain 'N' and resid 396 through 406 removed outlier: 3.583A pdb=" N LEU N 400 " --> pdb=" O ASP N 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 423 through 442 removed outlier: 3.509A pdb=" N SER N 442 " --> pdb=" O SER N 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 464 Processing helix chain 'N' and resid 471 through 488 removed outlier: 4.069A pdb=" N ASP N 475 " --> pdb=" O GLY N 471 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG N 485 " --> pdb=" O VAL N 481 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS N 486 " --> pdb=" O LYS N 482 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR N 487 " --> pdb=" O GLU N 483 " (cutoff:3.500A) Processing helix chain 'N' and resid 497 through 501 Processing helix chain 'N' and resid 502 through 508 Processing helix chain 'N' and resid 519 through 528 removed outlier: 3.581A pdb=" N ARG N 523 " --> pdb=" O ASN N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 539 Processing helix chain 'N' and resid 540 through 544 removed outlier: 3.644A pdb=" N THR N 543 " --> pdb=" O MET N 540 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU N 544 " --> pdb=" O LEU N 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 540 through 544' Processing helix chain 'N' and resid 579 through 586 removed outlier: 3.999A pdb=" N ASN N 586 " --> pdb=" O ALA N 582 " (cutoff:3.500A) Processing helix chain 'N' and resid 592 through 603 removed outlier: 4.134A pdb=" N VAL N 596 " --> pdb=" O ASP N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 666 through 676 removed outlier: 3.650A pdb=" N HIS N 670 " --> pdb=" O PRO N 666 " (cutoff:3.500A) Processing helix chain 'N' and resid 681 through 687 Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 78 through 83 Processing helix chain 'O' and resid 122 through 130 Processing helix chain 'O' and resid 155 through 161 Processing helix chain 'O' and resid 168 through 171 Processing helix chain 'O' and resid 172 through 185 removed outlier: 3.519A pdb=" N THR O 176 " --> pdb=" O GLY O 172 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 233 Processing helix chain 'O' and resid 234 through 242 Processing helix chain 'O' and resid 248 through 269 removed outlier: 4.119A pdb=" N ASN O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 302 removed outlier: 3.789A pdb=" N LEU O 292 " --> pdb=" O SER O 288 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU O 300 " --> pdb=" O LEU O 296 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE O 301 " --> pdb=" O TYR O 297 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER O 302 " --> pdb=" O ARG O 298 " (cutoff:3.500A) Processing helix chain 'O' and resid 311 through 315 removed outlier: 3.589A pdb=" N GLU O 315 " --> pdb=" O GLU O 312 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 373 Processing helix chain 'O' and resid 376 through 381 Processing helix chain 'O' and resid 396 through 406 removed outlier: 3.852A pdb=" N LEU O 400 " --> pdb=" O ASP O 396 " (cutoff:3.500A) Processing helix chain 'O' and resid 423 through 442 removed outlier: 3.782A pdb=" N SER O 442 " --> pdb=" O SER O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 472 through 488 removed outlier: 5.434A pdb=" N ARG O 485 " --> pdb=" O VAL O 481 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS O 486 " --> pdb=" O LYS O 482 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR O 487 " --> pdb=" O GLU O 483 " (cutoff:3.500A) Processing helix chain 'O' and resid 502 through 507 Processing helix chain 'O' and resid 519 through 528 removed outlier: 4.039A pdb=" N ARG O 523 " --> pdb=" O ASN O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 534 through 539 removed outlier: 3.895A pdb=" N GLY O 539 " --> pdb=" O GLU O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 544 removed outlier: 3.568A pdb=" N LEU O 544 " --> pdb=" O LEU O 541 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 25 removed outlier: 3.599A pdb=" N GLN P 15 " --> pdb=" O ASP P 11 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU P 25 " --> pdb=" O HIS P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 41 removed outlier: 3.975A pdb=" N VAL P 40 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER P 41 " --> pdb=" O GLY P 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 36 through 41' Processing helix chain 'P' and resid 52 through 64 Processing helix chain 'P' and resid 71 through 81 removed outlier: 4.163A pdb=" N ILE P 75 " --> pdb=" O LEU P 71 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE P 76 " --> pdb=" O LEU P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 101 Processing helix chain 'P' and resid 113 through 131 removed outlier: 3.558A pdb=" N ALA P 117 " --> pdb=" O SER P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 151 removed outlier: 4.024A pdb=" N ILE P 151 " --> pdb=" O TRP P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 175 Processing helix chain 'P' and resid 193 through 199 removed outlier: 3.708A pdb=" N GLU P 197 " --> pdb=" O ILE P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 265 Processing helix chain 'P' and resid 281 through 294 Processing helix chain 'P' and resid 306 through 309 Processing helix chain 'P' and resid 310 through 320 Processing helix chain 'P' and resid 356 through 359 Processing helix chain 'P' and resid 360 through 373 Processing helix chain 'R' and resid 11 through 24 removed outlier: 3.676A pdb=" N GLN R 15 " --> pdb=" O ASP R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 42 Processing helix chain 'R' and resid 52 through 64 Processing helix chain 'R' and resid 70 through 81 Processing helix chain 'R' and resid 87 through 101 removed outlier: 3.620A pdb=" N ILE R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 131 removed outlier: 3.664A pdb=" N GLU R 120 " --> pdb=" O ASN R 116 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN R 131 " --> pdb=" O GLU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 149 removed outlier: 3.519A pdb=" N ASN R 149 " --> pdb=" O ALA R 145 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 175 removed outlier: 3.642A pdb=" N LEU R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 199 removed outlier: 3.755A pdb=" N ASN R 199 " --> pdb=" O THR R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 265 Processing helix chain 'R' and resid 281 through 294 Processing helix chain 'R' and resid 306 through 309 Processing helix chain 'R' and resid 310 through 320 Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.650A pdb=" N GLY R 359 " --> pdb=" O PHE R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 373 removed outlier: 3.886A pdb=" N GLN R 373 " --> pdb=" O GLU R 369 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 24 Processing helix chain 'S' and resid 37 through 41 Processing helix chain 'S' and resid 52 through 63 Processing helix chain 'S' and resid 73 through 81 Processing helix chain 'S' and resid 87 through 101 removed outlier: 3.758A pdb=" N ILE S 101 " --> pdb=" O LEU S 97 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 108 removed outlier: 4.305A pdb=" N LYS S 106 " --> pdb=" O MET S 103 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE S 107 " --> pdb=" O SER S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 131 Processing helix chain 'S' and resid 139 through 151 removed outlier: 3.606A pdb=" N LYS S 143 " --> pdb=" O THR S 139 " (cutoff:3.500A) Processing helix chain 'S' and resid 166 through 175 Processing helix chain 'S' and resid 193 through 199 removed outlier: 4.189A pdb=" N GLU S 197 " --> pdb=" O ILE S 193 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN S 199 " --> pdb=" O THR S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 251 through 265 Processing helix chain 'S' and resid 280 through 294 removed outlier: 3.940A pdb=" N VAL S 286 " --> pdb=" O HIS S 282 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 309 Processing helix chain 'S' and resid 310 through 320 Processing helix chain 'S' and resid 360 through 373 Processing helix chain 'T' and resid 11 through 24 removed outlier: 3.861A pdb=" N GLN T 15 " --> pdb=" O ASP T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 42 Processing helix chain 'T' and resid 52 through 64 Processing helix chain 'T' and resid 69 through 83 removed outlier: 4.151A pdb=" N ILE T 75 " --> pdb=" O LEU T 71 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE T 76 " --> pdb=" O LEU T 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR T 82 " --> pdb=" O ASN T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 101 removed outlier: 3.514A pdb=" N ILE T 101 " --> pdb=" O LEU T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 131 Processing helix chain 'T' and resid 139 through 149 removed outlier: 3.556A pdb=" N ASN T 149 " --> pdb=" O ALA T 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 166 through 175 removed outlier: 3.567A pdb=" N LEU T 175 " --> pdb=" O ALA T 171 " (cutoff:3.500A) Processing helix chain 'T' and resid 193 through 199 removed outlier: 3.760A pdb=" N GLU T 197 " --> pdb=" O ILE T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 252 through 265 Processing helix chain 'T' and resid 281 through 294 Processing helix chain 'T' and resid 306 through 309 Processing helix chain 'T' and resid 310 through 320 Processing helix chain 'T' and resid 356 through 359 removed outlier: 3.639A pdb=" N GLY T 359 " --> pdb=" O PHE T 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 356 through 359' Processing helix chain 'T' and resid 360 through 373 removed outlier: 3.712A pdb=" N GLN T 373 " --> pdb=" O GLU T 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 24 removed outlier: 3.861A pdb=" N GLN F 15 " --> pdb=" O ASP F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 38 through 42 Processing helix chain 'F' and resid 52 through 64 Processing helix chain 'F' and resid 69 through 83 removed outlier: 4.151A pdb=" N ILE F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 101 removed outlier: 3.515A pdb=" N ILE F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 131 Processing helix chain 'F' and resid 139 through 149 removed outlier: 3.556A pdb=" N ASN F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 175 removed outlier: 3.566A pdb=" N LEU F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 193 through 199 removed outlier: 3.760A pdb=" N GLU F 197 " --> pdb=" O ILE F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 265 Processing helix chain 'F' and resid 281 through 294 Processing helix chain 'F' and resid 306 through 309 Processing helix chain 'F' and resid 310 through 320 Processing helix chain 'F' and resid 356 through 359 removed outlier: 3.638A pdb=" N GLY F 359 " --> pdb=" O PHE F 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 360 through 373 removed outlier: 3.712A pdb=" N GLN F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 24 removed outlier: 3.862A pdb=" N GLN Q 15 " --> pdb=" O ASP Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 38 through 42 Processing helix chain 'Q' and resid 52 through 64 Processing helix chain 'Q' and resid 69 through 83 removed outlier: 4.151A pdb=" N ILE Q 75 " --> pdb=" O LEU Q 71 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE Q 76 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR Q 82 " --> pdb=" O ASN Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 101 removed outlier: 3.515A pdb=" N ILE Q 101 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 131 Processing helix chain 'Q' and resid 139 through 149 removed outlier: 3.556A pdb=" N ASN Q 149 " --> pdb=" O ALA Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 175 removed outlier: 3.567A pdb=" N LEU Q 175 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 199 removed outlier: 3.761A pdb=" N GLU Q 197 " --> pdb=" O ILE Q 193 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 265 Processing helix chain 'Q' and resid 281 through 294 Processing helix chain 'Q' and resid 306 through 309 Processing helix chain 'Q' and resid 310 through 320 Processing helix chain 'Q' and resid 356 through 359 removed outlier: 3.639A pdb=" N GLY Q 359 " --> pdb=" O PHE Q 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 356 through 359' Processing helix chain 'Q' and resid 360 through 373 removed outlier: 3.711A pdb=" N GLN Q 373 " --> pdb=" O GLU Q 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 20 removed outlier: 6.486A pdb=" N ARG D 26 " --> pdb=" O GLN D 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 29 current: chain 'D' and resid 61 through 70 removed outlier: 7.068A