Starting phenix.real_space_refine on Tue Aug 26 23:17:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wof_37685/08_2025/8wof_37685.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wof_37685/08_2025/8wof_37685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wof_37685/08_2025/8wof_37685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wof_37685/08_2025/8wof_37685.map" model { file = "/net/cci-nas-00/data/ceres_data/8wof_37685/08_2025/8wof_37685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wof_37685/08_2025/8wof_37685.cif" } resolution = 3.3 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= 0.068 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 93 5.16 5 C 27435 2.51 5 N 7466 2.21 5 O 8108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s 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: 43102 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4041 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 24, 'TRANS': 522} Chain breaks: 2 Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 280 Unresolved non-hydrogen dihedrals: 181 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 5, 'ASN:plan1': 6, 'TYR:plan': 5, 'HIS:plan': 3, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 135 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: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2051 Classifications: {'peptide': 335} Incomplete info: {'truncation_to_alanine': 178} Link IDs: {'PTRANS': 16, 'TRANS': 318} Chain breaks: 2 Unresolved non-hydrogen bonds: 653 Unresolved non-hydrogen angles: 825 Unresolved non-hydrogen dihedrals: 524 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': 16, 'TYR:plan': 6, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 362 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: 4954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 4954 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 30, 'TRANS': 641} Chain breaks: 1 Unresolved non-hydrogen bonds: 334 Unresolved non-hydrogen angles: 417 Unresolved non-hydrogen dihedrals: 276 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 16, 'ASN:plan1': 8, 'ASP:plan': 6, 'TYR:plan': 5, 'ARG:plan': 5, 'HIS:plan': 4, 'GLN:plan1': 6, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 216 Chain: "N" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 3644 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 325} Link IDs: {'PTRANS': 25, 'TRANS': 587} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1225 Unresolved non-hydrogen angles: 1558 Unresolved non-hydrogen dihedrals: 1013 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': 24, 'TRP:plan': 5, 'GLU:plan': 37, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 746 Chain: "O" Number of atoms: 4968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 4968 Classifications: {'peptide': 673} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 30, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 328 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 7, 'ASN:plan1': 8, 'TYR:plan': 5, 'HIS:plan': 5, 'GLN:plan1': 6, 'PHE:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 206 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: "Q" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2345 Classifications: {'peptide': 342} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'PTRANS': 18, 'TRANS': 323} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 415 Unresolved non-hydrogen angles: 519 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 14, 'GLU:plan': 14, 'ARG:plan': 7, 'HIS:plan': 1, 'ASN:plan1': 8, 'PHE:plan': 3, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 233 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: "B" Number of atoms: 3827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 3827 Classifications: {'peptide': 522} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 2 Unresolved non-hydrogen bonds: 315 Unresolved non-hydrogen angles: 395 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASN:plan1': 8, 'GLU:plan': 10, 'HIS:plan': 5, 'TYR:plan': 5, 'GLN:plan1': 6, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 196 Time building chain proxies: 11.98, per 1000 atoms: 0.28 Number of scatterers: 43102 At special positions: 0 Unit cell: (150.342, 186.938, 229.469, 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 93 16.00 O 8108 8.00 N 7466 7.00 C 27435 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 2.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11354 Finding SS restraints... Secondary structure from input PDB file: 247 helices and 43 sheets defined 41.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 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: 3.554A 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: 4.078A pdb=" N ASN D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 302 removed outlier: 3.990A pdb=" N LEU D 292 " --> pdb=" O SER D 288 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 301 " --> pdb=" O TYR D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 315 removed outlier: 3.549A pdb=" N GLU D 315 " --> pdb=" O GLU D 312 " (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: 3.808A pdb=" N LEU D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 442 removed outlier: 3.872A 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: 6.340A 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: 3.608A 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: 3.749A pdb=" N HIS J 21 " --> pdb=" O SER J 17 " (cutoff:3.500A) removed outlier: 3.657A 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: 3.514A 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: 3.746A 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: 3.749A 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: 4.383A pdb=" N THR K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.553A 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: 3.739A 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: 3.968A 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: 3.560A pdb=" N LEU L 292 " --> pdb=" O SER L 288 " (cutoff:3.500A) removed outlier: 4.238A 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: 3.855A 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: 5.443A 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: 3.680A pdb=" N ARG L 523 " --> pdb=" O ASN L 519 " (cutoff:3.500A) Processing helix chain 'L' and resid 534 through 539 removed outlier: 4.027A 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: 3.591A pdb=" N ASN L 586 " --> pdb=" O ALA L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 592 through 603 removed outlier: 4.145A 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: 3.953A pdb=" N LEU M 80 " --> pdb=" O PRO M 76 " (cutoff:3.500A) removed outlier: 3.562A 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: 3.541A 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: 4.136A pdb=" N ASN M 252 " --> pdb=" O GLY M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 288 through 302 removed outlier: 3.618A pdb=" N LEU M 292 " --> pdb=" O SER M 288 " (cutoff:3.500A) removed outlier: 4.519A 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: 3.901A 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: 3.528A 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: 3.564A pdb=" N GLN M 508 " --> pdb=" O THR M 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 529 removed outlier: 3.821A 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: 3.555A 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: 3.645A 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: 3.527A 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: 5.153A 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: 3.641A pdb=" N THR N 543 " --> pdb=" O MET N 540 " (cutoff:3.500A) removed outlier: 3.692A 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: 4.135A 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: 4.120A pdb=" N ASN O 252 " --> pdb=" O GLY O 248 " (cutoff:3.500A) Processing helix chain 'O' and resid 288 through 302 removed outlier: 3.788A pdb=" N LEU O 292 " --> pdb=" O SER O 288 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLU O 300 " --> pdb=" O LEU O 296 " (cutoff:3.500A) removed outlier: 3.586A 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: 3.590A 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: 5.436A pdb=" N ARG O 485 " --> pdb=" O VAL O 481 " (cutoff:3.500A) removed outlier: 6.858A 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: 4.040A pdb=" N ARG O 523 " --> pdb=" O ASN O 519 " (cutoff:3.500A) Processing helix chain 'O' and resid 534 through 539 removed outlier: 3.896A 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 'O' and resid 579 through 586 removed outlier: 3.615A pdb=" N ASN O 586 " --> pdb=" O ALA O 582 " (cutoff:3.500A) Processing helix chain 'O' and resid 592 through 603 removed outlier: 3.968A pdb=" N VAL O 596 " --> pdb=" O ASP O 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 666 through 676 removed outlier: 3.807A pdb=" N HIS O 670 " --> pdb=" O PRO O 666 " (cutoff:3.500A) Processing helix chain 'O' and resid 681 through 687 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: 3.583A 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: 3.846A 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: 4.350A 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: 3.559A pdb=" N ALA P 117 " --> pdb=" O SER P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 151 removed outlier: 4.023A 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: 3.709A 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 'Q' and resid 11 through 24 removed outlier: 3.729A 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: 3.873A pdb=" N ILE Q 75 " --> pdb=" O LEU Q 71 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE Q 76 " --> pdb=" O LEU Q 72 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR Q 82 " --> pdb=" O ASN Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 101 removed outlier: 3.734A pdb=" N ILE Q 101 " --> pdb=" O LEU Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 105 removed outlier: 4.526A pdb=" N GLY Q 105 " --> pdb=" O PRO Q 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 102 through 105' Processing helix chain 'Q' and resid 113 through 131 Processing helix chain 'Q' and resid 139 through 151 removed outlier: 3.684A pdb=" N ASN Q 149 " --> pdb=" O ALA Q 145 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ILE Q 151 " --> pdb=" O TRP Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 175 removed outlier: 3.658A pdb=" N LEU Q 175 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 199 Processing helix chain 'Q' and resid 252 through 265 removed outlier: 3.595A pdb=" N GLN Q 259 " --> pdb=" O VAL Q 255 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 294 Processing helix chain 'Q' and resid 306 through 309 removed outlier: 3.524A pdb=" N ASN Q 309 " --> pdb=" O VAL Q 306 " (cutoff:3.500A) No H-bonds generated for '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: 3.852A 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 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: 3.622A 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: 3.649A 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: 3.888A 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: 3.857A 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: 3.607A 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: 4.188A pdb=" N GLU S 197 " --> pdb=" O ILE S 193 " (cutoff:3.500A) removed outlier: 3.728A 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: 3.941A 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: 3.862A 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: 3.905A pdb=" N THR T 82 " --> pdb=" O ASN T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 101 removed outlier: 3.515A 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: 3.555A 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: 3.759A 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: 3.638A 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: 3.713A pdb=" N GLN T 373 " --> pdb=" O GLU T 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 168 through 171 Processing helix chain 'B' and resid 172 through 185 removed outlier: 3.554A pdb=" N THR B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 234 through 242 Processing helix chain 'B' and resid 248 through 269 removed outlier: 4.078A pdb=" N ASN B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 removed outlier: 3.990A pdb=" N LEU B 292 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 301 " --> pdb=" O TYR B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 315 removed outlier: 3.549A pdb=" N GLU B 315 " --> pdb=" O GLU B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 376 through 381 Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.808A pdb=" N LEU B 400 " --> pdb=" O ASP B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 442 removed outlier: 3.871A pdb=" N SER B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 464 Processing helix chain 'B' and resid 472 through 488 removed outlier: 5.459A pdb=" N ARG B 485 " --> pdb=" O VAL B 481 