pdb=" N ASN D 62 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU D 97 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE D 64 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER D 91 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL D 70 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N TRP D 89 " --> pdb=" O VAL D 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 104 through 106 current: chain 'L' and resid 25 through 29 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 25 through 29 current: chain 'L' and resid 61 through 71 removed outlier: 6.990A pdb=" N ASN L 62 " --> pdb=" O GLU L 97 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU L 97 " --> pdb=" O ASN L 62 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE L 64 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N SER L 91 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N VAL L 70 " --> pdb=" O TRP L 89 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N TRP L 89 " --> pdb=" O VAL L 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 104 through 106 current: chain 'M' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 24 through 29 current: chain 'M' and resid 61 through 71 removed outlier: 6.899A pdb=" N LEU M 63 " --> pdb=" O GLU M 97 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU M 97 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N GLY M 65 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL M 95 " --> pdb=" O GLY M 65 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N VAL M 67 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN M 93 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN M 69 " --> pdb=" O SER M 91 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TRP M 89 " --> pdb=" O GLY M 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 104 through 106 current: chain 'N' and resid 24 through 28 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 24 through 28 current: chain 'N' and resid 61 through 71 removed outlier: 6.874A pdb=" N LEU N 63 " --> pdb=" O GLU N 97 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU N 97 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY N 65 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL N 95 " --> pdb=" O GLY N 65 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VAL N 67 " --> pdb=" O GLN N 93 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLN N 93 " --> pdb=" O VAL N 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 104 through 106 current: chain 'O' and resid 25 through 29 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 25 through 29 current: chain 'O' and resid 61 through 71 removed outlier: 7.202A pdb=" N ASN O 62 " --> pdb=" O GLU O 97 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU O 97 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE O 64 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL O 95 " --> pdb=" O PHE O 64 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER O 91 " --> pdb=" O SER O 68 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N VAL O 70 " --> pdb=" O TRP O 89 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N TRP O 89 " --> pdb=" O VAL O 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 150 through 153 removed outlier: 6.626A pdb=" N ALA D 151 " --> pdb=" O LEU D 140 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA D 164 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 493 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 456 " --> pdb=" O MET D 492 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL D 494 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU D 458 " --> pdb=" O VAL D 494 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 459 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE D 195 " --> pdb=" O SER D 412 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE D 414 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D 197 " --> pdb=" O PHE D 414 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU D 224 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL D 214 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 179 through 180 removed outlier: 5.850A pdb=" N PHE J 180 " --> pdb=" O LEU J 208 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LYS J 210 " --> pdb=" O PHE J 180 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N PHE J 32 " --> pdb=" O PHE J 160 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA J 31 " --> pdb=" O ILE J 272 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N CYS J 274 " --> pdb=" O ALA J 31 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE J 33 " --> pdb=" O CYS J 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'J' and resid 188 through 189 removed outlier: 3.625A pdb=" N ALA J 189 " --> pdb=" O ARG J 228 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 324 through 326 Processing sheet with id=AA7, first strand: chain 'K' and resid 33 through 34 removed outlier: 5.940A pdb=" N PHE K 180 " --> pdb=" O LEU K 208 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N LYS K 210 " --> pdb=" O PHE K 180 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 43 through 44 Processing sheet with id=AA9, first strand: chain 'K' and resid 183 through 184 removed outlier: 3.747A pdb=" N VAL K 184 " --> pdb=" O PHE K 190 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE K 190 " --> pdb=" O VAL K 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 270 through 273 removed outlier: 7.466A pdb=" N LEU K 271 " --> pdb=" O TYR K 300 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N LEU K 302 " --> pdb=" O LEU K 271 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N THR K 273 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE K 299 " --> pdb=" O ILE K 324 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU K 326 " --> pdb=" O ILE K 299 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLY K 301 " --> pdb=" O LEU K 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.891A pdb=" N TYR L 45 " --> pdb=" O LYS L 38 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 150 through 153 removed outlier: 6.742A pdb=" N ALA L 151 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET L 560 " --> pdb=" O ILE L 551 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA L 514 " --> pdb=" O ILE L 550 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ALA L 164 " --> pdb=" O PHE L 513 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL L 456 " --> pdb=" O MET L 492 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL L 494 " --> pdb=" O VAL L 456 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU L 458 " --> pdb=" O VAL L 494 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU L 459 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE L 195 " --> pdb=" O SER L 412 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE L 414 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL L 197 " --> pdb=" O PHE L 414 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU L 224 " --> pdb=" O ALA L 212 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL L 214 " --> pdb=" O LEU L 224 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 303 through 304 Processing sheet with id=AB5, first strand: chain 'L' and resid 616 through 618 removed outlier: 3.893A pdb=" N LEU L 617 " --> pdb=" O ILE L 641 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU L 653 " --> pdb=" O LEU L 639 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE L 641 " --> pdb=" O GLU L 651 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLU L 651 " --> pdb=" O ILE L 641 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 150 through 153 removed outlier: 3.981A pdb=" N GLY M 141 " --> pdb=" O ALA M 151 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL M 153 " --> pdb=" O SER M 139 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N SER M 139 " --> pdb=" O VAL M 153 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU M 459 " --> pdb=" O PHE M 198 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ILE M 195 " --> pdb=" O SER M 412 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE M 414 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL M 197 " --> pdb=" O PHE M 414 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N LYS M 213 " --> pdb=" O ILE M 413 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ASP M 415 " --> pdb=" O LYS M 213 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR M 215 " --> pdb=" O ASP M 415 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU M 224 " --> pdb=" O ALA M 212 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL M 214 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 638 through 642 removed outlier: 3.564A pdb=" N SER M 640 " --> pdb=" O GLU M 653 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE M 652 " --> pdb=" O TYR M 660 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 39 through 40 Processing sheet with id=AB9, first strand: chain 'N' and resid 150 through 154 removed outlier: 6.532A pdb=" N ALA N 151 " --> pdb=" O LEU N 140 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN N 142 " --> pdb=" O ILE N 563 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 224 through 225 removed outlier: 8.108A pdb=" N LEU N 224 " --> pdb=" O ALA N 212 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N VAL N 214 " --> pdb=" O LEU N 224 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS N 213 " --> pdb=" O ILE N 413 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE N 195 " --> pdb=" O SER N 412 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N PHE N 414 " --> pdb=" O ILE N 195 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL N 197 " --> pdb=" O PHE N 414 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU N 459 " --> pdb=" O PHE N 198 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU N 454 " --> pdb=" O GLY N 490 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N MET N 492 " --> pdb=" O LEU N 454 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL N 456 " --> pdb=" O MET N 492 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL N 494 " --> pdb=" O VAL N 456 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU N 458 " --> pdb=" O VAL N 494 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA N 164 " --> pdb=" O PHE N 513 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 641 through 642 Processing sheet with id=AC3, first strand: chain 'O' and resid 39 through 40 Processing sheet with id=AC4, first strand: chain 'O' and resid 150 through 153 removed outlier: 6.533A pdb=" N ALA O 151 " --> pdb=" O LEU O 140 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU O 493 " --> pdb=" O SER O 163 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU O 459 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE O 195 " --> pdb=" O SER O 412 " (cutoff:3.500A) removed outlier: 7.861A pdb=" N PHE O 414 " --> pdb=" O ILE O 195 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL O 197 " --> pdb=" O PHE O 414 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS O 213 " --> pdb=" O ILE O 413 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 303 through 304 removed outlier: 3.620A pdb=" N TYR O 352 " --> pdb=" O HIS O 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 9 through 10 removed outlier: 3.602A pdb=" N ILE P 332 " --> pdb=" O LEU P 325 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA P 31 " --> pdb=" O ILE P 272 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N CYS P 274 " --> pdb=" O ALA P 31 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ILE P 33 " --> pdb=" O CYS P 274 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE P 159 " --> pdb=" O TRP P 209 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'P' and resid 217 through 219 removed outlier: 3.703A pdb=" N TRP P 227 " --> pdb=" O GLN P 218 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 9 through 10 removed outlier: 6.590A pdb=" N LEU R 271 " --> pdb=" O TYR R 300 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU R 302 " --> pdb=" O LEU R 271 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR R 273 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ALA R 31 " --> pdb=" O ILE R 272 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N CYS R 274 " --> pdb=" O ALA R 31 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE R 33 " --> pdb=" O CYS R 274 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ILE R 159 " --> pdb=" O TRP R 209 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 183 through 184 Processing sheet with id=AD1, first strand: chain 'R' and resid 217 through 219 removed outlier: 3.619A pdb=" N TRP R 227 " --> pdb=" O GLN R 218 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 207 through 210 removed outlier: 6.622A pdb=" N VAL S 157 " --> pdb=" O LYS S 207 " (cutoff:3.500A) removed outlier: 8.146A pdb=" N TRP S 209 " --> pdb=" O VAL S 157 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE S 159 " --> pdb=" O TRP S 209 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE S 30 " --> pdb=" O GLU S 158 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE S 160 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE S 32 " --> pdb=" O PHE S 160 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA S 31 " --> pdb=" O ILE S 272 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS S 274 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE S 33 " --> pdb=" O CYS S 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'S' and resid 43 through 44 Processing sheet with id=AD4, first strand: chain 'S' and resid 183 through 184 removed outlier: 3.896A pdb=" N VAL S 184 " --> pdb=" O PHE S 190 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE S 190 " --> pdb=" O VAL S 184 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'S' and resid 302 through 303 Processing sheet with id=AD6, first strand: chain 'T' and resid 9 through 10 removed outlier: 3.686A pdb=" N ALA T 331 " --> pdb=" O GLY T 338 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE T 33 " --> pdb=" O CYS T 274 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE T 32 " --> pdb=" O PHE T 160 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU T 208 " --> pdb=" O PHE T 180 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'T' and resid 217 through 219 Processing sheet with id=AD8, first strand: chain 'F' and resid 9 through 10 removed outlier: 3.686A pdb=" N ALA F 331 " --> pdb=" O GLY F 338 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE F 33 " --> pdb=" O CYS F 274 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE F 32 " --> pdb=" O PHE F 160 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU F 208 " --> pdb=" O PHE F 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 217 through 219 Processing sheet with id=AE1, first strand: chain 'Q' and resid 9 through 10 removed outlier: 3.686A pdb=" N ALA Q 331 " --> pdb=" O GLY Q 338 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE Q 33 " --> pdb=" O CYS Q 274 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE Q 32 " --> pdb=" O PHE Q 160 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU Q 208 " --> pdb=" O PHE Q 180 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 217 through 219 1679 hydrogen bonds defined for protein. 4785 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: 9.25 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13686 1.34 - 1.46: 8675 1.46 - 1.58: 19371 1.58 - 1.70: 0 1.70 - 1.82: 149 Bond restraints: 41881 Sorted by residual: bond pdb=" N GLY N 680 " pdb=" CA GLY N 680 " ideal model delta sigma weight residual 1.447 1.477 -0.029 1.03e-02 9.43e+03 8.11e+00 bond pdb=" N LYS N 681 " pdb=" CA LYS N 681 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.20e+00 bond pdb=" N GLU N 677 " pdb=" CA GLU N 677 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.71e+00 bond pdb=" N SER N 678 " pdb=" CA SER N 678 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 5.05e+00 bond pdb=" C MET S 251 " pdb=" N PRO S 252 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.22e+00 ... (remaining 41876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 55868 1.41 - 2.82: 1012 2.82 - 4.23: 252 4.23 - 5.64: 53 5.64 - 7.05: 15 Bond angle restraints: 57200 Sorted by residual: angle pdb=" C ASP K 109 " pdb=" CA ASP K 109 " pdb=" CB ASP K 109 " ideal model delta sigma weight residual 116.63 110.53 6.10 1.16e+00 7.43e-01 2.76e+01 angle pdb=" C GLU P 111 " pdb=" CA GLU P 111 " pdb=" CB GLU P 111 " ideal model delta sigma weight residual 115.79 109.87 5.92 1.19e+00 7.06e-01 2.47e+01 angle pdb=" N VAL M 217 " pdb=" CA VAL M 217 " pdb=" C VAL M 217 " ideal model delta sigma weight residual 112.96 108.48 4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N ILE F 115 " pdb=" CA ILE F 115 " pdb=" C ILE F 115 " ideal model delta sigma weight residual 111.90 108.51 3.39 8.10e-01 1.52e+00 1.75e+01 angle pdb=" N ILE T 115 " pdb=" CA ILE T 115 " pdb=" C ILE T 115 " ideal model delta sigma weight residual 111.90 108.55 3.35 8.10e-01 1.52e+00 1.71e+01 ... (remaining 57195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 23168 17.83 - 35.67: 1503 35.67 - 53.50: 204 53.50 - 71.33: 55 71.33 - 89.16: 18 Dihedral angle restraints: 24948 sinusoidal: 8333 harmonic: 16615 Sorted by residual: dihedral pdb=" CA GLU S 197 " pdb=" C GLU S 197 " pdb=" N GLU S 198 " pdb=" CA GLU S 198 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA ARG O 161 " pdb=" C ARG O 161 " pdb=" N HIS O 162 " pdb=" CA HIS O 162 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ILE N 34 " pdb=" C ILE N 34 " pdb=" N SER N 35 " pdb=" CA SER N 35 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 24945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 4544 0.036 - 0.072: 1572 0.072 - 0.108: 539 0.108 - 0.144: 158 0.144 - 0.181: 7 Chirality restraints: 6820 Sorted by residual: chirality pdb=" CG LEU L 427 " pdb=" CB LEU L 427 " pdb=" CD1 LEU L 427 " pdb=" CD2 LEU L 427 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.15e-01 chirality pdb=" CA GLU S 197 " pdb=" N GLU S 197 " pdb=" C GLU S 197 " pdb=" CB GLU S 197 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.90e-01 chirality pdb=" CA GLU K 128 " pdb=" N GLU K 128 " pdb=" C GLU K 128 " pdb=" CB GLU K 128 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 6817 not shown) Planarity restraints: 7395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE F 83 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO F 84 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO F 84 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO F 84 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE T 83 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.83e+00 pdb=" N PRO T 84 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO T 84 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO T 84 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Q 83 " 0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO Q 84 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO Q 84 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO Q 84 " 0.036 5.00e-02 4.00e+02 ... (remaining 7392 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 435 2.64 - 3.20: 37788 3.20 - 3.77: 59669 3.77 - 4.33: 77379 4.33 - 4.90: 131006 Nonbonded interactions: 306277 Sorted by model distance: nonbonded pdb=" OH TYR K 179 " pdb=" N SER Q 186 " model vdw 2.073 3.120 nonbonded pdb=" O ASP R 165 " pdb=" NZ LYS R 210 " model vdw 2.202 3.120 nonbonded pdb=" O SER L 302 " pdb=" OG SER L 354 " model vdw 2.211 3.040 nonbonded pdb=" NE2 GLN R 218 " pdb=" O THR R 230 " model vdw 2.241 3.120 nonbonded pdb=" OH TYR L 204 " pdb=" OE2 GLU L 459 " model vdw 2.243 3.040 ... (remaining 306272 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 'D' selection = (chain 'O' and (resid 10 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 36 or (resid 45 and (name N or nam \ e CA or name C or name O or name CB )) or resid 46 through 301 or resid 359 thro \ ugh 371 or (resid 372 and (name N or name CA or name C or name O or name CB )) o \ r resid 373 through 565)) } ncs_group { reference = (chain 'F' and ((resid 13 through 15 and (name N or name CA or name C or name O \ or name CB )) or resid 16 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 21 and (name N or na \ me CA or name C or name O or name CB )) or resid 22 through 23 or (resid 24 thro \ ugh 28 and (name N or name CA or name C or name O or name CB )) or resid 29 or ( \ resid 30 through 36 and (name N or name CA or name C or name O or name CB )) or \ resid 37 through 39 or (resid 40 through 47 and (name N or name CA or name C or \ name O or name CB )) or resid 48 or (resid 49 through 50 and (name N or name CA \ or name C or name O or name CB )) or resid 51 or (resid 52 through 54 and (name \ N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 and (nam \ e N or name CA or name C or name O or name CB )) or resid 57 through 58 or (resi \ d 59 through 60 and (name N or name CA or name C or name O or name CB )) or resi \ d 61 or (resid 62 through 63 and (name N or name CA or name C or name O or name \ CB )) or (resid 72 through 78 and (name N or name CA or name C or name O or name \ CB )) or resid 79 or (resid 80 through 83 and (name N or name CA or name C or n \ ame O or name CB )) or resid 84 through 86 or (resid 87 through 91 and (name N o \ r name CA or name C or name O or name CB )) or resid 92 through 93 or (resid 94 \ and (name N or name CA or name C or name O or name CB )) or resid 95 or (resid 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 03 or (resid 104 and (name N or name CA or name C or name O or name CB )) or res \ id 105 through 114 or (resid 115 through 118 and (name N or name CA or name C or \ name O or name CB )) or resid 119 or (resid 120 and (name N or name CA or name \ C or name O or name CB )) or resid 121 through 123 or (resid 124 and (name N or \ name CA or name C or name O or name CB )) or resid 125 or (resid 126 through 129 \ and (name N or name CA or name C or name O or name CB )) or resid 130 through 1 \ 31 or (resid 132 through 133 and (name N or name CA or name C or name O or name \ CB )) or resid 134 through 136 or (resid 137 through 139 and (name N or name CA \ or name C or name O or name CB )) or resid 140 through 142 or (resid 143 and (na \ me N or name CA or name C or name O or name CB )) or resid 144 through 146 or (r \ esid 147 and (name N or name CA or name C or name O or name CB )) or resid 148 t \ hrough 150 or (resid 151 through 158 and (name N or name CA or name C or name O \ or name CB )) or resid 159 or (resid 160 and (name N or name CA or name C or nam \ e O or name CB )) or resid 161 through 162 or (resid 163 through 166 and (name N \ or name CA or name C or name O or name CB )) or resid 167 or (resid 168 through \ 171 and (name N or name CA or name C or name O or name CB )) or resid 172 or (r \ esid 173 through 177 and (name N or name CA or name C or name O or name CB )) or \ resid 178 through 185 or (resid 186 through 190 and (name N or name CA or name \ C or name O or name CB )) or resid 191 or (resid 192 and (name N or name CA or n \ ame C or name O or name CB )) or resid 193 through 196 or (resid 197 and (name N \ or name CA or name C or name O or name CB )) or resid 198 through 203 or (resid \ 204 and (name N or name CA or name C or name O or name CB )) or resid 205 throu \ gh 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) or \ resid 208 through 209 or (resid 210 through 211 and (name N or name CA or name \ C or name O or name CB )) or resid 212 through 214 or (resid 215 through 216 and \ (name N or name CA or name C or name O or name CB )) or resid 217 or (resid 218 \ through 226 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 27 through 229 or (resid 230 and (name N or name CA or name C or name O or name \ CB )) or resid 231 or (resid 232 through 233 and (name N or name CA or name C or \ name O or name CB )) or (resid 234 through 239 and (name N or name CA or name C \ or name O or name CB )) or resid 240 through 242 or (resid 243 through 251 and \ (name N or name CA or name C or name O or name CB )) or resid 252 or (resid 253 \ through 254 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 5 or (resid 256 through 258 and (name N or name CA or name C or name O or name C \ B )) or resid 259 through 263 or (resid 264 through 266 and (name N or name CA o \ r name C or name O or name CB )) or resid 267 through 269 or (resid 270 and (nam \ e N or name CA or name C or name O or name CB )) or resid 271 or (resid 272 thro \ ugh 273 and (name N or name CA or name C or name O or name CB )) or resid 274 th \ rough 277 or (resid 278 through 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 or (resid 283 through 285 and (name N or name CA or na \ me C or name O or name CB )) or resid 286 through 288 or (resid 289 and (name N \ or name CA or name C or name O or name CB )) or resid 290 through 291 or (resid \ 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or (re \ sid 294 and (name N or name CA or name C or name O or name CB )) or resid 295 or \ (resid 296 