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LYS B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 487 " --> pdb=" O GLU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'B' and resid 502 through 507 Processing helix chain 'B' and resid 519 through 529 removed outlier: 3.963A pdb=" N ARG B 523 " --> pdb=" O ASN B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 539 removed outlier: 3.716A pdb=" N GLY B 539 " --> pdb=" O GLU B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 544 removed outlier: 3.608A pdb=" N LEU B 544 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 586 removed outlier: 3.531A pdb=" N LYS B 583 " --> pdb=" O ASP B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 603 Processing helix chain 'B' and resid 666 through 675 removed outlier: 3.978A pdb=" N HIS B 670 " --> pdb=" O PRO B 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 687 Processing sheet with id=AA1, first strand: chain 'D' and resid 13 through 20 removed outlier: 6.487A 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: 7.067A pdb=" N ASN D 62 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLU D 97 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 7.261A 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: 7.680A 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: 4.818A pdb=" N GLU L 97 " --> pdb=" O ASN L 62 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N PHE L 64 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N SER L 91 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.138A 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: 6.898A pdb=" N LEU M 63 " --> pdb=" O GLU M 97 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLU M 97 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY M 65 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL M 95 " --> pdb=" O GLY M 65 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N VAL M 67 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 6.017A 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 '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: 7.201A pdb=" N ASN O 62 " --> pdb=" O GLU O 97 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU O 97 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 7.214A 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: 6.793A 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: 7.598A 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: 6.627A 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: 6.723A pdb=" N VAL D 456 " --> pdb=" O MET D 492 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL D 494 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.484A 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: 6.528A 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: 6.706A 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: 6.953A pdb=" N VAL D 214 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AA4, 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: 7.833A 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: 7.830A 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=AA5, first strand: chain 'J' and resid 43 through 44 Processing sheet with id=AA6, first strand: chain 'J' and resid 188 through 189 removed outlier: 3.624A pdb=" N ALA J 189 " --> pdb=" O ARG J 228 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 324 through 326 Processing sheet with id=AA8, 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=AA9, first strand: chain 'K' and resid 43 through 44 Processing sheet with id=AB1, 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=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 270 through 273 removed outlier: 7.465A pdb=" N LEU K 271 " --> pdb=" O TYR K 300 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N LEU K 302 " --> pdb=" O LEU K 271 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N THR K 273 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE K 299 " --> pdb=" O ILE K 324 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LEU K 326 " --> pdb=" O ILE K 299 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY K 301 " --> pdb=" O LEU K 326 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.890A pdb=" N TYR L 45 " --> pdb=" O LYS L 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 150 through 153 removed outlier: 6.743A pdb=" N ALA L 151 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET L 560 " --> pdb=" O ILE L 551 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA L 514 " --> pdb=" O ILE L 550 " (cutoff:3.500A) removed outlier: 7.169A 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: 7.553A 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: 6.544A 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: 8.148A pdb=" N LEU L 224 " --> pdb=" O ALA L 212 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL L 214 " --> pdb=" O LEU L 224 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 303 through 304 Processing sheet with id=AB6, 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: 6.623A 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=AB7, first strand: chain 'M' and resid 150 through 153 removed outlier: 3.982A 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: 6.658A pdb=" N ILE M 195 " --> pdb=" O SER M 412 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N PHE M 414 " --> pdb=" O ILE M 195 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL M 197 " --> pdb=" O PHE M 414 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS M 213 " --> pdb=" O ILE M 413 " (cutoff:3.500A) removed outlier: 7.333A 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: 6.504A pdb=" N VAL M 214 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 638 through 642 removed outlier: 3.565A 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=AB9, first strand: chain 'N' and resid 16 through 17 removed outlier: 3.685A pdb=" N THR N 16 " --> pdb=" O VAL N 28 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 24 through 28 current: chain 'N' and resid 61 through 70 removed outlier: 6.875A pdb=" N LEU N 63 " --> pdb=" O GLU N 97 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU N 97 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLY N 65 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N VAL N 95 " --> pdb=" O GLY N 65 " (cutoff:3.500A) removed outlier: 5.194A 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) Processing sheet with id=AC1, first strand: chain 'N' and resid 39 through 40 Processing sheet with id=AC2, first strand: chain 'N' and resid 150 through 154 removed outlier: 6.530A 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=AC3, first strand: chain 'N' and resid 224 through 225 removed outlier: 8.109A pdb=" N LEU N 224 " --> pdb=" O ALA N 212 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL N 214 " --> pdb=" O LEU N 224 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N LYS N 213 " --> pdb=" O ILE N 413 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE N 195 " --> pdb=" O SER N 412 " (cutoff:3.500A) removed outlier: 6.812A 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: 4.196A pdb=" N GLU N 459 " --> pdb=" O PHE N 198 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU N 454 " --> pdb=" O GLY N 490 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N MET N 492 " --> pdb=" O LEU N 454 " (cutoff:3.500A) removed outlier: 6.516A 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: 6.265A 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=AC4, first strand: chain 'N' and resid 641 through 642 Processing sheet with id=AC5, first strand: chain 'O' and resid 39 through 40 Processing sheet with id=AC6, 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: 3.580A 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: 7.860A 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=AC7, first strand: chain 'O' and resid 303 through 304 removed outlier: 3.621A pdb=" N TYR O 352 " --> pdb=" O HIS O 304 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 616 through 618 removed outlier: 3.747A pdb=" N LEU O 617 " --> pdb=" O ILE O 641 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER O 640 " --> pdb=" O GLU O 653 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU O 651 " --> pdb=" O GLY O 642 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 9 through 10 removed outlier: 3.603A 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: 8.311A 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=AD1, 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=AD2, first strand: chain 'Q' and resid 9 through 10 removed outlier: 6.158A pdb=" N ALA Q 269 " --> pdb=" O LEU Q 298 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N TYR Q 300 " --> pdb=" O ALA Q 269 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N LEU Q 271 " --> pdb=" O TYR Q 300 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU Q 302 " --> pdb=" O LEU Q 271 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR Q 273 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA Q 31 " --> pdb=" O ILE Q 272 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N CYS Q 274 " --> pdb=" O ALA Q 31 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE Q 33 " --> pdb=" O CYS Q 274 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ILE Q 30 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N PHE Q 160 " --> pdb=" O ILE Q 30 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N PHE Q 32 " --> pdb=" O PHE Q 160 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE Q 159 " --> pdb=" O TRP Q 209 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 183 through 184 Processing sheet with id=AD4, first strand: chain 'Q' and resid 217 through 219 Processing sheet with id=AD5, first strand: chain 'R' and resid 9 through 10 removed outlier: 6.589A 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: 6.207A 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=AD6, first strand: chain 'R' and resid 183 through 184 Processing sheet with id=AD7, 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=AD8, 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: 7.950A pdb=" N PHE S 160 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE S 32 " --> pdb=" O PHE S 160 " (cutoff:3.500A) removed outlier: 6.209A 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=AD8 Processing sheet with id=AD9, first strand: chain 'S' and resid 43 through 44 Processing sheet with id=AE1, first strand: chain 'S' and resid 183 through 184 removed outlier: 3.897A 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=AE2, first strand: chain 'S' and resid 302 through 303 Processing sheet with id=AE3, first strand: chain 'T' and resid 9 through 10 removed outlier: 3.685A pdb=" N ALA T 331 " --> pdb=" O GLY T 338 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE T 33 " --> pdb=" O CYS T 274 " (cutoff:3.500A) removed outlier: 5.860A 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=AE4, first strand: chain 'T' and resid 217 through 219 Processing sheet with id=AE5, first strand: chain 'B' and resid 224 through 225 removed outlier: 8.392A pdb=" N LEU B 224 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL B 214 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE B 195 " --> pdb=" O SER B 412 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE B 414 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 197 " --> pdb=" O PHE B 414 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU B 459 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 456 " --> pdb=" O MET B 492 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL B 494 " --> pdb=" O VAL B 456 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU B 458 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 493 " --> pdb=" O SER B 163 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ALA B 164 " --> pdb=" O PHE B 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AE7, first strand: chain 'B' and resid 616 through 618 1736 hydrogen bonds defined for protein. 