through 299 and (name N or name CA or name C or name O or name CB )) \ or resid 300 through 302 or (resid 303 through 320 and (name N or name CA or na \ me C or name O or name CB )) or resid 321 or (resid 322 through 333 and (name N \ or name CA or name C or name O or name CB )) or resid 334 or (resid 335 through \ 337 and (name N or name CA or name C or name O or name CB )) or resid 338 or res \ id 359 or (resid 360 through 365 and (name N or name CA or name C or name O or n \ ame CB )) or resid 366 or (resid 367 through 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 or (resid 373 and (name N or name CA or n \ ame C or name O or name CB )))) selection = (chain 'J' and (resid 13 through 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 21 and (name N or nam \ e CA or name C or name O or name CB )) or resid 22 through 29 or (resid 30 throu \ gh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throu \ gh 40 or (resid 41 through 47 and (name N or name CA or name C or name O or name \ CB )) or resid 48 or (resid 49 through 50 and (name N or name CA or name C or n \ ame O or name CB )) or resid 51 through 52 or (resid 53 through 54 and (name N o \ r name CA or name C or name O or name CB )) or resid 55 through 63 or (resid 72 \ through 78 and (name N or name CA or name C or name O or name CB )) or resid 79 \ or (resid 80 through 83 and (name N or name CA or name C or name O or name CB )) \ or resid 84 through 87 or (resid 88 through 91 and (name N or name CA or name C \ or name O or name CB )) or resid 92 through 93 or (resid 94 and (name N or name \ CA or name C or name O or name CB )) or resid 95 or (resid 96 and (name N or na \ me CA or name C or name O or name CB )) or resid 97 through 99 or (resid 100 thr \ ough 101 and (name N or name CA or name C or name O or name CB )) or resid 102 t \ hrough 103 or (resid 104 and (name N or name CA or name C or name O or name CB ) \ ) or resid 105 through 115 or (resid 116 through 118 and (name N or name CA or n \ ame C or name O or name CB )) or resid 119 or (resid 120 and (name N or name CA \ or name C or name O or name CB )) or resid 121 through 125 or (resid 126 through \ 129 and (name N or 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through 136 or (resid 137 through 139 and (name N or name CA \ or name C or name O or name CB )) or resid 140 through 142 or (resid 143 and (na \ me N or name CA or name C or name O or name CB )) or resid 144 through 146 or (r \ esid 147 and (name N or name CA or name C or name O or name CB )) or resid 148 t \ hrough 150 or (resid 151 through 158 and (name N or name CA or name C or name O \ or name CB )) or resid 159 or (resid 160 and (name N or name CA or name C or nam \ e O or name CB )) or resid 161 through 162 or (resid 163 through 166 and (name N \ or name CA or name C or name O or name CB )) or resid 167 or (resid 168 through \ 171 and (name N or name CA or name C or name O or name CB )) or resid 172 or (r \ esid 173 through 177 and (name N or name CA or name C or name O or name CB )) or \ resid 178 through 185 or (resid 186 through 190 and (name N or name CA or name \ C or name O or name CB )) or resid 191 or (resid 192 and (name N or name CA or n \ ame C or name O or name CB )) 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name CB )) or resid 252 or (resid 253 \ through 254 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 5 or (resid 256 through 258 and (name N or name CA or name C or name O or name C \ B )) or resid 259 through 263 or (resid 264 through 266 and (name N or name CA o \ r name C or name O or name CB )) or resid 267 through 269 or (resid 270 and (nam \ e N or name CA or name C or name O or name CB )) or resid 271 or (resid 272 thro \ ugh 273 and (name N or name CA or name C or name O or name CB )) or resid 274 th \ rough 277 or (resid 278 through 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 or (resid 283 through 285 and (name N or name CA or na \ me C or name O or name CB )) or resid 286 through 288 or (resid 289 and (name N \ or name CA or name C or name O or name CB )) or resid 290 through 291 or (resid \ 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or (re \ sid 294 and (name N or name CA or name C or name 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)) or resid 259 through 2 \ 63 or (resid 264 through 266 and (name N or name CA or name C or name O or name \ CB )) or resid 267 through 269 or (resid 270 and (name N or name CA or name C or \ name O or name CB )) or resid 271 or (resid 272 through 273 and (name N or name \ CA or name C or name O or name CB )) or resid 274 through 277 or (resid 278 thr \ ough 281 and (name N or name CA or name C or name O or name CB )) or resid 282 o \ r (resid 283 through 285 and (name N or name CA or name C or name O or name CB ) \ ) or resid 286 through 288 or (resid 289 and (name N or name CA or name C or nam \ e O or name CB )) or resid 290 through 291 or (resid 292 and (name N or name CA \ or name C or name O or name CB )) or resid 293 or (resid 294 and (name N or name \ CA or name C or name O or name CB )) or resid 295 or (resid 296 through 299 and \ (name N or name CA or name C or name O or name CB )) or resid 300 through 302 o \ r (resid 303 through 320 and (name N or name CA or name C or name 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)) or resid \ 102 through 103 or (resid 104 and (name N or name CA or name C or name O or name \ CB )) or (resid 105 through 112 and (name N or name CA or name C or name O or n \ ame CB )) or resid 113 through 115 or (resid 116 through 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N or \ name CA or name C or name O or name CB )) or resid 121 through 123 or (resid 124 \ and (name N or name CA or name C or name O or name CB )) or resid 125 or (resid \ 126 through 129 and (name N or name CA or name C or name O or name CB )) or res \ id 130 or (resid 131 through 133 and (name N or name CA or name C or name O or n \ ame CB )) or resid 134 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB )) or resid 140 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB )) or resid 148 through 150 or (resid 151 \ through 158 and (name N or name CA or name C or name O or name CB )) or resid 1 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or name CB ) \ ) or resid 336 through 337 or resid 352 through 355 or (resid 356 and (name N or \ name CA or name C or name O or name CB )) or (resid 357 through 362 and (name N \ or name CA or name C or name O or name CB )) or resid 363 or (resid 364 through \ 365 and (name N or name CA or name C or name O or name CB )) or resid 366 throu \ gh 369 or (resid 370 and (name N or name CA or name C or name O or name CB )) or \ resid 371 or (resid 372 through 373 and (name N or name CA or name C or name O \ or name CB )) or resid 374 or (resid 375 through 379 and (name N or name CA or n \ ame C or name O or name CB )) or resid 380 or (resid 381 through 384 and (name N \ or name CA or name C or name O or name CB )) or resid 385 through 387 or (resid \ 388 through 390 and (name N or name CA or name C or name O or name CB )) or res \ id 391 or (resid 392 through 399 and (name N or name CA or name C or name O or n \ ame CB )) or resid 400 through 404 or (resid 405 and (name N or name CA or name \ C or name O or name CB )) or resid 406 or (resid 407 through 410 and (name N or \ name CA or name C or name O or name CB )) or resid 411 through 413 or (resid 414 \ through 416 and (name N or name CA or name C or name O or name CB )) or resid 4 \ 17 through 420 or (resid 421 and (name N or name CA or name C or name O or name \ CB )) or resid 422 or (resid 423 through 427 and (name N or name CA or name C or \ name O or name CB )) or resid 428 through 431 or (resid 432 and (name N or name \ CA or name C or name O or name CB )) or resid 433 through 434 or (resid 435 thr \ ough 437 and (name N or name CA or name C or name O or name CB )) or resid 438 t \ hrough 439 or (resid 440 through 441 and (name N or name CA or name C or name O \ or name CB )) or resid 442 or (resid 443 through 445 and (name N or name CA or n \ ame C or name O or name CB )) or resid 446 or (resid 447 and (name N or name CA \ or name C or name O or name CB )) or resid 448 through 449 or (resid 450 through \ 452 and (name N or name CA or name C or name O or name CB )) or resid 453 throu \ gh 458 or (resid 459 through 461 and (name N or name CA or name C or name O or n \ ame CB )) or resid 462 through 466 or (resid 467 through 468 and (name N or name \ CA or name C or name O or name CB )) or resid 469 or (resid 470 and (name N or \ name CA or name C or name O or name CB )) or resid 471 or (resid 472 through 473 \ and (name N or name CA or name C or name O or name CB )) or resid 474 through 4 \ 80 or (resid 481 through 483 and (name N or name CA or name C or name O or name \ CB )) or resid 484 or (resid 485 through 487 and (name N or name CA or name C or \ name O or name CB )) or resid 488 through 490 or (resid 491 through 492 and (na \ me N or name CA or name C or name O or name CB )) or resid 493 through 496 or (r \ esid 497 and (name N or name CA or name C or name O or name CB )) or resid 498 t \ hrough 499 or (resid 500 and (name N or name CA or name C or name O or name CB ) \ ) or resid 501 through 507 or (resid 508 and (name N or name CA or name C or nam \ e O or name CB )) or resid 509 through 521 or (resid 522 and (name N or name CA \ or name C or name O or name CB )) or resid 523 through 530 or (resid 531 through \ 535 and (name N or name CA or name C or name O or name CB )) or resid 536 or (r \ esid 537 through 538 and (name N or name CA or name C or name O or name CB )) or \ resid 539 or (resid 540 and (name N or name CA or name C or name O or name CB ) \ ) or resid 541 through 547 or (resid 548 through 549 and (name N or name CA or n \ ame C or name O or name CB )) or resid 550 through 553 or (resid 554 through 558 \ and (name N or name CA or name C or name O or name CB )) or resid 559 or (resid \ 560 through 562 and (name N or name CA or name C or name O or name CB )) or res \ id 563 or (resid 564 and (name N or name CA or name C or name O or name CB )) or \ resid 565 through 571 or (resid 572 and (name N or name CA or name C or name O \ or name CB )) or resid 573 or (resid 574 through 577 and (name N or name CA or n \ ame C or name O or name CB )) or resid 578 or (resid 579 through 580 and (name N \ or name CA or name C or name O or name CB )) or resid 581 through 582 or (resid \ 583 through 584 and (name N or name CA or name C or name O or name CB )) or res \ id 585 or (resid 586 through 590 and (name N or name CA or name C or name O or n \ ame CB )) or resid 591 or (resid 592 and (name N or name CA or name C or name O \ or name CB )) or resid 593 through 594 or (resid 595 and (name N or name CA or n \ ame C or name O or name CB )) or resid 596 through 599 or (resid 600 and (name N \ or name CA or name C or name O or name CB )) or resid 601 or (resid 602 through \ 609 and (name N or name CA or name C or name O or name CB )) or (resid 640 thro \ ugh 641 and (name N or name CA or name C or name O or name CB )) or (resid 642 t \ hrough 653 and (name N or name CA or name C or name O or name CB )) or resid 654 \ through 657 or (resid 658 through 660 and (name N or name CA or name C or name \ O or name CB )) or resid 661 through 663 or (resid 664 through 665 and (name N o \ r name CA or name C or name O or name CB )) or resid 666 through 667 or (resid 6 \ 68 through 669 and (name N or name CA or name C or name O or name CB )) or resid \ 670 or (resid 671 through 679 and (name N or name CA or name C or name O or nam \ e CB )) or (resid 680 through 684 and (name N or name CA or name C or name O or \ name CB )) or resid 685 through 686 or (resid 687 through 695 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'N' and (resid 15 through 160 or (resid 161 and (name N or name CA or nam \ e C or name O or name CB )) or resid 162 through 608 or (resid 609 through 641 a \ nd (name N or name CA or name C or name O or name CB )) or resid 642 through 695 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.610 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 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 : 0.002 0.053 41881 Z= 0.119 Angle : 0.515 7.052 57200 Z= 0.283 Chirality : 0.043 0.181 6820 Planarity : 0.004 0.065 7395 Dihedral : 12.356 89.165 14208 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.72 % Favored : 94.11 % Rotamer: Outliers : 0.03 % Allowed : 0.78 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.12), residues: 5668 helix: 1.63 (0.12), residues: 2135 sheet: -1.11 (0.20), residues: 745 loop : -1.16 (0.12), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 470 TYR 0.015 0.001 TYR J 253 PHE 0.016 0.001 PHE F 361 TRP 0.012 0.001 TRP T 147 HIS 0.005 0.001 HIS M 162 Details of bonding type rmsd covalent geometry : bond 0.00230 (41881) covalent geometry : angle 0.51516 (57200) hydrogen bonds : bond 0.17323 ( 1679) hydrogen bonds : angle 6.62459 ( 4785) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 828 time to evaluate : 1.881 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: D 137 TYR cc_start: 0.8031 (m-80) cc_final: 0.7827 (m-80) REVERT: D 376 TYR cc_start: 0.7018 (m-80) cc_final: 0.6577 (m-80) REVERT: D 416 LEU cc_start: 0.8803 (mt) cc_final: 0.8131 (pp) REVERT: D 428 ILE cc_start: 0.8407 (mt) cc_final: 0.7605 (mt) REVERT: D 464 TYR cc_start: 0.5766 (m-80) cc_final: 0.4953 (m-10) REVERT: D 493 LEU cc_start: 0.8495 (mt) cc_final: 0.8232 (mm) REVERT: D 535 GLU cc_start: 0.7988 (tt0) cc_final: 0.7550 (tm-30) REVERT: D 560 MET cc_start: 0.5899 (ptp) cc_final: 0.5351 (ptp) REVERT: J 94 TYR cc_start: 0.8434 (t80) cc_final: 0.8079 (t80) REVERT: J 98 LEU cc_start: 0.8747 (mt) cc_final: 0.8446 (tt) REVERT: M 296 LEU cc_start: 0.8964 (mt) cc_final: 0.8420 (tp) REVERT: M 679 HIS cc_start: 0.6569 (m-70) cc_final: 0.6217 (m90) REVERT: N 142 ASN cc_start: 0.7361 (m-40) cc_final: 0.6858 (p0) REVERT: N 525 HIS cc_start: 0.8319 (t70) cc_final: 0.8118 (t-170) REVERT: N 544 LEU cc_start: 0.8164 (mt) cc_final: 0.7940 (mt) REVERT: O 84 PRO cc_start: 0.8536 (Cg_endo) cc_final: 0.8313 (Cg_exo) REVERT: P 276 TYR cc_start: 0.8789 (t80) cc_final: 0.8346 (t80) REVERT: R 12 THR cc_start: 0.5775 (p) cc_final: 0.5362 (t) REVERT: R 38 CYS cc_start: 0.7161 (m) cc_final: 0.5643 (m) REVERT: R 254 LEU cc_start: 0.8062 (tp) cc_final: 0.7493 (pp) REVERT: R 261 LYS cc_start: 0.8199 (ttmm) cc_final: 0.7977 (tppt) REVERT: F 22 VAL cc_start: 0.7770 (t) cc_final: 0.7150 (p) REVERT: F 256 MET cc_start: 0.4183 (mmm) cc_final: 0.3272 (ptp) REVERT: Q 96 ARG cc_start: 0.8294 (mtt180) cc_final: 0.7694 (mtm180) REVERT: Q 304 TYR cc_start: 0.7165 (t80) cc_final: 0.6417 (p90) outliers start: 1 outliers final: 1 residues processed: 828 average time/residue: 0.2637 time to fit residues: 352.2386 Evaluate side-chains 374 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 162 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 394 optimal weight: 5.9990 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 0.0670 chunk 497 optimal weight: 0.8980 chunk 414 optimal weight: 0.4980 chunk 310 optimal weight: 7.9990 chunk 488 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 0.0570 overall best weight: 1.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 110 GLN D 462 HIS J 137 ASN J 199 ASN J 309 ASN ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 266 GLN L 182 GLN N 462 HIS P 99 GLN R 309 ASN S 199 ASN T 116 ASN F 21 HIS F 116 ASN ** F 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 155 HIS F 218 GLN ** F 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 HIS Q 116 ASN Q 218 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.126993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.092145 restraints weight = 125933.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.089502 restraints weight = 78808.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089744 restraints weight = 83271.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.089874 restraints weight = 75156.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090276 restraints weight = 64616.913| |-----------------------------------------------------------------------------| r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 41881 Z= 0.132 Angle : 0.571 15.457 57200 Z= 0.292 Chirality : 0.045 0.279 6820 Planarity : 0.004 0.060 7395 Dihedral : 3.833 33.637 6061 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.09 % Rotamer: Outliers : 1.62 % Allowed : 9.51 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.12), residues: 5668 helix: 1.62 (0.12), residues: 2167 sheet: -1.01 (0.20), residues: 730 loop : -1.19 (0.12), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 228 TYR 0.030 0.001 TYR Q 253 PHE 0.023 0.001 PHE O 294 TRP 0.033 0.001 TRP N 385 HIS 0.019 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00300 (41881) covalent geometry : angle 0.57115 (57200) hydrogen bonds : bond 0.03485 ( 1679) hydrogen bonds : angle 4.93667 ( 4785) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 406 time to evaluate : 1.751 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: D 177 VAL cc_start: 0.9228 (t) cc_final: 0.8977 (t) REVERT: D 204 TYR cc_start: 0.7646 (m-80) cc_final: 0.6933 (m-80) REVERT: D 376 TYR cc_start: 0.7007 (m-80) cc_final: 0.6732 (m-80) REVERT: D 414 PHE cc_start: 0.6678 (m-80) cc_final: 0.5662 (m-80) REVERT: D 416 LEU cc_start: 0.8887 (mt) cc_final: 0.8549 (pp) REVERT: D 535 GLU cc_start: 0.8331 (tt0) cc_final: 0.7689 (tm-30) REVERT: J 98 LEU cc_start: 0.9013 (mt) cc_final: 0.8584 (tt) REVERT: J 119 GLU cc_start: 0.8534 (pt0) cc_final: 0.8092 (pt0) REVERT: J 197 GLU cc_start: 0.8349 (mp0) cc_final: 0.8135 (mp0) REVERT: J 257 MET cc_start: 0.8863 (mmm) cc_final: 0.8597 (mmm) REVERT: L 535 GLU cc_start: 0.7984 (tp30) cc_final: 0.7783 (tp30) REVERT: M 296 LEU cc_start: 0.9302 (mt) cc_final: 0.8728 (tp) REVERT: N 105 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6374 (pm20) REVERT: N 367 LEU cc_start: 0.8512 (tt) cc_final: 0.8238 (pp) REVERT: N 433 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8501 (ttp80) REVERT: N 517 MET cc_start: 0.8449 (mtp) cc_final: 0.8109 (mtp) REVERT: N 525 HIS cc_start: 0.8704 (t70) cc_final: 0.8411 (t-170) REVERT: O 239 LEU cc_start: 0.9306 (mt) cc_final: 0.9003 (tt) REVERT: R 12 THR cc_start: 0.5395 (p) cc_final: 0.5017 (t) REVERT: R 38 CYS cc_start: 0.6987 (m) cc_final: 0.6471 (m) REVERT: R 157 VAL cc_start: 0.6552 (t) cc_final: 0.6328 (p) REVERT: R 217 TRP cc_start: 0.7342 (m-10) cc_final: 0.6387 (m-10) REVERT: R 258 ASP cc_start: 0.8200 (m-30) cc_final: 0.7843 (t0) REVERT: R 312 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7688 (pm20) REVERT: R 316 MET cc_start: 0.8350 (mtm) cc_final: 0.7522 (ptp) REVERT: R 330 ARG cc_start: 0.7253 (mtm180) cc_final: 0.6976 (mtm180) REVERT: F 256 MET cc_start: 0.3774 (mmm) cc_final: 0.3427 (mpp) REVERT: Q 56 LEU cc_start: 0.8707 (mt) cc_final: 0.8050 (tp) REVERT: Q 96 ARG cc_start: 0.8373 (mtt180) cc_final: 0.7657 (mtm180) REVERT: Q 98 LEU cc_start: 0.8436 (mt) cc_final: 0.8183 (tt) REVERT: Q 304 TYR cc_start: 0.7411 (t80) cc_final: 0.6695 (p90) outliers start: 62 outliers final: 36 residues processed: 455 average time/residue: 0.2429 time to fit residues: 185.6150 Evaluate side-chains 367 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 331 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain J residue 88 ILE Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 421 SER Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain M residue 684 ASN Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 162 HIS Chi-restraints excluded: chain N residue 462 HIS Chi-restraints excluded: chain N residue 596 VAL Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain O residue 518 ASN Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain S residue 77 GLN Chi-restraints excluded: chain T residue 49 LEU Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 169 GLU Chi-restraints excluded: chain T residue 306 VAL Chi-restraints excluded: chain Q residue 194 ARG Chi-restraints excluded: chain Q residue 230 THR Chi-restraints excluded: chain Q residue 283 ILE Chi-restraints excluded: chain Q residue 368 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 485 optimal weight: 2.9990 chunk 553 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 279 optimal weight: 50.0000 chunk 120 optimal weight: 2.9990 chunk 436 optimal weight: 5.9990 chunk 197 optimal weight: 4.9990 chunk 87 optimal weight: 20.0000 chunk 214 optimal weight: 5.9990 chunk 451 optimal weight: 1.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 199 ASN ** K 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 GLN N 462 HIS ** S 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 212 HIS T 218 GLN F 142 HIS ** F 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 199 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.123445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086556 restraints weight = 124983.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.085708 restraints weight = 80168.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.085479 restraints weight = 69321.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085683 restraints weight = 63971.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.085826 restraints weight = 62219.256| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 41881 Z= 0.195 Angle : 0.581 13.203 57200 Z= 0.299 Chirality : 0.045 0.224 6820 Planarity : 0.004 0.056 7395 Dihedral : 4.001 29.661 6061 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.49 % Rotamer: Outliers : 2.25 % Allowed : 11.41 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.12), residues: 5668 helix: 1.66 (0.12), residues: 2160 sheet: -1.03 (0.20), residues: 748 loop : -1.16 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG N 545 TYR 0.025 0.001 TYR Q 253 PHE 0.017 0.002 PHE S 263 TRP 0.037 0.001 TRP F 147 HIS 0.033 0.001 HIS N 462 Details of bonding type rmsd covalent geometry : bond 0.00451 (41881) covalent geometry : angle 0.58081 (57200) hydrogen bonds : bond 0.03511 ( 1679) hydrogen bonds : angle 4.69573 ( 4785) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 334 time to evaluate : 1.713 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: D 204 TYR cc_start: 0.7714 (m-80) cc_final: 0.6927 (m-80) REVERT: D 441 TRP cc_start: 0.8308 (m100) cc_final: 0.7292 (t60) REVERT: D 535 GLU cc_start: 0.8316 (tt0) cc_final: 0.7701 (tm-30) REVERT: J 197 GLU cc_start: 0.8152 (mp0) cc_final: 0.7842 (mp0) REVERT: J 210 LYS cc_start: 0.7508 (mtpt) cc_final: 0.7289 (mtpt) REVERT: K 128 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8833 (pm20) REVERT: L 535 GLU cc_start: 0.7664 (tp30) cc_final: 0.7426 (tp30) REVERT: M 296 LEU cc_start: 0.9373 (mt) cc_final: 0.8779 (tp) REVERT: N 105 GLU cc_start: 0.7467 (mm-30) cc_final: 0.6325 (pm20) REVERT: N 256 ASP cc_start: 0.6865 (m-30) cc_final: 0.6465 (p0) REVERT: N 517 MET cc_start: 0.8660 (mtp) cc_final: 0.8459 (mtp) REVERT: N 670 HIS cc_start: 0.5812 (OUTLIER) cc_final: 0.5431 (p-80) REVERT: O 19 ASP cc_start: 0.7966 (m-30) cc_final: 0.7509 (t0) REVERT: O 491 MET cc_start: 0.8701 (tpp) cc_final: 0.7900 (tpp) REVERT: R 12 THR cc_start: 0.5252 (p) cc_final: 0.4820 (t) REVERT: R 38 CYS cc_start: 0.6984 (m) cc_final: 0.6503 (m) REVERT: R 258 ASP cc_start: 0.8282 (m-30) cc_final: 0.7843 (t0) REVERT: R 316 MET cc_start: 0.8301 (mtm) cc_final: 0.7560 (ptp) REVERT: R 330 ARG cc_start: 0.7058 (mtm180) cc_final: 0.6810 (mtm180) REVERT: F 217 TRP cc_start: 0.3009 (m-10) cc_final: 0.2493 (m-10) REVERT: F 256 MET cc_start: 0.4182 (mmm) cc_final: 0.3278 (ptp) REVERT: F 281 GLN cc_start: 0.6036 (mm-40) cc_final: 0.5538 (tm-30) REVERT: Q 56 LEU cc_start: 0.8843 (mt) cc_final: 0.8199 (tp) REVERT: Q 96 ARG cc_start: 0.8412 (mtt180) cc_final: 0.7612 (mtm180) outliers start: 86 outliers final: 55 residues processed: 403 average time/residue: 0.2455 time to fit residues: 166.2600 Evaluate side-chains 345 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 288 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain L residue 16 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 SER Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 80 LEU Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain M residue 684 ASN Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 505 ILE Chi-restraints excluded: chain N residue 596 VAL Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 24 ASN Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 228 ILE Chi-restraints excluded: chain O residue 235 CYS Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain O residue 472 ILE Chi-restraints excluded: chain O residue 518 ASN Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 287 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 286 VAL Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain Q residue 194 ARG Chi-restraints excluded: chain Q residue 283 ILE Chi-restraints excluded: chain Q residue 368 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 0 optimal weight: 10.0000 chunk 426 optimal weight: 7.9990 chunk 337 optimal weight: 0.6980 chunk 89 optimal weight: 4.9990 chunk 539 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 chunk 354 optimal weight: 1.9990 chunk 502 optimal weight: 20.0000 chunk 286 optimal weight: 3.9990 chunk 307 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 GLN ** S 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 311 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.122804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086056 restraints weight = 121267.