4929 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: 9.93 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8299 1.33 - 1.45: 10248 1.45 - 1.57: 25217 1.57 - 1.69: 0 1.69 - 1.81: 154 Bond restraints: 43918 Sorted by residual: bond pdb=" N GLU N 451 " pdb=" CA GLU N 451 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.31e-02 5.83e+03 9.29e+00 bond pdb=" N LEU N 454 " pdb=" CA LEU N 454 " ideal model delta sigma weight residual 1.454 1.491 -0.037 1.29e-02 6.01e+03 8.04e+00 bond pdb=" N GLY N 680 " pdb=" CA GLY N 680 " ideal model delta sigma weight residual 1.447 1.476 -0.028 1.03e-02 9.43e+03 7.58e+00 bond pdb=" N LYS N 681 " pdb=" CA LYS N 681 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.14e+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 5.63e+00 ... (remaining 43913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 58618 1.40 - 2.79: 1058 2.79 - 4.19: 265 4.19 - 5.59: 53 5.59 - 6.98: 17 Bond angle restraints: 60011 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 116.63 110.62 6.01 1.16e+00 7.43e-01 2.69e+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 2.48e+01 angle pdb=" N VAL M 217 " pdb=" CA VAL M 217 " pdb=" C VAL M 217 " ideal model delta sigma weight residual 112.96 108.47 4.49 1.00e+00 1.00e+00 2.02e+01 angle pdb=" N ILE T 115 " pdb=" CA ILE T 115 " pdb=" C ILE T 115 " ideal model delta sigma weight residual 111.90 108.57 3.33 8.10e-01 1.52e+00 1.69e+01 angle pdb=" C GLU R 197 " pdb=" N GLU R 198 " pdb=" CA GLU R 198 " ideal model delta sigma weight residual 120.31 114.72 5.59 1.52e+00 4.33e-01 1.35e+01 ... (remaining 60006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 24360 17.84 - 35.67: 1498 35.67 - 53.51: 217 53.51 - 71.35: 50 71.35 - 89.18: 16 Dihedral angle restraints: 26141 sinusoidal: 8569 harmonic: 17572 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 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+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 180.00 154.36 25.64 0 5.00e+00 4.00e-02 2.63e+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 180.00 154.74 25.26 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 26138 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 4743 0.036 - 0.072: 1709 0.072 - 0.107: 530 0.107 - 0.143: 177 0.143 - 0.179: 12 Chirality restraints: 7171 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 8.01e-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 6.93e-01 chirality pdb=" CA LEU N 454 " pdb=" N LEU N 454 " pdb=" C LEU N 454 " pdb=" CB LEU N 454 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.81e-01 ... (remaining 7168 not shown) Planarity restraints: 7779 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG N 450 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ARG N 450 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG N 450 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU N 451 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE T 83 " -0.043 5.00e-02 4.00e+02 6.55e-02 6.87e+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 P 83 " 0.033 5.00e-02 4.00e+02 5.00e-02 4.01e+00 pdb=" N PRO P 84 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO P 84 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO P 84 " 0.028 5.00e-02 4.00e+02 ... (remaining 7776 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 322 2.57 - 3.15: 35352 3.15 - 3.74: 63969 3.74 - 4.32: 81230 4.32 - 4.90: 140063 Nonbonded interactions: 320936 Sorted by model distance: nonbonded pdb=" CB SER N 192 " pdb=" O TRP B 584 " model vdw 1.989 3.440 nonbonded pdb=" OD1 ASN M 154 " pdb=" OD1 ASP M 156 " model vdw 2.046 3.040 nonbonded pdb=" OG1 THR S 82 " pdb=" CG PRO T 102 " model vdw 2.133 3.440 nonbonded pdb=" O ASP S 246 " pdb=" OE1 GLU T 285 " model vdw 2.152 3.040 nonbonded pdb=" CB SER N 36 " pdb=" NH1 ARG Q 28 " model vdw 2.152 3.520 ... (remaining 320931 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 'B' and (resid 153 or (resid 154 and (name N or name CA or name C or name \ O or name CB )) or resid 155 or (resid 156 through 157 and (name N or name CA o \ r name C or name O or name CB )) or resid 158 through 159 or (resid 160 and (nam \ e N or name CA or name C or name O or name CB )) or resid 161 through 170 or (re \ sid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 th \ rough 175 or (resid 176 through 177 and (name N or name CA or name C or name O o \ r name CB )) or resid 178 through 179 or (resid 180 through 181 and (name N or n \ ame CA or name C or name O or name CB )) or resid 182 or (resid 183 through 184 \ and (name N or name CA or name C or name O or name CB )) or resid 185 through 18 \ 6 or (resid 187 through 190 and (name N or name CA or name C or name O or name C \ B )) or resid 191 through 196 or (resid 197 through 199 and (name N or name CA o \ r name C or name O or name CB )) or resid 200 through 202 or (resid 203 and (nam \ e N or name CA or name C or name O or name CB )) or resid 204 through 207 or (re \ sid 208 through 209 and (name N or name CA or name C or name O or name CB )) or \ resid 210 or (resid 211 through 212 and (name N or name CA or name C or name O o \ r name CB )) or resid 213 through 215 or (resid 216 and (name N or name CA or na \ me C or name O or name CB )) or resid 217 or (resid 218 and (name N or name CA o \ r name C or name O or name CB )) or resid 219 through 228 or (resid 229 and (nam \ e N or name CA or name C or name O or name CB )) or resid 230 through 232 or (re \ sid 233 through 235 and (name N or name CA or name C or name O or name CB )) or \ resid 236 or (resid 237 through 238 and (name N or name CA or name C or name O o \ r name CB )) or resid 239 through 242 or (resid 243 and (name N or name CA or na \ me C or name O or name CB )) or resid 244 through 245 or (resid 246 through 247 \ and (name N or name CA or name C or name O or name CB )) or resid 248 or (resid \ 249 and (name N or name CA or name C or name O or name CB )) or resid 250 or (re \ sid 251 through 254 and (name N or name CA or name C or name O or name CB )) or \ resid 255 through 256 or (resid 257 through 272 and (name N or name CA or name C \ or name O or name CB )) or resid 273 or (resid 274 through 282 and (name N or n \ ame CA or name C or name O or name CB )) or resid 283 through 286 or (resid 287 \ through 307 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 8 or (resid 309 through 310 and (name N or name CA or name C or name O or name C \ B )) or resid 311 through 316 or resid 330 through 331 or (resid 332 through 335 \ and (name N or name CA or name C or name O or name CB )) or resid 336 through 3 \ 37 or resid 352 through 355 or (resid 356 and (name N or name CA or name C or na \ me O or name CB )) or (resid 357 through 362 and (name N or name CA or 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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 (name N or name CA or name C o \ r name O or name CB )) or resid 144 through 146 or (resid 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 148 through 150 or (resid 151 th \ rough 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 name O or name CB )) or resid \ 161 through 162 or (resid 163 through 166 and (name N or name CA or name C or na \ me 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 (resid 173 through 177 and (n \ ame 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 )) o \ r resid 191 or (resid 192 and (name N or name CA or name C or name O or name CB \ )) or resid 193 through 196 or (resid 197 through 201 and (name N or name CA or \ name C or name O or name CB )) or resid 202 through 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 (resi \ d 210 through 211 and (name N or name CA or name C or name O or name CB )) or re \ sid 212 through 214 or (resid 215 through 216 and (name N or name CA or name C o \ r name O or name CB )) or resid 217 or (resid 218 through 226 and (name N or nam \ e CA or name C or name O or name CB )) or resid 227 through 229 or (resid 230 an \ d (name N or name CA or name C or name O or name CB )) or resid 231 or (resid 23 \ 2 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 res \ id 240 through 241 or (resid 242 and (name N or name CA or name C or name O or n \ ame CB )) or resid 251 through 252 or (resid 253 through 254 and (name N or name \ CA or name C or name O or name CB )) or resid 255 or (resid 256 through 258 and \ (name N or name CA or name C or name O or name CB )) or resid 259 through 263 o \ r (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 nam \ e 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 through \ 281 and (name N or name CA or name C or name O or name CB )) or resid 282 or (r \ esid 283 through 287 and (name N or name CA or name C or name O or name CB )) or \ resid 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 nam \ e 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 or (resid 303 thr \ ough 333 and (name N or name CA or name C or name O or name CB )) or resid 334 o \ r (resid 335 through 337 and (name N or name CA or name C or name O or name CB ) \ ) or resid 338 or resid 359 or (resid 360 through 365 and (name N or name CA or \ name C or name O or name 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 (n \ ame N or name CA or name C or name O or name CB )))) selection = (chain 'S' 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 29 or (resid 30 thro \ ugh 36 and (name N or name CA or name C or name O or name CB )) or resid 37 thro \ ugh 38 or (resid 39 through 47 and (name N or name CA or name C or name O or nam \ e 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 through 52 or (resid 53 through 54 and (name N \ or name CA or name C or name O or name CB )) or resid 55 or (resid 56 through 60 \ and (name N or name CA or name C or name O or name CB )) or resid 61 or (resid \ 62 through 83 and (name N or name CA or name C or name O or name CB )) or resid \ 84 through 86 or (resid 87 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 nam \ e C or name O or name CB )) or resid 95 or (resid 96 and (name N or name CA or n \ ame C or name O or name CB )) or resid 97 or (resid 98 through 101 and (name N o \ r name CA or name C or name O or name CB )) or resid 102 through 103 or (resid 1 \ 04 and (name N or name CA or name C or name O or name CB )) or (resid 105 throug \ h 112 and (name N or name CA or name C or name O or name CB )) or resid 113 thro \ ugh 115 or (resid 116 through 120 and (name N or name CA or name C or name O or \ name CB )) or resid 121 or (resid 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 or (resid 124 through 129 and (name N or name CA or \ name C or name O or name CB )) or resid 130 or (resid 131 through 133 and (name \ N or name CA or name C or name O or name CB )) or resid 134 through 138 or (resi \ d 139 and (name N or name CA or name C or name O or name CB )) or resid 140 thro \ ugh 146 or (resid 147 and (name N or name CA or name C or name O or name CB )) o \ r 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 159 or (resid 160 and (name N or name CA or \ name C or name O or name CB )) or resid 161 through 162 or (resid 163 through 16 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 167 or (resi \ d 168 through 171 and (name N or name CA or name C or name O or name CB )) or re \ sid 172 through 185 or (resid 186 through 190 and (name N or name CA or name C o \ r name O or name CB )) or resid 191 through 196 or (resid 197 through 201 and (n \ ame N or name CA or name C or name O or name CB )) or resid 202 through 203 or ( \ resid 204 and (name N or name CA or name C or name O or name CB )) or resid 205 \ 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 through 222 or (resid 22 \ 3 through 226 and (name N or name CA or name C or name O or name CB )) or resid \ 227 through 231 or (resid 232 through 233 and (name N or name CA or name C or na \ me 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 251 through 252 or (resi \ d 253 through 254 and (name N or name CA or name C or name O or name CB )) or re \ sid 255 through 256 or (resid 257 through 258 and (name N or name CA or name C o \ r name O or name CB )) or resid 259 through 271 or (resid 272 through 273 and (n \ ame N or name CA or name C or name O or name CB )) or resid 274 through 277 or ( \ resid 278 through 281 and (name N or name CA or name C or name O or name CB )) o \ r resid 282 or (resid 283 through 287 and (name N or name CA or name C or name O \ or name CB )) or resid 288 through 303 or (resid 304 through 333 and (name N or \ name CA or name C or name O or name CB )) or resid 334 through 338 or resid 359 \ or (resid 360 through 365 and (name N or name CA or name C or name O or name CB \ )) or resid 366 through 367 or (resid 368 through 371 and (name N or name CA or \ name C or name O or name CB )) or resid 372 through 373)) selection = (chain 'T' 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 38 or (resid 39 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 through \ 60 and (name N or name CA or name C or name O or name CB )) or resid 61 or (resi \ d 62 through 63 and (name N or name CA or name C or name O or name CB )) or (res \ id 72 through 83 and (name N or name CA or name C or name O or name CB )) or res \ id 84 through 86 or (resid 87 through 91 and (name N or name CA or name C or nam \ e 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 name CA o \ r name C or name O or name CB )) or resid 97 or (resid 98 through 101 and (name \ N or name CA or name C or name O or name CB )) or resid 102 through 103 or (resi \ d 104 and (name N or name CA or name C or name O or name CB )) or resid 105 thro \ ugh 114 or (resid 115 through 120 and (name N or name CA or name C or name O or \ name CB )) or resid 121 or (resid 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 or (resid 124 through 129 and (name N or name CA or \ name C or name O or name CB )) or resid 130 through 131 or (resid 132 through 13 \ 3 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 (name N or name CA or name C o \ r name O or name CB )) or resid 144 through 146 or (resid 147 and (name N or nam \ e CA or name C or name O or name CB )) or resid 148 through 150 or (resid 151 th \ rough 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 name O or name CB )) or resid \ 161 through 162 or (resid 163 through 166 and (name N or name CA or name C or na \ me 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 (resid 173 through 177 and (n \ ame 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 )) o \ r resid 191 or (resid 192 and (name N or name CA or name C or name O or name CB \ )) or resid 193 through 196 or (resid 197 through 201 and (name N or name CA or \ name C or name O or name CB )) or resid 202 through 203 or (resid 204 and (name \ N or name CA or name C or name O or name CB )) or resid 205 through 206 or (resi \ d 207 and (name N or name CA or name C or name O or name CB )) or resid 208 thro \ ugh 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 nam \ e CA or name C or name O or name CB )) or resid 217 or (resid 218 through 226 an \ d (name N or name CA or name C or name O or name CB )) or resid 227 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 n \ ame CB )) or resid 240 through 242 or resid 251 through 252 or (resid 253 throug \ h 254 and (name N or name CA or name C or name O or name CB )) or resid 255 or ( \ resid 256 through 258 and (name N or name CA or name C or name O or name CB )) o \ r resid 259 through 263 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 27 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 274 through \ 277 or (resid 278 through 281 and (name N or name CA or name C or name O or name \ CB )) or resid 282 or (resid 283 through 287 and (name N or name CA or name C o \ r name O or name CB )) or resid 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 (resid 294 and (name \ N or name CA or name C or name O or name CB )) or resid 295 or (resid 296 throug \ h 299 and (name N or name CA or name C or name O or name CB )) or resid 300 thro \ ugh 302 or (resid 303 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 resid 359 or (resid 360 through 365 a \ nd (name N or name CA or name C or name O or name CB )) or resid 366 or (resid 3 \ 67 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 name C or name O or name CB )))) } ncs_group { reference = (chain 'L' and ((resid 9 through 10 and (name N or name CA or name C or name O o \ r name CB )) or resid 11 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 401 or (resid 402 and (name N o \ r name CA or name C or name O or name CB )) or resid 403 through 446 or (resid 4 \ 47 and (name N or name CA or name C or name O or name CB )) or resid 448 through \ 696)) selection = (chain 'M' and (resid 9 through 29 or (resid 30 through 33 and (name N or name C \ A or name C or name O or name CB )) or resid 34 through 678 or (resid 679 and (n \ ame N or name CA or name C or name O or name CB )) or resid 680 through 696)) selection = (chain 'O' and (resid 9 through 160 or (resid 161 and (name N or name CA or name \ C or name O or name CB )) or resid 162 through 401 or (resid 402 and (name N or \ name CA or name C or name O or name CB )) or resid 403 through 446 or (resid 44 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 448 through \ 570 or (resid 571 and (name N or name CA or name C or name O or name CB )) or re \ sid 572 through 696)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.060 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.130 Process input model: 40.330 Find NCS groups from input model: 1.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 0.054 43918 Z= 0.116 Angle : 0.510 6.982 60011 Z= 0.280 Chirality : 0.043 0.179 7171 Planarity : 0.003 0.066 7779 Dihedral : 12.095 89.183 14787 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.36 % Favored : 94.49 % Rotamer: Outliers : 0.03 % Allowed : 0.53 % Favored : 99.44 % 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: -0.14 (0.11), residues: 6007 helix: 1.55 (0.12), residues: 2204 sheet: -1.01 (0.20), residues: 779 loop : -1.09 (0.11), residues: 3024 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 Q 367 TRP 0.024 0.001 TRP B 584 HIS 0.005 0.001 HIS B 670 Details of bonding type rmsd covalent geometry : bond 0.00224 (43918) covalent geometry : angle 0.50973 (60011) hydrogen bonds : bond 0.17330 ( 1736) hydrogen bonds : angle 6.65611 ( 4929) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1154 time to evaluate : 1.297 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: D 256 ASP cc_start: 0.8057 (m-30) cc_final: 0.7822 (t0) REVERT: D 289 ILE cc_start: 0.8054 (tp) cc_final: 0.7836 (tp) REVERT: D 367 LEU cc_start: 0.8279 (tt) cc_final: 0.7857 (mm) REVERT: D 485 ARG cc_start: 0.8151 (ttt-90) cc_final: 0.7836 (ttm-80) REVERT: J 95 ILE cc_start: 0.8810 (mt) cc_final: 0.8505 (tp) REVERT: J 96 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7482 (mtt180) REVERT: J 119 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8262 (pt0) REVERT: J 129 GLU cc_start: 0.8560 (tp30) cc_final: 0.8155 (mm-30) REVERT: J 262 LEU cc_start: 0.8988 (mp) cc_final: 0.8752 (mm) REVERT: K 124 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8787 (mm-30) REVERT: K 193 ILE cc_start: 0.8441 (tt) cc_final: 0.8213 (pt) REVERT: K 195 THR cc_start: 0.7929 (p) cc_final: 0.6978 (p) REVERT: K 196 ILE cc_start: 0.8489 (mt) cc_final: 0.8242 (tt) REVERT: L 637 ASN cc_start: 0.7648 (p0) cc_final: 0.7308 (m110) REVERT: M 28 VAL cc_start: 0.8408 (t) cc_final: 0.8199 (p) REVERT: M 61 ILE cc_start: 0.7266 (pt) cc_final: 0.6818 (pt) REVERT: M 331 SER cc_start: 0.8286 (m) cc_final: 0.8071 (p) REVERT: M 427 LEU cc_start: 0.8043 (pp) cc_final: 0.7628 (pp) REVERT: N 117 LYS cc_start: 0.7421 (mptt) cc_final: 0.7149 (tttt) REVERT: O 156 ASP cc_start: 0.8096 (m-30) cc_final: 0.7829 (m-30) REVERT: O 263 LEU cc_start: 0.9200 (mt) cc_final: 0.8913 (mt) REVERT: O 381 ASN cc_start: 0.8314 (t0) cc_final: 0.7908 (t0) REVERT: O 691 TYR cc_start: 0.7558 (m-80) cc_final: 0.7162 (m-10) REVERT: P 94 TYR cc_start: 0.8201 (t80) cc_final: 0.7926 (t80) REVERT: P 193 ILE cc_start: 0.8809 (tt) cc_final: 0.7880 (tt) REVERT: Q 34 ILE cc_start: 0.7786 (mt) cc_final: 0.7571 (pt) REVERT: Q 88 ILE cc_start: 0.7988 (mm) cc_final: 0.7460 (pt) REVERT: Q 124 GLU cc_start: 0.6483 (mm-30) cc_final: 0.5959 (mm-30) REVERT: Q 155 HIS cc_start: 0.7814 (m170) cc_final: 0.7191 (m170) REVERT: Q 164 TYR cc_start: 0.5554 (m-80) cc_final: 0.4778 (m-10) REVERT: Q 183 PHE cc_start: 0.8039 (m-80) cc_final: 0.7760 (m-80) REVERT: Q 340 TRP cc_start: 0.5323 (m100) cc_final: 0.4364 (m100) REVERT: R 28 ARG cc_start: 0.7446 (mtp180) cc_final: 0.7055 (mtp85) REVERT: R 38 CYS cc_start: 0.7361 (m) cc_final: 0.7038 (m) REVERT: R 96 ARG cc_start: 0.8412 (mtp85) cc_final: 0.8183 (ptt180) REVERT: R 155 HIS cc_start: 0.7268 (m-70) cc_final: 0.6998 (m170) REVERT: R 159 ILE cc_start: 0.7504 (mt) cc_final: 0.7238 (tt) REVERT: R 261 LYS cc_start: 0.8587 (ttmm) cc_final: 0.8311 (ptmm) REVERT: R 278 TYR cc_start: 0.7873 (m-80) cc_final: 0.6810 (m-80) REVERT: R 289 GLN cc_start: 0.8193 (mm110) cc_final: 0.7993 (tp40) REVERT: R 298 LEU cc_start: 0.8431 (tp) cc_final: 0.8170 (tp) REVERT: R 314 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7719 (mtmt) REVERT: R 316 MET cc_start: 0.7939 (ttm) cc_final: 0.7470 (ttm) REVERT: S 79 LEU cc_start: 0.7822 (pp) cc_final: 0.7593 (tt) REVERT: S 83 ILE cc_start: 0.6987 (mt) cc_final: 0.6528 (mt) REVERT: S 98 LEU cc_start: 0.8418 (mt) cc_final: 0.7942 (mt) REVERT: S 163 ASN cc_start: 0.8036 (m-40) cc_final: 0.7579 (m-40) REVERT: S 212 HIS cc_start: 0.8372 (m90) cc_final: 0.7895 (m-70) REVERT: S 309 ASN cc_start: 0.8301 (m110) cc_final: 0.8089 (m-40) REVERT: S 326 LEU cc_start: 0.6912 (mt) cc_final: 0.6524 (tt) REVERT: T 257 MET cc_start: 0.9067 (mmt) cc_final: 0.8786 (mmt) REVERT: B 225 LYS cc_start: 0.6261 (ttmt) cc_final: 0.6004 (ttmm) REVERT: B 395 LYS cc_start: 0.7893 (mttt) cc_final: 0.7654 (mmmm) REVERT: B 402 GLU cc_start: 0.9054 (tt0) cc_final: 0.8738 (mm-30) REVERT: B 470 ARG cc_start: 0.7444 (mmm160) cc_final: 0.6684 (tpm170) REVERT: B 525 HIS cc_start: 0.5022 (t70) cc_final: 0.4796 (t-170) REVERT: B 538 MET cc_start: 0.6588 (mmm) cc_final: 0.6332 (mmm) REVERT: B 583 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6811 (mmtp) REVERT: B 603 LYS cc_start: 0.8322 (mtmt) cc_final: 0.7348 (tppt) REVERT: B 647 SER cc_start: 0.6340 (m) cc_final: 0.6056 (p) REVERT: B 695 ARG cc_start: 0.6307 (ttm170) cc_final: 0.6056 (ttp-110) outliers start: 1 outliers final: 0 residues processed: 1154 average time/residue: 0.2268 time to fit residues: 419.5050 Evaluate side-chains 562 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 394 optimal weight: 6.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 488 optimal weight: 0.0870 chunk 366 optimal weight: 0.0040 chunk 597 optimal weight: 20.0000 overall best weight: 3.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 142 ASN D 182 GLN D 508 GLN D 518 ASN J 239 HIS L 69 GLN L 87 HIS L 518 ASN M 49 GLN M 119 HIS N 252 ASN N 462 HIS N 496 GLN O 394 ASN Q 116 ASN Q 170 GLN Q 265 ASN ** Q 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 292 GLN S 116 ASN S 259 GLN T 116 ASN T 155 HIS T 212 HIS T 218 GLN T 363 HIS B 670 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.088951 restraints weight = 94019.326| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 3.19 r_work: 0.3099 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.174 43918 Z= 0.287 Angle : 0.715 12.746 60011 Z= 0.373 Chirality : 0.050 0.228 7171 Planarity : 0.005 0.067 7779 Dihedral : 4.623 32.220 6420 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.74 % Favored : 93.12 % Rotamer: Outliers : 3.14 % Allowed : 10.84 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.11), residues: 6007 helix: 1.13 (0.11), residues: 2212 sheet: -1.15 (0.20), residues: 756 loop : -1.27 (0.11), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG M 251 TYR 0.026 0.002 TYR M 464 PHE 0.022 0.002 PHE R 367 TRP 0.038 0.002 TRP B 600 HIS 0.008 0.002 HIS M 670 Details of bonding type rmsd covalent geometry : bond 0.00694 (43918) covalent geometry : angle 0.71521 (60011) hydrogen bonds : bond 0.04595 ( 1736) hydrogen bonds : angle 5.13997 ( 4929) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 556 time to evaluate : 1.962 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 127 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8952 (mttp) REVERT: D 367 LEU cc_start: 0.8463 (tt) cc_final: 0.8097 (mm) REVERT: D 525 HIS cc_start: 0.8085 (t70) cc_final: 0.7440 (t-170) REVERT: J 210 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7804 (mtpt) REVERT: J 239 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6346 (t70) REVERT: J 253 TYR cc_start: 0.7888 (t80) cc_final: 0.7425 (t80) REVERT: J 257 MET cc_start: 0.8676 (mmt) cc_final: 0.7892 (mmt) REVERT: K 19 LEU cc_start: 0.7367 (tp) cc_final: 0.6942 (pp) REVERT: K 128 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: K 228 ARG cc_start: 0.7817 (ttp80) cc_final: 0.7422 (tmm-80) REVERT: K 259 GLN cc_start: 0.8777 (tp40) cc_final: 0.8428 (mp10) REVERT: K 282 HIS cc_start: 0.7913 (OUTLIER) cc_final: 0.7109 (m-70) REVERT: K 300 TYR cc_start: 0.7110 (m-10) cc_final: 0.6866 (m-80) REVERT: L 535 GLU cc_start: 0.8227 (mp0) cc_final: 0.8017 (mp0) REVERT: M 93 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8581 (tt0) REVERT: M 135 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8474 (ttpp) REVERT: M 272 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8315 (tm-30) REVERT: M 295 ASP cc_start: 0.8675 (m-30) cc_final: 0.8451 (m-30) REVERT: M 331 SER cc_start: 0.8989 (m) cc_final: 0.8770 (p) REVERT: M 362 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9089 (ttpp) REVERT: M 370 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8768 (mp) REVERT: M 459 GLU cc_start: 0.8550 (tp30) cc_final: 0.8003 (tt0) REVERT: M 486 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.8363 (ptmt) REVERT: N 117 LYS cc_start: 0.7940 (OUTLIER) cc_final: 0.7455 (tttp) REVERT: N 162 HIS cc_start: 0.8307 (m-70) cc_final: 0.7873 (m-70) REVERT: N 213 LYS cc_start: 0.8303 (mmtm) cc_final: 0.8076 (mmtt) REVERT: N 255 ILE cc_start: 0.8121 (mt) cc_final: 0.7896 (pt) REVERT: N 489 ILE cc_start: 0.8022 (mt) cc_final: 0.7754 (tt) REVERT: O 41 ASP cc_start: 0.8028 (t0) cc_final: 0.7794 (t0) REVERT: O 381 ASN cc_start: 0.8820 (t0) cc_final: 0.8284 (t0) REVERT: O 663 TYR cc_start: 0.7865 (m-10) cc_final: 0.7450 (m-10) REVERT: O 691 TYR cc_start: 0.7985 (m-80) cc_final: 0.7759 (m-10) REVERT: P 26 ASP cc_start: 0.8291 (p0) cc_final: 0.7819 (t0) REVERT: P 94 TYR cc_start: 0.8605 (t80) cc_final: 0.7922 (t80) REVERT: P 169 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7998 (mm-30) REVERT: P 258 ASP cc_start: 0.9115 (t70) cc_final: 0.8906 (t0) REVERT: Q 21 HIS cc_start: 0.7963 (OUTLIER) cc_final: 0.7630 (m90) REVERT: Q 164 TYR cc_start: 0.5723 (m-80) cc_final: 0.4886 (m-10) REVERT: Q 175 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8715 (tp) REVERT: Q 218 GLN cc_start: 0.5231 (mt0) cc_final: 0.4935 (tt0) REVERT: Q 261 LYS cc_start: 0.8308 (mmtp) cc_final: 0.7380 (tmtt) REVERT: R 28 ARG cc_start: 0.7427 (mtp180) cc_final: 0.6969 (mtp85) REVERT: R 38 CYS cc_start: 0.7353 (m) cc_final: 0.7022 (m) REVERT: R 43 ARG cc_start: 0.7216 (tpp80) cc_final: 0.6538 (tpp80) REVERT: R 153 ARG cc_start: 0.5843 (ttm110) cc_final: 0.5615 (mtt-85) REVERT: R 155 HIS cc_start: 0.7673 (m-70) cc_final: 0.7355 (m170) REVERT: R 164 TYR cc_start: 0.4641 (m-80) cc_final: 0.3887 (m-80) REVERT: R 209 TRP cc_start: 0.6733 (m-10) cc_final: 0.6532 (m-90) REVERT: R 261 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8275 (ptmm) REVERT: R 278 TYR cc_start: 0.8009 (m-80) cc_final: 0.7408 (m-80) REVERT: R 298 LEU cc_start: 0.8731 (tp) cc_final: 0.8442 (mt) REVERT: R 314 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7663 (mtmt) REVERT: S 79 LEU cc_start: 0.8180 (pp) cc_final: 0.7936 (tt) REVERT: S 83 ILE cc_start: 0.7986 (mt) cc_final: 0.7525 (mt) REVERT: S 163 ASN cc_start: 0.8183 (m-40) cc_final: 0.7496 (m-40) REVERT: S 164 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.6564 (m-80) REVERT: S 210 LYS cc_start: 0.8252 (mtmt) cc_final: 0.7665 (mtmt) REVERT: S 212 HIS cc_start: 0.8926 (m90) cc_final: 0.8212 (m-70) REVERT: S 309 ASN cc_start: 0.8409 (m110) cc_final: 0.8054 (m-40) REVERT: T 188 ARG cc_start: 0.7552 (tpp80) cc_final: 0.7063 (tpt-90) REVERT: T 257 MET cc_start: 0.8999 (mmt) cc_final: 0.8738 (mmt) REVERT: T 357 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8071 (mmtm) REVERT: B 182 GLN cc_start: 0.5470 (mt0) cc_final: 0.5118 (mm-40) REVERT: B 402 GLU cc_start: 0.9054 (tt0) cc_final: 0.8813 (mm-30) REVERT: B 603 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7363 (tppt) REVERT: B 644 GLU cc_start: 0.6540 (tt0) cc_final: 0.6327 (pp20) REVERT: B 684 ASN cc_start: 0.6385 (OUTLIER) cc_final: 0.6130 (p0) REVERT: B 695 ARG cc_start: 0.6099 (ttm170) cc_final: 0.5697 (ttp-110) outliers start: 124 outliers final: 64 residues processed: 642 average time/residue: 0.1989 time to fit residues: 211.6536 Evaluate side-chains 538 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 460 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 239 HIS Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 306 VAL Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 274 CYS Chi-restraints excluded: chain K residue 282 HIS Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 454 LEU Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 135 LYS Chi-restraints excluded: chain M residue 159 VAL Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 296 LEU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain M residue 362 LYS Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 379 LEU Chi-restraints excluded: chain M residue 486 LYS Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain M residue 554 GLU Chi-restraints excluded: chain M residue 614 ILE Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 224 LEU Chi-restraints excluded: chain N residue 401 LEU Chi-restraints excluded: chain N residue 419 MET Chi-restraints excluded: chain N residue 495 SER Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 99 GLN Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 21 HIS Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain R residue 57 THR Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 321 SER Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 77 GLN Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 194 ARG Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 76 ILE Chi-restraints excluded: chain T residue 155 HIS Chi-restraints excluded: chain T residue 371 ILE Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 521 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 687 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 139 optimal weight: 1.9990 chunk 456 optimal weight: 8.9990 chunk 367 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 156 optimal weight: 0.0770 chunk 276 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 193 optimal weight: 0.9990 chunk 509 optimal weight: 9.9990 chunk 368 optimal weight: 0.6980 chunk 481 optimal weight: 9.9990 overall best weight: 0.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 100 GLN J 239 HIS M 49 GLN N 69 GLN O 602 GLN Q 78 ASN Q 265 ASN R 142 HIS S 116 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.137865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092075 restraints weight = 93121.368| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.40 r_work: 0.3130 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 43918 Z= 0.102 Angle : 0.517 8.056 60011 Z= 0.266 Chirality : 0.044 0.179 7171 Planarity : 0.004 0.060 7779 Dihedral : 3.965 29.734 6420 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.94 % Favored : 94.96 % Rotamer: Outliers : 2.15 % Allowed : 13.01 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.11 (0.11), residues: 6007 helix: 1.58 (0.12), residues: 2213 sheet: -0.80 (0.20), residues: 721 loop : -1.16 (0.11), residues: 3073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 268 TYR 0.014 0.001 TYR R 179 PHE 0.019 0.001 PHE J 263 TRP 0.038 0.001 TRP B 584 HIS 0.016 0.001 HIS T 155 Details of bonding type rmsd covalent geometry : bond 0.00229 (43918) covalent geometry : angle 0.51677 (60011) hydrogen bonds : bond 0.03140 ( 1736) hydrogen bonds : angle 4.60368 ( 4929) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 527 time to evaluate : 1.388 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 69 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: D 256 ASP cc_start: 0.8194 (m-30) cc_final: 0.7889 (t0) REVERT: D 367 LEU cc_start: 0.8450 (tt) cc_final: 0.8191 (mm) REVERT: D 525 HIS cc_start: 0.8037 (t70) cc_final: 0.7766 (t-170) REVERT: J 164 TYR cc_start: 0.6996 (m-10) cc_final: 0.6575 (m-80) REVERT: J 197 GLU cc_start: 0.8475 (mp0) cc_final: 0.7963 (mp0) REVERT: J 239 HIS cc_start: 0.6788 (OUTLIER) cc_final: 0.6431 (t70) REVERT: K 259 GLN cc_start: 0.8802 (tp40) cc_final: 0.8374 (mp10) REVERT: K 282 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7261 (m-70) REVERT: L 535 GLU cc_start: 0.8303 (mp0) cc_final: 0.8087 (mp0) REVERT: M 93 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: M 135 LYS cc_start: 0.8824 (ptpt) cc_final: 0.8468 (mmmt) REVERT: M 272 GLU cc_start: 0.8526 (tm-30) cc_final: 0.8193 (tm-30) REVERT: M 295 ASP cc_start: 0.8733 (m-30) cc_final: 0.8463 (m-30) REVERT: M 331 SER cc_start: 0.8986 (m) cc_final: 0.8636 (p) REVERT: M 370 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8731 (mp) REVERT: M 689 ASN cc_start: 0.8750 (p0) cc_final: 0.8420 (p0) REVERT: N 117 LYS cc_start: 0.7801 (OUTLIER) cc_final: 0.7421 (tttp) REVERT: N 162 HIS cc_start: 0.7936 (m-70) cc_final: 0.7409 (m-70) REVERT: O 41 ASP cc_start: 0.8038 (t0) cc_final: 0.7798 (t0) REVERT: O 156 ASP cc_start: 0.8892 (m-30) cc_final: 0.8638 (m-30) REVERT: P 94 TYR cc_start: 0.8637 (t80) cc_final: 0.8387 (t80) REVERT: Q 124 GLU cc_start: 0.5940 (mm-30) cc_final: 0.5707 (mm-30) REVERT: Q 164 TYR cc_start: 0.5754 (m-80) cc_final: 0.4899 (m-10) REVERT: Q 169 GLU cc_start: 0.9093 (mp0) cc_final: 0.8578 (pm20) REVERT: Q 203 SER cc_start: 0.8648 (m) cc_final: 0.8350 (t) REVERT: Q 261 LYS cc_start: 0.8207 (mmtp) cc_final: 0.7272 (tmtt) REVERT: Q 367 PHE cc_start: 0.8459 (t80) cc_final: 0.8239 (t80) REVERT: R 28 ARG cc_start: 0.7413 (mtp180) cc_final: 0.6996 (mtp85) REVERT: R 43 ARG cc_start: 0.7219 (tpp80) cc_final: 0.6834 (tpp80) REVERT: R 164 TYR cc_start: 0.4973 (m-80) cc_final: 0.4503 (m-80) REVERT: R 278 TYR cc_start: 0.7997 (m-80) cc_final: 0.6967 (m-80) REVERT: R 314 LYS cc_start: 0.8076 (mtpt) cc_final: 0.7722 (mtmt) REVERT: R 341 LYS cc_start: 0.7004 (mmmt) cc_final: 0.6504 (mmmt) REVERT: S 83 ILE cc_start: 0.8057 (mt) cc_final: 0.7675 (mt) REVERT: S 120 GLU cc_start: 0.9401 (mp0) cc_final: 0.9043 (mp0) REVERT: S 163 ASN cc_start: 0.8171 (m-40) cc_final: 0.7635 (m-40) REVERT: S 169 GLU cc_start: 0.8820 (pm20) cc_final: 0.8576 (pm20) REVERT: S 210 LYS cc_start: 0.8116 (mtmt) cc_final: 0.7716 (mtpt) REVERT: S 212 HIS cc_start: 0.8981 (m90) cc_final: 0.8347 (m-70) REVERT: S 309 ASN cc_start: 0.8412 (m110) cc_final: 0.8023 (m-40) REVERT: T 169 GLU cc_start: 0.8599 (mp0) cc_final: 0.7715 (mp0) REVERT: T 257 MET cc_start: 0.8987 (mmt) cc_final: 0.8700 (mmt) REVERT: B 182 GLN cc_start: 0.5149 (mt0) cc_final: 0.4835 (mm-40) REVERT: B 402 GLU cc_start: 0.9030 (tt0) cc_final: 0.8735 (mm-30) REVERT: B 541 LEU cc_start: 0.6867 (mt) cc_final: 0.6628 (tt) REVERT: B 603 LYS cc_start: 0.8293 (mtmt) cc_final: 0.7275 (tppt) REVERT: B 644 GLU cc_start: 0.6026 (tt0) cc_final: 0.5811 (tm-30) REVERT: B 695 ARG cc_start: 0.6097 (ttm170) cc_final: 0.5701 (ttp-110) outliers start: 85 outliers final: 44 residues processed: 585 average time/residue: 0.1996 time to fit residues: 194.8444 Evaluate side-chains 511 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 461 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 239 HIS Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain K residue 282 HIS Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain M residue 554 GLU Chi-restraints excluded: chain M residue 614 ILE Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain N residue 419 MET Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 99 GLN Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 242 HIS Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain S residue 77 GLN Chi-restraints excluded: chain S residue 194 ARG Chi-restraints excluded: chain S residue 361 PHE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 687 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 529 optimal weight: 5.9990 chunk 501 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 597 optimal weight: 7.9990 chunk 487 optimal weight: 1.9990 chunk 555 optimal weight: 10.0000 chunk 276 optimal weight: 7.9990 chunk 560 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 200 optimal weight: 0.9980 chunk 189 optimal weight: 0.4980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 290 HIS D 518 ASN J 100 GLN J 170 GLN J 239 HIS L 49 GLN M 49 GLN ** M 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 69 GLN Q 218 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.134022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087144 restraints weight = 93525.593| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 3.18 r_work: 0.3065 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.141 43918 Z= 0.240 Angle : 0.593 10.527 60011 Z= 0.306 Chirality : 0.046 0.219 7171 Planarity : 0.004 0.049 7779 Dihedral : 4.246 30.399 6420 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.49 % Favored : 93.44 % Rotamer: Outliers : 3.09 % Allowed : 13.77 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.11), residues: 6007 helix: 1.47 (0.12), residues: 2232 sheet: -1.03 (0.19), residues: 802 loop : -1.24 (0.11), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O 268 TYR 0.031 0.002 TYR B 487 PHE 0.021 0.002 PHE B 440 TRP 0.049 0.002 TRP B 584 HIS 0.010 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00575 (43918) covalent geometry : angle 0.59315 (60011) hydrogen bonds : bond 0.03800 ( 1736) hydrogen bonds : angle 4.67351 ( 4929) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 459 time to evaluate : 1.545 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 98 GLU cc_start: 0.8457 (tt0) cc_final: 0.8069 (tm-30) REVERT: D 127 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8814 (mttt) REVERT: D 256 ASP cc_start: 0.8140 (m-30) cc_final: 0.7832 (t0) REVERT: D 277 ASP cc_start: 0.8093 (m-30) cc_final: 0.7576 (t0) REVERT: D 525 HIS cc_start: 0.8149 (t70) cc_final: 0.7910 (t-170) REVERT: J 119 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8153 (pt0) REVERT: J 197 GLU cc_start: 0.8458 (mp0) cc_final: 0.7997 (mp0) REVERT: J 239 HIS cc_start: 0.6812 (OUTLIER) cc_final: 0.6281 (t-90) REVERT: J 261 LYS cc_start: 0.8761 (tmtt) cc_final: 0.8551 (tptt) REVERT: K 19 LEU cc_start: 0.7460 (tp) cc_final: 0.7122 (pp) REVERT: K 259 GLN cc_start: 0.8778 (tp40) cc_final: 0.8371 (mp10) REVERT: K 282 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.7580 (m-70) REVERT: M 93 GLN cc_start: 0.9024 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: M 111 TYR cc_start: 0.8932 (m-80) cc_final: 0.8459 (m-80) REVERT: M 272 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8080 (tm-30) REVERT: M 295 ASP cc_start: 0.8726 (m-30) cc_final: 0.8460 (m-30) REVERT: M 370 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8784 (mp) REVERT: M 486 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8649 (ptmt) REVERT: M 689 ASN cc_start: 0.8817 (p0) cc_final: 0.8514 (p0) REVERT: N 117 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7442 (tttm) REVERT: O 41 ASP cc_start: 0.8044 (t0) cc_final: 0.7829 (t0) REVERT: O 691 TYR cc_start: 0.7769 (m-10) cc_final: 0.7473 (m-80) REVERT: P 26 ASP cc_start: 0.8400 (p0) cc_final: 0.7730 (t0) REVERT: P 94 TYR cc_start: 0.8688 (t80) cc_final: 0.8408 (t80) REVERT: Q 164 TYR cc_start: 0.5689 (m-80) cc_final: 0.4770 (m-10) REVERT: Q 169 GLU cc_start: 0.9071 (mp0) cc_final: 0.8614 (pm20) REVERT: Q 187 LYS cc_start: 0.7114 (ptmt) cc_final: 0.6904 (pttt) REVERT: Q 261 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7282 (tmtt) REVERT: Q 315 ASP cc_start: 0.8808 (m-30) cc_final: 0.8333 (p0) REVERT: R 28 ARG cc_start: 0.7449 (mtp180) cc_final: 0.6915 (mtp180) REVERT: R 43 ARG cc_start: 0.7318 (tpp80) cc_final: 0.6973 (tpp80) REVERT: R 164 TYR cc_start: 0.4894 (m-80) cc_final: 0.4455 (m-80) REVERT: R 209 TRP cc_start: 0.5885 (m-90) cc_final: 0.5574 (m-90) REVERT: R 278 TYR cc_start: 0.7911 (m-80) cc_final: 0.7480 (m-80) REVERT: R 314 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7772 (mtmt) REVERT: S 89 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6945 (mp0) REVERT: S 120 