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.084467 restraints weight = 88112.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084835 restraints weight = 72044.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.085240 restraints weight = 62312.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.085450 restraints weight = 54111.984| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 41881 Z= 0.174 Angle : 0.559 13.694 57200 Z= 0.286 Chirality : 0.044 0.221 6820 Planarity : 0.004 0.058 7395 Dihedral : 3.975 28.959 6059 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 2.69 % Allowed : 12.56 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.12), residues: 5668 helix: 1.67 (0.12), residues: 2159 sheet: -1.03 (0.20), residues: 745 loop : -1.18 (0.12), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 433 TYR 0.026 0.001 TYR Q 253 PHE 0.021 0.001 PHE R 183 TRP 0.046 0.001 TRP F 147 HIS 0.013 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00409 (41881) covalent geometry : angle 0.55859 (57200) hydrogen bonds : bond 0.03249 ( 1679) hydrogen bonds : angle 4.48249 ( 4785) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 319 time to evaluate : 1.252 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: D 204 TYR cc_start: 0.7563 (m-80) cc_final: 0.6893 (m-80) REVERT: D 376 TYR cc_start: 0.7110 (m-10) cc_final: 0.6845 (m-10) REVERT: D 441 TRP cc_start: 0.8349 (m100) cc_final: 0.7121 (t60) REVERT: D 535 GLU cc_start: 0.8174 (tt0) cc_final: 0.7632 (tm-30) REVERT: J 94 TYR cc_start: 0.8934 (t80) cc_final: 0.8709 (t80) REVERT: J 165 ASP cc_start: 0.8004 (p0) cc_final: 0.7628 (p0) REVERT: J 210 LYS cc_start: 0.7475 (mtpt) cc_final: 0.7267 (mtpt) REVERT: K 128 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8818 (pm20) REVERT: L 535 GLU cc_start: 0.7644 (tp30) cc_final: 0.7377 (tp30) REVERT: M 296 LEU cc_start: 0.9317 (mt) cc_final: 0.8662 (tp) REVERT: M 590 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: N 105 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6097 (pm20) REVERT: N 225 LYS cc_start: 0.8321 (tptp) cc_final: 0.8039 (tmtt) REVERT: N 256 ASP cc_start: 0.6877 (m-30) cc_final: 0.6493 (p0) REVERT: N 670 HIS cc_start: 0.6125 (OUTLIER) cc_final: 0.5699 (p-80) REVERT: O 239 LEU cc_start: 0.9438 (mt) cc_final: 0.9172 (tt) REVERT: O 491 MET cc_start: 0.8653 (tpp) cc_final: 0.7866 (tpp) REVERT: P 92 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8439 (mm) REVERT: R 12 THR cc_start: 0.5325 (p) cc_final: 0.4898 (t) REVERT: R 38 CYS cc_start: 0.7121 (m) cc_final: 0.6638 (m) REVERT: R 157 VAL cc_start: 0.6809 (t) cc_final: 0.6568 (p) REVERT: R 217 TRP cc_start: 0.7375 (m-10) cc_final: 0.6597 (m-10) REVERT: R 330 ARG cc_start: 0.6975 (mtm180) cc_final: 0.6711 (mtm180) REVERT: S 168 MET cc_start: 0.8383 (tpp) cc_final: 0.8129 (tpp) REVERT: F 256 MET cc_start: 0.4286 (mmm) cc_final: 0.3633 (mpp) REVERT: Q 56 LEU cc_start: 0.8733 (mt) cc_final: 0.8096 (tp) REVERT: Q 96 ARG cc_start: 0.8420 (mtt180) cc_final: 0.7542 (mtm180) outliers start: 103 outliers final: 63 residues processed: 406 average time/residue: 0.2212 time to fit residues: 151.4148 Evaluate side-chains 351 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 284 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain L residue 40 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 SER Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 605 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 184 ILE Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 468 ASP Chi-restraints excluded: chain M residue 590 GLN Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain M residue 684 ASN Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 502 ASP Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 24 ASN Chi-restraints excluded: chain O residue 159 VAL Chi-restraints excluded: chain O residue 228 ILE Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain O residue 472 ILE Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 287 LEU Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 286 VAL Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain Q residue 194 ARG Chi-restraints excluded: chain Q residue 283 ILE Chi-restraints excluded: chain Q residue 368 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 73 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 415 optimal weight: 8.9990 chunk 58 optimal weight: 30.0000 chunk 215 optimal weight: 20.0000 chunk 498 optimal weight: 2.9990 chunk 182 optimal weight: 0.4980 chunk 274 optimal weight: 0.0670 chunk 497 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 137 ASN L 110 GLN ** S 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.123434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.086870 restraints weight = 121407.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.085741 restraints weight = 79471.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.085957 restraints weight = 67807.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086129 restraints weight = 65314.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.086426 restraints weight = 54647.929| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41881 Z= 0.117 Angle : 0.522 12.875 57200 Z= 0.264 Chirality : 0.043 0.217 6820 Planarity : 0.004 0.055 7395 Dihedral : 3.792 26.980 6059 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.82 % Favored : 94.11 % Rotamer: Outliers : 2.25 % Allowed : 13.92 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.12), residues: 5668 helix: 1.78 (0.12), residues: 2155 sheet: -0.90 (0.20), residues: 731 loop : -1.14 (0.12), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 433 TYR 0.026 0.001 TYR Q 253 PHE 0.015 0.001 PHE S 263 TRP 0.058 0.001 TRP F 147 HIS 0.011 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00268 (41881) covalent geometry : angle 0.52194 (57200) hydrogen bonds : bond 0.02876 ( 1679) hydrogen bonds : angle 4.32854 ( 4785) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 333 time to evaluate : 1.599 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: D 204 TYR cc_start: 0.7595 (m-80) cc_final: 0.6970 (m-80) REVERT: D 376 TYR cc_start: 0.7153 (m-10) cc_final: 0.6783 (m-10) REVERT: D 441 TRP cc_start: 0.8326 (m100) cc_final: 0.7227 (t60) REVERT: D 474 ILE cc_start: 0.8592 (tt) cc_final: 0.8294 (pt) REVERT: D 535 GLU cc_start: 0.8194 (tt0) cc_final: 0.7511 (tm-30) REVERT: D 560 MET cc_start: 0.6228 (ptp) cc_final: 0.5912 (ptt) REVERT: J 94 TYR cc_start: 0.8990 (t80) cc_final: 0.8778 (t80) REVERT: J 210 LYS cc_start: 0.7462 (mtpt) cc_final: 0.7200 (mtpt) REVERT: J 257 MET cc_start: 0.8881 (mmm) cc_final: 0.8668 (mmm) REVERT: K 128 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8813 (pm20) REVERT: L 535 GLU cc_start: 0.7660 (tp30) cc_final: 0.7420 (tp30) REVERT: M 296 LEU cc_start: 0.9309 (mt) cc_final: 0.8639 (tp) REVERT: M 590 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7972 (tm-30) REVERT: N 105 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6295 (pm20) REVERT: N 225 LYS cc_start: 0.8341 (tptp) cc_final: 0.8015 (tmtt) REVERT: N 256 ASP cc_start: 0.6910 (m-30) cc_final: 0.6480 (p0) REVERT: N 367 LEU cc_start: 0.8536 (tt) cc_final: 0.8186 (pp) REVERT: N 670 HIS cc_start: 0.6063 (OUTLIER) cc_final: 0.5652 (p-80) REVERT: O 491 MET cc_start: 0.8600 (tpp) cc_final: 0.7774 (tpp) REVERT: R 12 THR cc_start: 0.5275 (p) cc_final: 0.4860 (t) REVERT: R 38 CYS cc_start: 0.7159 (m) cc_final: 0.6649 (m) REVERT: R 157 VAL cc_start: 0.6862 (t) cc_final: 0.6645 (p) REVERT: R 195 THR cc_start: 0.6051 (p) cc_final: 0.5258 (p) REVERT: R 258 ASP cc_start: 0.8196 (m-30) cc_final: 0.7802 (t0) REVERT: R 303 GLN cc_start: 0.6731 (OUTLIER) cc_final: 0.6432 (mp-120) REVERT: R 316 MET cc_start: 0.8257 (mtm) cc_final: 0.7379 (ptp) REVERT: R 330 ARG cc_start: 0.6875 (mtm180) cc_final: 0.6587 (mtm180) REVERT: F 256 MET cc_start: 0.4343 (mmm) cc_final: 0.3742 (mpp) REVERT: Q 56 LEU cc_start: 0.8727 (mt) cc_final: 0.8105 (tp) REVERT: Q 96 ARG cc_start: 0.8361 (mtt180) cc_final: 0.7538 (mtm180) outliers start: 86 outliers final: 60 residues processed: 400 average time/residue: 0.2194 time to fit residues: 148.7679 Evaluate side-chains 349 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 285 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 190 PHE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain J residue 137 ASN Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 SER Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 184 ILE Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 468 ASP Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 590 GLN Chi-restraints excluded: chain M residue 684 ASN Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 162 HIS Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 502 ASP Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 24 ASN Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 228 ILE Chi-restraints excluded: chain O residue 235 CYS Chi-restraints excluded: chain O residue 472 ILE Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 518 ASN Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain R residue 8 SER Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain R residue 303 GLN Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 287 LEU Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 72 LEU Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 286 VAL Chi-restraints excluded: chain Q residue 194 ARG Chi-restraints excluded: chain Q residue 368 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 224 optimal weight: 3.9990 chunk 477 optimal weight: 20.0000 chunk 476 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 515 optimal weight: 8.9990 chunk 356 optimal weight: 3.9990 chunk 512 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 59 optimal weight: 9.9990 chunk 128 optimal weight: 4.9990 chunk 396 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 201 HIS J 116 ASN M 69 GLN N 119 HIS P 212 HIS P 218 GLN R 116 ASN ** S 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 170 GLN ** S 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 15 GLN F 116 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 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 = 0.3987 r_free = 0.3987 target = 0.118757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.081969 restraints weight = 124988.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.080615 restraints weight = 82494.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080265 restraints weight = 75983.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.080427 restraints weight = 76503.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.080648 restraints weight = 64310.961| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.153 41881 Z= 0.322 Angle : 0.702 13.942 57200 Z= 0.360 Chirality : 0.048 0.192 6820 Planarity : 0.005 0.064 7395 Dihedral : 4.661 32.091 6059 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.40 % Favored : 91.51 % Rotamer: Outliers : 3.13 % Allowed : 14.83 % Favored : 82.03 % 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 aren not related in a simple way. whole: -0.39 (0.11), residues: 5668 helix: 1.38 (0.12), residues: 2156 sheet: -1.39 (0.19), residues: 775 loop : -1.26 (0.12), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 433 TYR 0.024 0.002 TYR Q 253 PHE 0.018 0.002 PHE L 513 TRP 0.067 0.002 TRP F 147 HIS 0.013 0.002 HIS M 162 Details of bonding type rmsd covalent geometry : bond 0.00754 (41881) covalent geometry : angle 0.70161 (57200) hydrogen bonds : bond 0.04121 ( 1679) hydrogen bonds : angle 4.77667 ( 4785) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 288 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 87 HIS cc_start: 0.6502 (p-80) cc_final: 0.6273 (p-80) REVERT: D 204 TYR cc_start: 0.7435 (m-80) cc_final: 0.7020 (m-80) REVERT: D 376 TYR cc_start: 0.7188 (m-10) cc_final: 0.6918 (m-10) REVERT: D 441 TRP cc_start: 0.8339 (m100) cc_final: 0.7205 (t60) REVERT: D 459 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6558 (tm-30) REVERT: J 197 GLU cc_start: 0.8054 (mp0) cc_final: 0.7766 (mp0) REVERT: J 210 LYS cc_start: 0.7473 (mtpt) cc_final: 0.7190 (mtpt) REVERT: K 128 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8818 (pm20) REVERT: M 459 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7732 (tt0) REVERT: M 590 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8177 (tm-30) REVERT: N 256 ASP cc_start: 0.6986 (m-30) cc_final: 0.6519 (p0) REVERT: N 367 LEU cc_start: 0.8627 (tt) cc_final: 0.8098 (mt) REVERT: N 527 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9132 (mm) REVERT: N 662 TYR cc_start: 0.6726 (m-80) cc_final: 0.6355 (m-10) REVERT: N 670 HIS cc_start: 0.6044 (OUTLIER) cc_final: 0.5769 (p-80) REVERT: O 239 LEU cc_start: 0.9487 (mt) cc_final: 0.9269 (tt) REVERT: O 491 MET cc_start: 0.8633 (tpp) cc_final: 0.7972 (tpt) REVERT: P 92 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8535 (mm) REVERT: P 257 MET cc_start: 0.8697 (mmm) cc_final: 0.8480 (mmm) REVERT: R 12 THR cc_start: 0.5443 (p) cc_final: 0.5039 (t) REVERT: R 38 CYS cc_start: 0.7068 (m) cc_final: 0.6534 (m) REVERT: R 157 VAL cc_start: 0.6880 (t) cc_final: 0.6675 (p) REVERT: R 330 ARG cc_start: 0.6746 (mtm180) cc_final: 0.6477 (mtm180) REVERT: F 256 MET cc_start: 0.4329 (mmm) cc_final: 0.3467 (ptp) REVERT: Q 96 ARG cc_start: 0.8427 (mtt180) cc_final: 0.7365 (mtp180) outliers start: 120 outliers final: 78 residues processed: 390 average time/residue: 0.1991 time to fit residues: 132.7153 Evaluate side-chains 335 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 250 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 459 GLU Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 153 VAL Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 370 LEU Chi-restraints excluded: chain L residue 421 SER Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 430 ILE Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain M residue 459 GLU Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 590 GLN Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain M residue 684 ASN Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 502 ASP Chi-restraints excluded: chain N residue 505 ILE Chi-restraints excluded: chain N residue 527 LEU Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 24 ASN Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 218 THR Chi-restraints excluded: chain O residue 235 CYS Chi-restraints excluded: chain O residue 379 LEU Chi-restraints excluded: chain O residue 472 ILE Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 517 MET Chi-restraints excluded: chain O residue 518 ASN Chi-restraints excluded: chain O residue 538 MET Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 325 LEU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain S residue 23 LEU Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 287 LEU Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 115 ILE Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 286 VAL Chi-restraints excluded: chain T residue 306 VAL Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 168 MET Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain Q residue 283 ILE Chi-restraints excluded: chain Q residue 368 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 57 optimal weight: 8.9990 chunk 266 optimal weight: 0.0980 chunk 354 optimal weight: 1.9990 chunk 259 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 350 optimal weight: 0.6980 chunk 557 optimal weight: 0.2980 chunk 275 optimal weight: 30.0000 chunk 169 optimal weight: 0.9980 chunk 212 optimal weight: 30.0000 chunk 174 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 170 GLN ** S 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 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 = 0.4035 r_free = 0.4035 target = 0.121787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.085278 restraints weight = 121344.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.084076 restraints weight = 80958.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.084208 restraints weight = 68194.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084467 restraints weight = 64689.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.084612 restraints weight = 57839.025| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 41881 Z= 0.102 Angle : 0.551 13.646 57200 Z= 0.277 Chirality : 0.044 0.229 6820 Planarity : 0.004 0.058 7395 Dihedral : 4.019 28.961 6059 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 1.93 % Allowed : 16.48 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.12), residues: 5668 helix: 1.66 (0.12), residues: 2170 sheet: -1.19 (0.20), residues: 730 loop : -1.21 (0.12), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG R 43 TYR 0.026 0.001 TYR Q 253 PHE 0.014 0.001 PHE S 263 TRP 0.065 0.001 TRP F 147 HIS 0.010 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00228 (41881) covalent geometry : angle 0.55105 (57200) hydrogen bonds : bond 0.02904 ( 1679) hydrogen bonds : angle 4.35654 ( 4785) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 295 time to evaluate : 1.387 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: D 19 ASP cc_start: 0.6940 (m-30) cc_final: 0.6725 (m-30) REVERT: D 87 HIS cc_start: 0.6328 (p-80) cc_final: 0.6087 (p-80) REVERT: D 204 TYR cc_start: 0.7410 (m-80) cc_final: 0.6892 (m-80) REVERT: D 414 PHE cc_start: 0.6375 (m-80) cc_final: 0.6040 (t80) REVERT: D 441 TRP cc_start: 0.8344 (m100) cc_final: 0.7217 (t60) REVERT: D 474 ILE cc_start: 0.8545 (tt) cc_final: 0.8329 (pt) REVERT: J 210 LYS cc_start: 0.7374 (mtpt) cc_final: 0.7162 (mtpt) REVERT: J 287 LEU cc_start: 0.8960 (pp) cc_final: 0.8684 (tt) REVERT: K 128 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8812 (pm20) REVERT: M 296 LEU cc_start: 0.9339 (mt) cc_final: 0.8596 (tp) REVERT: M 590 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8114 (tm-30) REVERT: N 256 ASP cc_start: 0.6990 (m-30) cc_final: 0.6528 (p0) REVERT: N 367 LEU cc_start: 0.8581 (tt) cc_final: 0.8096 (mt) REVERT: N 670 HIS cc_start: 0.5823 (OUTLIER) cc_final: 0.5479 (p-80) REVERT: O 239 LEU cc_start: 0.9492 (mt) cc_final: 0.9276 (tt) REVERT: O 491 MET cc_start: 0.8630 (tpp) cc_final: 0.7809 (tpp) REVERT: P 257 MET cc_start: 0.8508 (mmm) cc_final: 0.8048 (mmm) REVERT: R 12 THR cc_start: 0.5396 (p) cc_final: 0.4956 (t) REVERT: R 38 CYS cc_start: 0.7093 (m) cc_final: 0.6679 (m) REVERT: R 195 THR cc_start: 0.6357 (p) cc_final: 0.6086 (p) REVERT: R 258 ASP cc_start: 0.8269 (m-30) cc_final: 0.7858 (p0) REVERT: R 330 ARG cc_start: 0.6687 (mtm180) cc_final: 0.6391 (mtm180) REVERT: F 256 MET cc_start: 0.4338 (mmm) cc_final: 0.3437 (ptp) REVERT: Q 56 LEU cc_start: 0.8554 (mt) cc_final: 0.7748 (tp) REVERT: Q 96 ARG cc_start: 0.8411 (mtt180) cc_final: 0.7345 (mtp180) outliers start: 74 outliers final: 56 residues processed: 355 average time/residue: 0.1953 time to fit residues: 117.9677 Evaluate side-chains 328 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 269 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 83 GLU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain L residue 421 SER Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 430 ILE Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 590 GLN Chi-restraints excluded: chain M residue 684 ASN Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 502 ASP Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 24 ASN Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 228 ILE Chi-restraints excluded: chain O residue 235 CYS Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 518 ASN Chi-restraints excluded: chain O residue 540 MET Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 287 LEU Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 286 VAL Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 43 ARG Chi-restraints excluded: chain Q residue 368 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 179 optimal weight: 20.0000 chunk 514 optimal weight: 20.0000 chunk 555 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 364 optimal weight: 2.9990 chunk 170 optimal weight: 0.9980 chunk 426 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 117 optimal weight: 0.0470 chunk 140 optimal weight: 3.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 137 ASN O 49 GLN S 78 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.120876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.084171 restraints weight = 122300.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.084005 restraints weight = 82337.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083366 restraints weight = 68890.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083785 restraints weight = 67319.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083965 restraints weight = 57936.107| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 41881 Z= 0.145 Angle : 0.555 13.111 57200 Z= 0.281 Chirality : 0.044 0.215 6820 Planarity : 0.004 0.055 7395 Dihedral : 3.990 28.145 6059 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.83 % Favored : 93.12 % Rotamer: Outliers : 2.04 % Allowed : 16.61 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.12), residues: 5668 helix: 1.70 (0.12), residues: 2147 sheet: -1.18 (0.20), residues: 737 loop : -1.15 (0.12), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 433 TYR 0.022 0.001 TYR Q 253 PHE 0.015 0.001 PHE S 263 TRP 0.051 0.001 TRP F 147 HIS 0.010 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00337 (41881) covalent geometry : angle 0.55451 (57200) hydrogen bonds : bond 0.03027 ( 1679) hydrogen bonds : angle 4.32957 ( 4785) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 274 time to evaluate : 1.674 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: D 19 ASP cc_start: 0.7042 (m-30) cc_final: 0.6785 (m-30) REVERT: D 204 TYR cc_start: 0.7523 (m-80) cc_final: 0.6948 (m-80) REVERT: D 441 TRP cc_start: 0.8369 (m100) cc_final: 0.7267 (t60) REVERT: D 474 ILE cc_start: 0.8476 (tt) cc_final: 0.8261 (pt) REVERT: J 210 LYS cc_start: 0.7343 (mtpt) cc_final: 0.7027 (mtpt) REVERT: J 287 LEU cc_start: 0.9049 (pp) cc_final: 0.8834 (tt) REVERT: K 128 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8835 (pm20) REVERT: M 590 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: N 256 ASP cc_start: 0.7049 (m-30) cc_final: 0.6515 (p0) REVERT: N 670 HIS cc_start: 0.5841 (OUTLIER) cc_final: 0.5593 (p-80) REVERT: O 105 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7013 (pm20) REVERT: O 239 LEU cc_start: 0.9505 (mt) cc_final: 0.9286 (tt) REVERT: O 491 MET cc_start: 0.8671 (tpp) cc_final: 0.7885 (tpp) REVERT: P 92 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8491 (mm) REVERT: P 257 MET cc_start: 0.8538 (mmm) cc_final: 0.8238 (mmm) REVERT: R 12 THR cc_start: 0.5452 (p) cc_final: 0.5040 (t) REVERT: R 38 CYS cc_start: 0.7269 (m) cc_final: 0.6908 (m) REVERT: R 147 TRP cc_start: 0.5719 (t60) cc_final: 0.5432 (t60) REVERT: R 195 THR cc_start: 0.6395 (p) cc_final: 0.6068 (p) REVERT: R 258 ASP cc_start: 0.8267 (m-30) cc_final: 0.7922 (p0) REVERT: R 330 ARG cc_start: 0.6713 (mtm180) cc_final: 0.6451 (mtm180) REVERT: F 256 MET cc_start: 0.4196 (mmm) cc_final: 0.3336 (ptp) REVERT: Q 96 ARG cc_start: 0.8390 (mtt180) cc_final: 0.7325 (mtp180) outliers start: 78 outliers final: 61 residues processed: 338 average time/residue: 0.1979 time to fit residues: 114.0874 Evaluate side-chains 332 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 266 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 GLU Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 292 LEU Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 SER Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 430 ILE Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 590 GLN Chi-restraints excluded: chain M residue 684 ASN Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 502 ASP Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 24 ASN Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 218 THR Chi-restraints excluded: chain O residue 235 CYS Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 517 MET Chi-restraints excluded: chain O residue 518 ASN Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain R residue 155 HIS Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 287 LEU Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 286 VAL Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain Q residue 40 VAL Chi-restraints excluded: chain Q residue 43 ARG Chi-restraints excluded: chain Q residue 368 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 510 optimal weight: 4.9990 chunk 522 optimal weight: 0.0570 chunk 79 optimal weight: 20.0000 chunk 292 optimal weight: 9.9990 chunk 23 optimal weight: 30.0000 chunk 556 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 434 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 401 optimal weight: 20.0000 chunk 498 optimal weight: 0.6980 overall best weight: 2.