GLU cc_start: 0.9427 (mp0) cc_final: 0.9017 (mp0) REVERT: S 163 ASN cc_start: 0.8176 (m-40) cc_final: 0.7589 (m-40) REVERT: S 164 TYR cc_start: 0.8313 (OUTLIER) cc_final: 0.6567 (m-80) REVERT: S 169 GLU cc_start: 0.8936 (pm20) cc_final: 0.8735 (pm20) REVERT: S 309 ASN cc_start: 0.8422 (m110) cc_final: 0.8081 (m110) REVERT: T 169 GLU cc_start: 0.8608 (mp0) cc_final: 0.7727 (mp0) REVERT: T 188 ARG cc_start: 0.7668 (tpp80) cc_final: 0.7156 (tpt-90) REVERT: T 257 MET cc_start: 0.8968 (mmt) cc_final: 0.8524 (mmt) REVERT: B 182 GLN cc_start: 0.5576 (mt0) cc_final: 0.5215 (mm-40) REVERT: B 402 GLU cc_start: 0.9002 (tt0) cc_final: 0.8719 (mm-30) REVERT: B 496 GLN cc_start: 0.5935 (pm20) cc_final: 0.5734 (pm20) REVERT: B 541 LEU cc_start: 0.7224 (mt) cc_final: 0.6815 (tt) REVERT: B 603 LYS cc_start: 0.8338 (mtmt) cc_final: 0.7311 (tppt) REVERT: B 695 ARG cc_start: 0.6166 (ttm170) cc_final: 0.5745 (ttp-110) outliers start: 122 outliers final: 73 residues processed: 549 average time/residue: 0.2148 time to fit residues: 196.2050 Evaluate side-chains 499 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 417 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 239 HIS Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 282 HIS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 282 HIS Chi-restraints excluded: chain L residue 332 LEU Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 454 LEU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 687 ILE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 486 LYS Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain N residue 155 ILE Chi-restraints excluded: chain N residue 419 MET Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 108 VAL Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 99 GLN Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 242 HIS Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain Q residue 370 GLU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 321 SER Chi-restraints excluded: chain S residue 89 GLU Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 194 ARG Chi-restraints excluded: chain S residue 361 PHE Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 371 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 687 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 398 optimal weight: 0.6980 chunk 341 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 chunk 374 optimal weight: 6.9990 chunk 190 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 147 optimal weight: 0.8980 chunk 101 optimal weight: 10.0000 chunk 405 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 overall best weight: 0.7318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 149 ASN J 239 HIS M 49 GLN O 201 HIS O 602 GLN Q 265 ASN T 21 HIS T 309 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.136533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.090686 restraints weight = 92981.400| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.44 r_work: 0.3099 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 43918 Z= 0.097 Angle : 0.503 7.657 60011 Z= 0.259 Chirality : 0.043 0.271 7171 Planarity : 0.004 0.045 7779 Dihedral : 3.881 29.211 6420 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 2.20 % Allowed : 15.24 % Favored : 82.56 % 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 (0.11), residues: 6007 helix: 1.71 (0.12), residues: 2221 sheet: -0.92 (0.19), residues: 795 loop : -1.14 (0.11), residues: 2991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 268 TYR 0.015 0.001 TYR R 179 PHE 0.019 0.001 PHE S 32 TRP 0.048 0.001 TRP B 584 HIS 0.011 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00217 (43918) covalent geometry : angle 0.50337 (60011) hydrogen bonds : bond 0.02804 ( 1736) hydrogen bonds : angle 4.38986 ( 4929) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 468 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8270 (mt0) REVERT: D 98 GLU cc_start: 0.8483 (tt0) cc_final: 0.8072 (tm-30) REVERT: D 127 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8710 (mttt) REVERT: D 256 ASP cc_start: 0.8149 (m-30) cc_final: 0.7825 (t0) REVERT: D 525 HIS cc_start: 0.8035 (t70) cc_final: 0.7757 (t-170) REVERT: J 119 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8289 (tm-30) REVERT: J 164 TYR cc_start: 0.7043 (m-80) cc_final: 0.6577 (m-80) REVERT: K 259 GLN cc_start: 0.8756 (tp40) cc_final: 0.8322 (mp10) REVERT: K 263 PHE cc_start: 0.8040 (t80) cc_final: 0.7828 (t80) REVERT: K 274 CYS cc_start: 0.7722 (m) cc_final: 0.7451 (p) REVERT: M 93 GLN cc_start: 0.8939 (OUTLIER) cc_final: 0.8731 (tt0) REVERT: M 111 TYR cc_start: 0.8887 (m-80) cc_final: 0.8455 (m-80) REVERT: M 135 LYS cc_start: 0.8899 (mmtm) cc_final: 0.8669 (ttmt) REVERT: M 272 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8049 (tm-30) REVERT: M 295 ASP cc_start: 0.8731 (m-30) cc_final: 0.8452 (m-30) REVERT: M 370 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8757 (mp) REVERT: M 459 GLU cc_start: 0.8607 (tp30) cc_final: 0.8284 (tt0) REVERT: M 689 ASN cc_start: 0.8792 (p0) cc_final: 0.8489 (p0) REVERT: N 117 LYS cc_start: 0.7869 (OUTLIER) cc_final: 0.7502 (tttm) REVERT: N 162 HIS cc_start: 0.7925 (m-70) cc_final: 0.7537 (m-70) REVERT: O 41 ASP cc_start: 0.7984 (t0) cc_final: 0.7696 (t0) REVERT: O 156 ASP cc_start: 0.8860 (m-30) cc_final: 0.8615 (m-30) REVERT: O 370 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8585 (mp) REVERT: P 94 TYR cc_start: 0.8667 (t80) cc_final: 0.8440 (t80) REVERT: P 316 MET cc_start: 0.9142 (ttp) cc_final: 0.8896 (ttm) REVERT: Q 164 TYR cc_start: 0.5597 (m-80) cc_final: 0.4671 (m-10) REVERT: Q 169 GLU cc_start: 0.9063 (mp0) cc_final: 0.8604 (pm20) REVERT: Q 261 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7247 (tmtt) REVERT: R 28 ARG cc_start: 0.7361 (mtp180) cc_final: 0.6634 (mtp180) REVERT: R 43 ARG cc_start: 0.7346 (tpp80) cc_final: 0.7009 (tpp80) REVERT: R 158 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7750 (mt-10) REVERT: R 164 TYR cc_start: 0.4982 (m-80) cc_final: 0.4536 (m-80) REVERT: R 278 TYR cc_start: 0.7909 (m-80) cc_final: 0.7452 (m-80) REVERT: R 296 ASN cc_start: 0.8212 (m-40) cc_final: 0.7764 (t0) REVERT: S 163 ASN cc_start: 0.8114 (m-40) cc_final: 0.7476 (m-40) REVERT: S 164 TYR cc_start: 0.8332 (OUTLIER) cc_final: 0.6593 (m-80) REVERT: S 169 GLU cc_start: 0.8846 (pm20) cc_final: 0.8599 (pm20) REVERT: S 210 LYS cc_start: 0.8153 (mtpp) cc_final: 0.7777 (mtpt) REVERT: S 309 ASN cc_start: 0.8339 (m110) cc_final: 0.7977 (m-40) REVERT: T 169 GLU cc_start: 0.8580 (mp0) cc_final: 0.8013 (mp0) REVERT: T 188 ARG cc_start: 0.7677 (tpp80) cc_final: 0.7204 (tpt-90) REVERT: T 257 MET cc_start: 0.8941 (mmt) cc_final: 0.8542 (mmt) REVERT: B 402 GLU cc_start: 0.8990 (tt0) cc_final: 0.8725 (mm-30) REVERT: B 517 MET cc_start: 0.6476 (mtt) cc_final: 0.5997 (mtt) REVERT: B 541 LEU cc_start: 0.7117 (mt) cc_final: 0.6835 (tt) REVERT: B 603 LYS cc_start: 0.8297 (mtmt) cc_final: 0.7242 (tppt) REVERT: B 695 ARG cc_start: 0.6103 (ttm170) cc_final: 0.5700 (ttp-110) outliers start: 87 outliers final: 49 residues processed: 533 average time/residue: 0.2052 time to fit residues: 180.4824 Evaluate side-chains 486 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 430 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 454 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain M residue 614 ILE Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 370 LEU Chi-restraints excluded: chain O residue 554 GLU Chi-restraints excluded: chain O residue 587 ASN Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 242 HIS Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 321 SER Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 194 ARG Chi-restraints excluded: chain S residue 361 PHE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 687 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 504 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 232 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 373 optimal weight: 4.9990 chunk 387 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 418 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 470 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.134556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087291 restraints weight = 93619.543| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.25 r_work: 0.3059 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.132 43918 Z= 0.203 Angle : 0.567 10.373 60011 Z= 0.292 Chirality : 0.045 0.354 7171 Planarity : 0.004 0.047 7779 Dihedral : 4.113 29.967 6420 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.43 % Favored : 93.51 % Rotamer: Outliers : 2.86 % Allowed : 15.37 % Favored : 81.77 % 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 (0.11), residues: 6007 helix: 1.60 (0.12), residues: 2227 sheet: -0.95 (0.19), residues: 798 loop : -1.20 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 96 TYR 0.014 0.001 TYR Q 141 PHE 0.022 0.002 PHE S 32 TRP 0.056 0.002 TRP B 584 HIS 0.011 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00494 (43918) covalent geometry : angle 0.56712 (60011) hydrogen bonds : bond 0.03556 ( 1736) hydrogen bonds : angle 4.55225 ( 4929) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 437 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: D 98 GLU cc_start: 0.8471 (tt0) cc_final: 0.8049 (tm-30) REVERT: D 127 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8748 (mttt) REVERT: D 277 ASP cc_start: 0.8143 (m-30) cc_final: 0.7611 (t0) REVERT: D 525 HIS cc_start: 0.8121 (t70) cc_final: 0.7859 (t-170) REVERT: J 119 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8143 (pt0) REVERT: J 129 GLU cc_start: 0.8330 (tp30) cc_final: 0.7882 (tm-30) REVERT: J 164 TYR cc_start: 0.7118 (m-80) cc_final: 0.6704 (m-80) REVERT: K 19 LEU cc_start: 0.7353 (tp) cc_final: 0.6958 (pp) REVERT: K 274 CYS cc_start: 0.7819 (m) cc_final: 0.7582 (p) REVERT: M 93 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8782 (tt0) REVERT: M 135 LYS cc_start: 0.8920 (mmtm) cc_final: 0.8653 (ttmt) REVERT: M 272 GLU cc_start: 0.8628 (tm-30) cc_final: 0.8040 (tm-30) REVERT: M 295 ASP cc_start: 0.8708 (m-30) cc_final: 0.8424 (m-30) REVERT: N 117 LYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7483 (tttm) REVERT: O 41 ASP cc_start: 0.7980 (t0) cc_final: 0.7736 (t0) REVERT: O 663 TYR cc_start: 0.7756 (m-10) cc_final: 0.7440 (m-10) REVERT: P 26 ASP cc_start: 0.8500 (p0) cc_final: 0.7571 (t0) REVERT: P 94 TYR cc_start: 0.8696 (t80) cc_final: 0.8395 (t80) REVERT: Q 164 TYR cc_start: 0.5495 (m-80) cc_final: 0.4589 (m-10) REVERT: Q 261 LYS cc_start: 0.8273 (mmtp) cc_final: 0.7354 (tmtt) REVERT: Q 300 TYR cc_start: 0.8079 (m-10) cc_final: 0.7838 (m-10) REVERT: Q 315 ASP cc_start: 0.8856 (m-30) cc_final: 0.8365 (p0) REVERT: R 28 ARG cc_start: 0.7382 (mtp180) cc_final: 0.6829 (mtp180) REVERT: R 43 ARG cc_start: 0.7322 (tpp80) cc_final: 0.6972 (tpp80) REVERT: R 164 TYR cc_start: 0.5037 (m-80) cc_final: 0.4568 (m-80) REVERT: R 168 MET cc_start: 0.7521 (tmm) cc_final: 0.6850 (tmm) REVERT: R 278 TYR cc_start: 0.7878 (m-80) cc_final: 0.7560 (m-10) REVERT: S 163 ASN cc_start: 0.8173 (m-40) cc_final: 0.7625 (m-40) REVERT: S 164 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6565 (m-80) REVERT: S 309 ASN cc_start: 0.8353 (m110) cc_final: 0.8001 (m-40) REVERT: T 188 ARG cc_start: 0.7537 (tpp80) cc_final: 0.7044 (tpt-90) REVERT: T 257 MET cc_start: 0.8935 (mmt) cc_final: 0.8524 (mmt) REVERT: B 196 ILE cc_start: 0.5533 (mm) cc_final: 0.5260 (tp) REVERT: B 402 GLU cc_start: 0.8950 (tt0) cc_final: 0.8567 (mm-30) REVERT: B 470 ARG cc_start: 0.8358 (mtt90) cc_final: 0.7960 (mpt180) REVERT: B 603 LYS cc_start: 0.8289 (mtmt) cc_final: 0.7231 (tppt) REVERT: B 695 ARG cc_start: 0.6047 (ttm170) cc_final: 0.5636 (ttp-110) outliers start: 113 outliers final: 80 residues processed: 524 average time/residue: 0.2363 time to fit residues: 206.1626 Evaluate side-chains 490 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 405 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 127 LYS Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 282 HIS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 454 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 687 ILE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 93 GLN Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 480 ILE Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 155 ILE Chi-restraints excluded: chain N residue 401 LEU Chi-restraints excluded: chain N residue 419 MET Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 292 LEU Chi-restraints excluded: chain O residue 554 GLU Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 587 ASN Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 325 LEU Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 242 HIS Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 265 ASN Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 321 SER Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 194 ARG Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 361 PHE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 371 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 687 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 446 optimal weight: 20.0000 chunk 326 optimal