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 137 ASN O 49 GLN ** S 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 156 GLN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.119614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082368 restraints weight = 123958.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.081712 restraints weight = 84543.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.081587 restraints weight = 77935.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.081835 restraints weight = 64033.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.082046 restraints weight = 61068.173| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 41881 Z= 0.198 Angle : 0.597 12.801 57200 Z= 0.303 Chirality : 0.045 0.254 6820 Planarity : 0.004 0.058 7395 Dihedral : 4.240 29.264 6059 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.29 % Favored : 92.61 % Rotamer: Outliers : 2.12 % Allowed : 16.77 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.12), residues: 5668 helix: 1.66 (0.12), residues: 2137 sheet: -1.30 (0.20), residues: 745 loop : -1.17 (0.12), residues: 2786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG N 433 TYR 0.022 0.001 TYR Q 253 PHE 0.015 0.001 PHE S 263 TRP 0.038 0.002 TRP F 147 HIS 0.010 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00463 (41881) covalent geometry : angle 0.59746 (57200) hydrogen bonds : bond 0.03366 ( 1679) hydrogen bonds : angle 4.43446 ( 4785) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 272 time to evaluate : 1.124 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: D 19 ASP cc_start: 0.7104 (m-30) cc_final: 0.6856 (m-30) REVERT: D 69 GLN cc_start: 0.7512 (mm-40) cc_final: 0.6906 (tm-30) REVERT: D 441 TRP cc_start: 0.8385 (m100) cc_final: 0.7259 (t60) REVERT: D 474 ILE cc_start: 0.8507 (tt) cc_final: 0.8235 (pt) REVERT: J 165 ASP cc_start: 0.7437 (p0) cc_final: 0.7126 (p0) REVERT: J 210 LYS cc_start: 0.7346 (mtpt) cc_final: 0.7054 (mtpt) REVERT: K 128 GLU cc_start: 0.9113 (OUTLIER) cc_final: 0.8860 (pm20) REVERT: L 670 HIS cc_start: 0.7185 (OUTLIER) cc_final: 0.6740 (p-80) REVERT: N 367 LEU cc_start: 0.8611 (tt) cc_final: 0.8246 (pp) REVERT: N 527 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.8905 (tt) REVERT: N 670 HIS cc_start: 0.5922 (OUTLIER) cc_final: 0.5566 (p-80) REVERT: O 239 LEU cc_start: 0.9523 (mt) cc_final: 0.9317 (tt) REVERT: O 538 MET cc_start: 0.8862 (mmm) cc_final: 0.8545 (mmm) REVERT: P 257 MET cc_start: 0.8464 (mmm) cc_final: 0.8254 (tpp) REVERT: R 12 THR cc_start: 0.5517 (p) cc_final: 0.5102 (t) REVERT: R 38 CYS cc_start: 0.7191 (m) cc_final: 0.6824 (m) REVERT: R 147 TRP cc_start: 0.5949 (t60) cc_final: 0.5711 (t60) REVERT: R 168 MET cc_start: 0.4491 (tpt) cc_final: 0.3973 (ttp) REVERT: R 195 THR cc_start: 0.6384 (p) cc_final: 0.6125 (p) REVERT: R 258 ASP cc_start: 0.8342 (m-30) cc_final: 0.7989 (p0) REVERT: R 330 ARG cc_start: 0.6768 (mtm180) cc_final: 0.6496 (mtm180) REVERT: F 256 MET cc_start: 0.4210 (mmm) cc_final: 0.3425 (ptp) REVERT: Q 96 ARG cc_start: 0.8402 (mtt180) cc_final: 0.7320 (mtp180) outliers start: 81 outliers final: 66 residues processed: 340 average time/residue: 0.2060 time to fit residues: 118.8739 Evaluate side-chains 329 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 259 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 166 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 SER Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 430 ILE Chi-restraints excluded: chain L residue 507 SER Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain M residue 684 ASN Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 502 ASP Chi-restraints excluded: chain N residue 527 LEU Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 24 ASN Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 218 THR Chi-restraints excluded: chain O residue 235 CYS Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 517 MET Chi-restraints excluded: chain O residue 518 ASN Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain R residue 155 HIS Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 287 LEU Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 286 VAL Chi-restraints excluded: chain Q residue 43 ARG Chi-restraints excluded: chain Q residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 398 optimal weight: 0.0270 chunk 512 optimal weight: 10.0000 chunk 567 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 413 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 308 optimal weight: 50.0000 chunk 408 optimal weight: 8.9990 chunk 399 optimal weight: 6.9990 chunk 431 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 137 ASN ** S 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.120606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084409 restraints weight = 121435.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083035 restraints weight = 80286.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083304 restraints weight = 69633.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.083517 restraints weight = 60821.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083676 restraints weight = 57767.853| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.5001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 41881 Z= 0.138 Angle : 0.570 14.584 57200 Z= 0.286 Chirality : 0.044 0.238 6820 Planarity : 0.004 0.082 7395 Dihedral : 4.046 28.051 6059 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.65 % Favored : 93.30 % Rotamer: Outliers : 1.91 % Allowed : 17.16 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.12), residues: 5668 helix: 1.74 (0.12), residues: 2135 sheet: -1.24 (0.20), residues: 746 loop : -1.17 (0.12), residues: 2787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG M 470 TYR 0.022 0.001 TYR Q 253 PHE 0.014 0.001 PHE S 263 TRP 0.036 0.001 TRP F 147 HIS 0.010 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00323 (41881) covalent geometry : angle 0.57028 (57200) hydrogen bonds : bond 0.02991 ( 1679) hydrogen bonds : angle 4.32740 ( 4785) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11336 Ramachandran restraints generated. 5668 Oldfield, 0 Emsley, 5668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 270 time to evaluate : 1.456 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: D 19 ASP cc_start: 0.7049 (m-30) cc_final: 0.6812 (m-30) REVERT: D 80 LEU cc_start: 0.6581 (tp) cc_final: 0.5766 (pp) REVERT: D 441 TRP cc_start: 0.8303 (m100) cc_final: 0.7052 (t60) REVERT: D 474 ILE cc_start: 0.8492 (tt) cc_final: 0.8172 (pt) REVERT: J 165 ASP cc_start: 0.7261 (p0) cc_final: 0.6975 (p0) REVERT: K 128 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8822 (pm20) REVERT: L 670 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6712 (p-80) REVERT: N 367 LEU cc_start: 0.8519 (tt) cc_final: 0.8057 (mt) REVERT: N 527 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8873 (tt) REVERT: N 670 HIS cc_start: 0.5935 (OUTLIER) cc_final: 0.5539 (p-80) REVERT: O 105 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6970 (pm20) REVERT: O 491 MET cc_start: 0.8626 (tpp) cc_final: 0.7828 (tpp) REVERT: O 538 MET cc_start: 0.8749 (mmm) cc_final: 0.8360 (mmp) REVERT: O 554 GLU cc_start: 0.8164 (pm20) cc_final: 0.7736 (pm20) REVERT: P 257 MET cc_start: 0.8453 (mmm) cc_final: 0.8162 (mmm) REVERT: R 12 THR cc_start: 0.5561 (p) cc_final: 0.5126 (t) REVERT: R 38 CYS cc_start: 0.7163 (m) cc_final: 0.6728 (m) REVERT: R 147 TRP cc_start: 0.6150 (t60) cc_final: 0.5912 (t60) REVERT: R 258 ASP cc_start: 0.8299 (m-30) cc_final: 0.7947 (p0) REVERT: R 330 ARG cc_start: 0.6845 (mtm180) cc_final: 0.6542 (mtm180) REVERT: F 256 MET cc_start: 0.4228 (mmm) cc_final: 0.3459 (ptp) REVERT: Q 96 ARG cc_start: 0.8406 (mtt180) cc_final: 0.7317 (mtp180) outliers start: 73 outliers final: 63 residues processed: 332 average time/residue: 0.2038 time to fit residues: 115.5389 Evaluate side-chains 327 residues out of total 5085 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 259 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 435 LEU Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain J residue 33 ILE Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 159 ILE Chi-restraints excluded: chain K residue 206 SER Chi-restraints excluded: chain K residue 264 LEU Chi-restraints excluded: chain K residue 266 GLN Chi-restraints excluded: chain L residue 60 TYR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 280 THR Chi-restraints excluded: chain L residue 334 VAL Chi-restraints excluded: chain L residue 421 SER Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain M residue 20 VAL Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 113 THR Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 277 ASP Chi-restraints excluded: chain M residue 489 ILE Chi-restraints excluded: chain M residue 576 LEU Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain M residue 684 ASN Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 428 ILE Chi-restraints excluded: chain N residue 502 ASP Chi-restraints excluded: chain N residue 505 ILE Chi-restraints excluded: chain N residue 527 LEU Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 24 ASN Chi-restraints excluded: chain O residue 105 GLU Chi-restraints excluded: chain O residue 156 ASP Chi-restraints excluded: chain O residue 218 THR Chi-restraints excluded: chain O residue 235 CYS Chi-restraints excluded: chain O residue 297 TYR Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 480 ILE Chi-restraints excluded: chain O residue 517 MET Chi-restraints excluded: chain P residue 23 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 169 GLU Chi-restraints excluded: chain P residue 197 GLU Chi-restraints excluded: chain P residue 333 ILE Chi-restraints excluded: chain R residue 259 GLN Chi-restraints excluded: chain R residue 273 THR Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 287 LEU Chi-restraints excluded: chain T residue 60 ILE Chi-restraints excluded: chain T residue 118 LEU Chi-restraints excluded: chain T residue 286 VAL Chi-restraints excluded: chain T residue 306 VAL Chi-restraints excluded: chain Q residue 43 ARG Chi-restraints excluded: chain Q residue 368 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 484 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 483 optimal weight: 0.9990 chunk 451 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 452 optimal weight: 0.9990 chunk 377 optimal weight: 0.8980 chunk 159 optimal weight: 4.9990 chunk 235 optimal weight: 3.9990 chunk 476 optimal weight: 5.9990 chunk 448 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 137 ASN S 309 ASN ** F 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN Q 309 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.121548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.085327 restraints weight = 122166.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.084643 restraints weight = 78702.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084571 restraints weight = 65691.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.084777 restraints weight = 68671.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.085059 restraints weight = 58031.357| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 41881 Z= 0.104 Angle : 0.547 20.884 57200 Z= 0.271 Chirality : 0.044 0.338 6820 Planarity : 0.004 0.056 7395 Dihedral : 3.778 26.317 6059 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 1.67 % Allowed : 17.18 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.12), residues: 5668 helix: 1.83 (0.12), residues: 2140 sheet: -1.05 (0.20), residues: 734 loop : -1.13 (0.12), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG N 433 TYR 0.025 0.001 TYR Q 253 PHE 0.013 0.001 PHE S 263 TRP 0.031 0.001 TRP F 147 HIS 0.009 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00239 (41881) covalent geometry : angle 0.54697 (57200) hydrogen bonds : bond 0.02702 ( 1679) hydrogen bonds : angle 4.21246 ( 4785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7021.58 seconds wall clock time: 121 minutes 44.58 seconds (7304.58 seconds total)