weight: 2.9990 chunk 281 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 438 optimal weight: 8.9990 chunk 579 optimal weight: 9.9990 chunk 480 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 448 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 508 GLN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN J 170 GLN ** M 508 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 62 ASN O 87 HIS O 182 GLN O 201 HIS O 602 GLN P 218 GLN S 78 ASN ** S 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN B 684 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.130381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.084050 restraints weight = 93674.993| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 3.39 r_work: 0.2974 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.211 43918 Z= 0.397 Angle : 0.749 10.010 60011 Z= 0.393 Chirality : 0.051 0.346 7171 Planarity : 0.005 0.057 7779 Dihedral : 5.208 30.355 6420 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.02 % Favored : 91.88 % Rotamer: Outliers : 3.70 % Allowed : 15.85 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.11), residues: 6007 helix: 0.93 (0.11), residues: 2231 sheet: -1.33 (0.19), residues: 802 loop : -1.56 (0.11), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 28 TYR 0.028 0.002 TYR L 60 PHE 0.033 0.003 PHE S 32 TRP 0.077 0.003 TRP B 584 HIS 0.013 0.002 HIS N 162 Details of bonding type rmsd covalent geometry : bond 0.00955 (43918) covalent geometry : angle 0.74923 (60011) hydrogen bonds : bond 0.05085 ( 1736) hydrogen bonds : angle 5.13632 ( 4929) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 398 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 50 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8166 (tp) REVERT: D 98 GLU cc_start: 0.8561 (tt0) cc_final: 0.8062 (tm-30) REVERT: D 277 ASP cc_start: 0.8256 (m-30) cc_final: 0.7785 (t0) REVERT: D 525 HIS cc_start: 0.8269 (t70) cc_final: 0.7865 (t-170) REVERT: J 119 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8115 (pt0) REVERT: J 129 GLU cc_start: 0.8295 (tp30) cc_final: 0.7927 (tm-30) REVERT: J 278 TYR cc_start: 0.7125 (m-80) cc_final: 0.6791 (m-80) REVERT: K 119 GLU cc_start: 0.8901 (pp20) cc_final: 0.8670 (pp20) REVERT: L 670 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6733 (p-80) REVERT: M 93 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8858 (tt0) REVERT: M 148 SER cc_start: 0.9325 (t) cc_final: 0.9078 (p) REVERT: M 364 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8794 (mp) REVERT: M 370 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8774 (mp) REVERT: N 117 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7851 (tttm) REVERT: O 41 ASP cc_start: 0.8092 (t0) cc_final: 0.7827 (t0) REVERT: O 60 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.7449 (t80) REVERT: O 156 ASP cc_start: 0.9056 (m-30) cc_final: 0.8777 (m-30) REVERT: Q 164 TYR cc_start: 0.5699 (m-80) cc_final: 0.4820 (m-10) REVERT: Q 187 LYS cc_start: 0.8128 (tppt) cc_final: 0.7607 (pttm) REVERT: R 43 ARG cc_start: 0.7567 (tpp80) cc_final: 0.7243 (tpp80) REVERT: R 155 HIS cc_start: 0.7730 (m-70) cc_final: 0.7360 (m170) REVERT: R 164 TYR cc_start: 0.5029 (m-80) cc_final: 0.4661 (m-80) REVERT: R 335 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8306 (mttt) REVERT: S 163 ASN cc_start: 0.8263 (m-40) cc_final: 0.7646 (m-40) REVERT: S 164 TYR cc_start: 0.8462 (OUTLIER) cc_final: 0.6689 (m-80) REVERT: S 309 ASN cc_start: 0.8285 (m110) cc_final: 0.7982 (m110) REVERT: T 96 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7038 (mtt90) REVERT: B 196 ILE cc_start: 0.5470 (mm) cc_final: 0.5098 (tp) REVERT: B 470 ARG cc_start: 0.8370 (mtt90) cc_final: 0.7970 (mpt180) REVERT: B 603 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7262 (tppt) REVERT: B 695 ARG cc_start: 0.6213 (ttm170) cc_final: 0.5891 (ttp-110) outliers start: 146 outliers final: 97 residues processed: 517 average time/residue: 0.2481 time to fit residues: 214.3013 Evaluate side-chains 480 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 374 time to evaluate : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 255 ILE Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 282 HIS Chi-restraints excluded: chain J residue 372 SER Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain K residue 293 THR Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 146 VAL Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 454 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain L residue 687 ILE 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 93 GLN Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 188 SER Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 364 LEU Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 379 LEU Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 480 ILE Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 653 GLU Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 155 ILE Chi-restraints excluded: chain N residue 401 LEU Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 554 GLU Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 587 ASN Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 325 LEU Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 242 HIS Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 282 HIS Chi-restraints excluded: chain R residue 321 SER Chi-restraints excluded: chain R residue 335 LYS Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain S residue 53 VAL Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 194 ARG Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 361 PHE Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 123 CYS Chi-restraints excluded: chain T residue 201 LEU Chi-restraints excluded: chain T residue 371 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 687 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 349 optimal weight: 5.9990 chunk 527 optimal weight: 0.2980 chunk 258 optimal weight: 8.9990 chunk 136 optimal weight: 0.9990 chunk 494 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 489 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** K 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 265 ASN S 78 ASN B 661 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.132566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.086464 restraints weight = 94244.180| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.45 r_work: 0.3013 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 43918 Z= 0.189 Angle : 0.583 9.311 60011 Z= 0.302 Chirality : 0.046 0.219 7171 Planarity : 0.004 0.055 7779 Dihedral : 4.570 29.723 6420 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.14 % Rotamer: Outliers : 2.86 % Allowed : 17.11 % Favored : 80.03 % 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: -0.57 (0.11), residues: 6007 helix: 1.28 (0.12), residues: 2229 sheet: -1.31 (0.19), residues: 774 loop : -1.43 (0.11), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG O 268 TYR 0.018 0.001 TYR R 179 PHE 0.022 0.002 PHE S 32 TRP 0.057 0.002 TRP B 584 HIS 0.010 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00457 (43918) covalent geometry : angle 0.58265 (60011) hydrogen bonds : bond 0.03643 ( 1736) hydrogen bonds : angle 4.72047 ( 4929) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 407 time to evaluate : 1.237 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 98 GLU cc_start: 0.8484 (tt0) cc_final: 0.7976 (tm-30) REVERT: D 251 ARG cc_start: 0.8363 (ttt-90) cc_final: 0.8107 (ttm-80) REVERT: D 277 ASP cc_start: 0.8140 (m-30) cc_final: 0.7677 (t0) REVERT: J 119 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8114 (pt0) REVERT: J 129 GLU cc_start: 0.8413 (tp30) cc_final: 0.8029 (tm-30) REVERT: J 278 TYR cc_start: 0.6930 (m-80) cc_final: 0.6657 (m-80) REVERT: L 670 HIS cc_start: 0.6984 (OUTLIER) cc_final: 0.6752 (p-80) REVERT: M 93 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8792 (tt0) REVERT: M 135 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8844 (ttmt) REVERT: M 364 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8714 (mp) REVERT: M 370 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8704 (mp) REVERT: N 117 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7891 (tttm) REVERT: O 41 ASP cc_start: 0.8059 (t0) cc_final: 0.7792 (t0) REVERT: O 60 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7240 (t80) REVERT: Q 169 GLU cc_start: 0.8912 (mp0) cc_final: 0.8448 (pm20) REVERT: Q 187 LYS cc_start: 0.8086 (tppt) cc_final: 0.7508 (pttm) REVERT: Q 217 TRP cc_start: 0.7903 (m100) cc_final: 0.7497 (m100) REVERT: Q 261 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7420 (tmtt) REVERT: Q 369 GLU cc_start: 0.8720 (tp30) cc_final: 0.8380 (tp30) REVERT: R 43 ARG cc_start: 0.7641 (tpp80) cc_final: 0.7322 (tpp80) REVERT: R 155 HIS cc_start: 0.7764 (m-70) cc_final: 0.7403 (m170) REVERT: R 164 TYR cc_start: 0.4951 (m-80) cc_final: 0.4540 (m-80) REVERT: R 168 MET cc_start: 0.7397 (tmm) cc_final: 0.6814 (tmm) REVERT: R 335 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8189 (mttt) REVERT: S 163 ASN cc_start: 0.8174 (m-40) cc_final: 0.7574 (m-40) REVERT: S 164 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.6759 (m-80) REVERT: S 169 GLU cc_start: 0.8883 (pm20) cc_final: 0.8597 (pm20) REVERT: S 282 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8299 (t70) REVERT: S 309 ASN cc_start: 0.8283 (m110) cc_final: 0.7987 (m110) REVERT: B 196 ILE cc_start: 0.5387 (mm) cc_final: 0.5049 (tp) REVERT: B 603 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7192 (tppt) REVERT: B 664 ASP cc_start: 0.5598 (t0) cc_final: 0.5375 (t0) REVERT: B 695 ARG cc_start: 0.6206 (ttm170) cc_final: 0.5933 (ttp-110) outliers start: 113 outliers final: 85 residues processed: 492 average time/residue: 0.2082 time to fit residues: 171.2278 Evaluate side-chains 478 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 384 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 249 SER Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 480 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 184 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 282 HIS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain L residue 155 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 454 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain L residue 687 ILE 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 93 GLN Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 166 LEU Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 364 LEU Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 379 LEU Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain M residue 581 THR Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 50 ILE Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 155 ILE Chi-restraints excluded: chain N residue 401 LEU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 60 TYR Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 554 GLU Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 587 ASN Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 205 TRP Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain Q residue 242 HIS Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 370 GLU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 179 TYR Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 282 HIS Chi-restraints excluded: chain R residue 321 SER Chi-restraints excluded: chain R residue 335 LYS Chi-restraints excluded: chain R residue 368 LEU Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 194 ARG Chi-restraints excluded: chain S residue 268 SER Chi-restraints excluded: chain S residue 282 HIS Chi-restraints excluded: chain S residue 361 PHE Chi-restraints excluded: chain T residue 22 VAL Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 123 CYS Chi-restraints excluded: chain T residue 371 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 235 CYS Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 527 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 665 VAL Chi-restraints excluded: chain B residue 684 ASN Chi-restraints excluded: chain B residue 687 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 532 optimal weight: 0.2980 chunk 329 optimal weight: 0.9980 chunk 570 optimal weight: 30.0000 chunk 23 optimal weight: 8.9990 chunk 389 optimal weight: 0.0060 chunk 453 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 344 optimal weight: 8.9990 chunk 471 optimal weight: 0.9990 chunk 318 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** K 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 518 ASN S 99 GLN S 116 ASN B 661 GLN B 684 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.135442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089043 restraints weight = 93064.508| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.22 r_work: 0.3085 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 43918 Z= 0.099 Angle : 0.539 12.871 60011 Z= 0.277 Chirality : 0.044 0.312 7171 Planarity : 0.004 0.077 7779 Dihedral : 4.057 29.108 6420 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 1.87 % Allowed : 18.18 % Favored : 79.95 % 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: -0.24 (0.11), residues: 6007 helix: 1.55 (0.12), residues: 2212 sheet: -1.03 (0.19), residues: 768 loop : -1.24 (0.11), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG O 268 TYR 0.020 0.001 TYR P 94 PHE 0.018 0.001 PHE S 263 TRP 0.074 0.002 TRP B 584 HIS 0.010 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00223 (43918) covalent geometry : angle 0.53851 (60011) hydrogen bonds : bond 0.02877 ( 1736) hydrogen bonds : angle 4.47287 ( 4929) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 439 time to evaluate : 1.497 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 69 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8343 (mt0) REVERT: D 98 GLU cc_start: 0.8466 (tt0) cc_final: 0.7991 (tm-30) REVERT: D 277 ASP cc_start: 0.8251 (m-30) cc_final: 0.7688 (t0) REVERT: D 293 TRP cc_start: 0.6988 (t60) cc_final: 0.6764 (t60) REVERT: D 525 HIS cc_start: 0.8056 (t-90) cc_final: 0.7704 (t-170) REVERT: J 119 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8096 (pt0) REVERT: J 129 GLU cc_start: 0.8269 (tp30) cc_final: 0.7873 (tm-30) REVERT: J 197 GLU cc_start: 0.8393 (mp0) cc_final: 0.7845 (mp0) REVERT: L 105 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8352 (mm-30) REVERT: L 670 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.6713 (p-80) REVERT: M 364 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8657 (mp) REVERT: M 370 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8751 (mp) REVERT: M 459 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8257 (tt0) REVERT: M 560 MET cc_start: 0.8773 (ptp) cc_final: 0.8571 (ptt) REVERT: N 117 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7860 (tttm) REVERT: N 162 HIS cc_start: 0.8155 (m-70) cc_final: 0.7952 (m-70) REVERT: O 41 ASP cc_start: 0.7958 (t0) cc_final: 0.7659 (t0) REVERT: O 156 ASP cc_start: 0.8867 (m-30) cc_final: 0.8641 (m-30) REVERT: P 292 GLN cc_start: 0.9094 (tt0) cc_final: 0.8842 (mt0) REVERT: P 316 MET cc_start: 0.9115 (ttp) cc_final: 0.8846 (ttm) REVERT: P 330 ARG cc_start: 0.8918 (mmt90) cc_final: 0.8512 (mmm-85) REVERT: Q 164 TYR cc_start: 0.6900 (m-80) cc_final: 0.6111 (m-80) REVERT: Q 169 GLU cc_start: 0.8907 (mp0) cc_final: 0.8511 (pm20) REVERT: Q 187 LYS cc_start: 0.8129 (tppt) cc_final: 0.7636 (pttm) REVERT: Q 217 TRP cc_start: 0.7859 (m100) cc_final: 0.7527 (m100) REVERT: Q 261 LYS cc_start: 0.8353 (mmtp) cc_final: 0.7455 (tmtt) REVERT: Q 369 GLU cc_start: 0.8686 (tp30) cc_final: 0.8224 (tp30) REVERT: R 43 ARG cc_start: 0.7659 (tpp80) cc_final: 0.7358 (tpp80) REVERT: R 155 HIS cc_start: 0.7730 (m-70) cc_final: 0.7336 (m170) REVERT: R 164 TYR cc_start: 0.5076 (m-80) cc_final: 0.4576 (m-80) REVERT: R 168 MET cc_start: 0.7462 (tmm) cc_final: 0.6835 (tmm) REVERT: S 163 ASN cc_start: 0.8154 (m-40) cc_final: 0.7544 (m-40) REVERT: S 164 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.6725 (m-80) REVERT: S 194 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7647 (ttm170) REVERT: S 309 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.7985 (m-40) REVERT: T 96 ARG cc_start: 0.7667 (mtt90) cc_final: 0.6996 (mtt90) REVERT: T 169 GLU cc_start: 0.8588 (mp0) cc_final: 0.8049 (mp0) REVERT: T 188 ARG cc_start: 0.7350 (tpp80) cc_final: 0.6643 (tpt-90) REVERT: T 257 MET cc_start: 0.8944 (mmt) cc_final: 0.8499 (mmt) REVERT: B 196 ILE cc_start: 0.5570 (mm) cc_final: 0.5270 (tp) REVERT: B 603 LYS cc_start: 0.8175 (mtmt) cc_final: 0.7079 (tppt) REVERT: B 695 ARG cc_start: 0.6154 (ttm170) cc_final: 0.5657 (ttp-110) outliers start: 74 outliers final: 56 residues processed: 493 average time/residue: 0.2336 time to fit residues: 190.2399 Evaluate side-chains 472 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 407 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 282 HIS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 454 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain L residue 687 ILE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 364 LEU Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 459 GLU Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 117 LYS Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 401 LEU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 240 SER Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 205 TRP Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain Q residue 242 HIS Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 370 GLU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 282 HIS Chi-restraints excluded: chain S residue 99 GLN Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 194 ARG Chi-restraints excluded: chain S residue 309 ASN Chi-restraints excluded: chain S residue 361 PHE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 687 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 485 optimal weight: 0.0870 chunk 373 optimal weight: 2.9990 chunk 418 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 500 optimal weight: 6.9990 chunk 451 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 498 optimal weight: 0.4980 chunk 423 optimal weight: 8.9990 chunk 434 optimal weight: 7.9990 overall best weight: 1.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 HIS ** Q 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 99 GLN B 661 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.134224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.087975 restraints weight = 93740.479| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.46 r_work: 0.3043 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 43918 Z= 0.147 Angle : 0.560 13.429 60011 Z= 0.286 Chirality : 0.045 0.223 7171 Planarity : 0.004 0.068 7779 Dihedral : 4.066 29.135 6420 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.29 % Favored : 93.66 % Rotamer: Outliers : 1.82 % Allowed : 18.30 % Favored : 79.87 % 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: -0.19 (0.11), residues: 6007 helix: 1.61 (0.12), residues: 2210 sheet: -1.05 (0.19), residues: 772 loop : -1.21 (0.11), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG O 268 TYR 0.035 0.001 TYR S 94 PHE 0.018 0.001 PHE S 32 TRP 0.056 0.001 TRP B 584 HIS 0.010 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00356 (43918) covalent geometry : angle 0.56017 (60011) hydrogen bonds : bond 0.03183 ( 1736) hydrogen bonds : angle 4.49322 ( 4929) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12014 Ramachandran restraints generated. 6007 Oldfield, 0 Emsley, 6007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 414 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 69 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8373 (mt0) REVERT: D 98 GLU cc_start: 0.8506 (tt0) cc_final: 0.7962 (tm-30) REVERT: D 293 TRP cc_start: 0.6894 (t60) cc_final: 0.6622 (t60) REVERT: J 119 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8054 (pt0) REVERT: J 129 GLU cc_start: 0.8316 (tp30) cc_final: 0.7916 (tm-30) REVERT: L 105 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8403 (mm-30) REVERT: L 670 HIS cc_start: 0.6968 (OUTLIER) cc_final: 0.6735 (p-80) REVERT: M 364 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8645 (mp) REVERT: M 370 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8834 (mp) REVERT: M 459 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: N 117 LYS cc_start: 0.8247 (mttt) cc_final: 0.7905 (tttm) REVERT: O 41 ASP cc_start: 0.7959 (t0) cc_final: 0.7696 (t0) REVERT: P 94 TYR cc_start: 0.8582 (t80) cc_final: 0.8098 (t80) REVERT: P 292 GLN cc_start: 0.9121 (tt0) cc_final: 0.8920 (tp40) REVERT: P 316 MET cc_start: 0.9147 (ttp) cc_final: 0.8867 (ttm) REVERT: P 330 ARG cc_start: 0.8932 (mmt90) cc_final: 0.8477 (mmm-85) REVERT: Q 169 GLU cc_start: 0.8870 (mp0) cc_final: 0.8381 (pm20) REVERT: Q 187 LYS cc_start: 0.8127 (tppt) cc_final: 0.7597 (pttm) REVERT: Q 210 LYS cc_start: 0.7898 (mmmt) cc_final: 0.7494 (mtpp) REVERT: Q 217 TRP cc_start: 0.7893 (m100) cc_final: 0.7609 (m100) REVERT: Q 261 LYS cc_start: 0.8304 (mmtp) cc_final: 0.7385 (tmtt) REVERT: R 43 ARG cc_start: 0.7696 (tpp80) cc_final: 0.7412 (tpp80) REVERT: R 155 HIS cc_start: 0.7746 (m-70) cc_final: 0.7372 (m170) REVERT: R 164 TYR cc_start: 0.5179 (m-80) cc_final: 0.4737 (m-80) REVERT: R 335 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8136 (mttt) REVERT: S 163 ASN cc_start: 0.8124 (m-40) cc_final: 0.7537 (m-40) REVERT: S 164 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.6679 (m-80) REVERT: S 194 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7644 (ttm170) REVERT: S 309 ASN cc_start: 0.8321 (m110) cc_final: 0.7981 (m-40) REVERT: T 96 ARG cc_start: 0.7706 (mtt90) cc_final: 0.6975 (mtt90) REVERT: T 169 GLU cc_start: 0.8669 (mp0) cc_final: 0.7816 (mp0) REVERT: T 257 MET cc_start: 0.8918 (mmt) cc_final: 0.8468 (mmt) REVERT: B 182 GLN cc_start: 0.5780 (mm-40) cc_final: 0.5313 (mm-40) REVERT: B 196 ILE cc_start: 0.5489 (mm) cc_final: 0.5191 (tp) REVERT: B 603 LYS cc_start: 0.8148 (mtmt) cc_final: 0.7086 (tppt) REVERT: B 695 ARG cc_start: 0.6167 (ttm170) cc_final: 0.5696 (ttp-110) outliers start: 72 outliers final: 59 residues processed: 469 average time/residue: 0.2420 time to fit residues: 189.1679 Evaluate side-chains 471 residues out of total 5378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 404 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 THR Chi-restraints excluded: chain D residue 69 GLN Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 177 VAL Chi-restraints excluded: chain J residue 206 SER Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 282 HIS Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 130 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 454 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain L residue 687 ILE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 122 THR Chi-restraints excluded: chain M residue 196 ILE Chi-restraints excluded: chain M residue 285 ILE Chi-restraints excluded: chain M residue 364 LEU Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain M residue 459 GLU Chi-restraints excluded: chain M residue 503 SER Chi-restraints excluded: chain M residue 562 THR Chi-restraints excluded: chain M residue 687 ILE Chi-restraints excluded: chain N residue 146 VAL Chi-restraints excluded: chain N residue 401 LEU Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain O residue 113 THR Chi-restraints excluded: chain O residue 145 SER Chi-restraints excluded: chain O residue 554 GLU Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain P residue 92 LEU Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 157 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 205 TRP Chi-restraints excluded: chain Q residue 214 SER Chi-restraints excluded: chain Q residue 242 HIS Chi-restraints excluded: chain Q residue 255 VAL Chi-restraints excluded: chain Q residue 370 GLU Chi-restraints excluded: chain R residue 90 ASP Chi-restraints excluded: chain R residue 115 ILE Chi-restraints excluded: chain R residue 172 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 264 LEU Chi-restraints excluded: chain R residue 282 HIS Chi-restraints excluded: chain R residue 335 LYS Chi-restraints excluded: chain S residue 99 GLN Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 164 TYR Chi-restraints excluded: chain S residue 184 VAL Chi-restraints excluded: chain S residue 194 ARG Chi-restraints excluded: chain S residue 361 PHE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 597 LEU Chi-restraints excluded: chain B residue 687 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 604 random chunks: chunk 304 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 503 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 435 optimal weight: 5.9990 chunk 452 optimal weight: 0.9980 chunk 324 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 428 optimal weight: 20.0000 chunk 241 optimal weight: 0.2980 chunk 323 optimal weight: 0.0030 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 131 ASN ** Q 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 99 GLN B 162 HIS ** B 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 661 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.133854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.089155 restraints weight = 93690.757| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 3.63 r_work: 0.3046 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.5679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 43918 Z= 0.121 Angle : 0.551 13.364 60011 Z= 0.281 Chirality : 0.044 0.229 7171 Planarity : 0.004 0.067 7779 Dihedral : 4.009 28.929 6420 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.91 % Favored : 94.06 % Rotamer: Outliers : 2.05 % Allowed : 18.23 % Favored : 79.72 % 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: -0.14 (0.11), residues: 6007 helix: 1.63 (0.12), residues: 2209 sheet: -0.96 (0.19), residues: 775 loop : -1.19 (0.11), residues: 3023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG O 268 TYR 0.020 0.001 TYR J 276 PHE 0.024 0.001 PHE Q 367 TRP 0.065 0.001 TRP B 584 HIS 0.010 0.001 HIS J 239 Details of bonding type rmsd covalent geometry : bond 0.00289 (43918) covalent geometry : angle 0.55094 (60011) hydrogen bonds : bond 0.03005 ( 1736) hydrogen bonds : angle 4.44183 ( 4929) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12665.11 seconds wall clock time: 216 minutes 19.44 seconds (12979.44 seconds total)