Starting phenix.real_space_refine on Tue Aug 26 20:57:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woc_37682/08_2025/8woc_37682.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woc_37682/08_2025/8woc_37682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8woc_37682/08_2025/8woc_37682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woc_37682/08_2025/8woc_37682.map" model { file = "/net/cci-nas-00/data/ceres_data/8woc_37682/08_2025/8woc_37682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woc_37682/08_2025/8woc_37682.cif" } resolution = 3.28 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= 0.059 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 88 5.16 5 C 26248 2.51 5 N 7138 2.21 5 O 7746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41220 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2434 Classifications: {'peptide': 354} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 15, 'TRANS': 338} Chain breaks: 2 Unresolved non-hydrogen bonds: 280 Unresolved non-hydrogen angles: 345 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'ASP:plan': 8, 'GLN:plan1': 4, 'GLU:plan': 9, 'TYR:plan': 3, 'HIS:plan': 3, 'ARG:plan': 8, 'ASN:plan1': 2, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 170 Chain: "D" Number of atoms: 4082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 554, 4082 Classifications: {'peptide': 554} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 26, 'TRANS': 527} Chain breaks: 2 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 303 Unresolved non-hydrogen dihedrals: 198 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, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 151 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: 4958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 4958 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 83} Link IDs: {'PTRANS': 30, 'TRANS': 641} Chain breaks: 1 Unresolved non-hydrogen bonds: 330 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 273 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 15, '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: 212 Chain: "N" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 3632 Classifications: {'peptide': 613} Incomplete info: {'truncation_to_alanine': 327} Link IDs: {'PTRANS': 25, 'TRANS': 587} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1237 Unresolved non-hydrogen angles: 1572 Unresolved non-hydrogen dihedrals: 1023 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'GLN:plan1': 14, 'ASN:plan1': 22, 'ASP:plan': 29, 'PHE:plan': 18, 'TYR:plan': 13, 'ARG:plan': 26, 'TRP:plan': 5, 'GLU:plan': 37, 'HIS:plan': 5} Unresolved non-hydrogen planarities: 756 Chain: "O" Number of atoms: 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: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1823 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 12, 'TRANS': 244} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 267 Unresolved non-hydrogen angles: 331 Unresolved non-hydrogen dihedrals: 217 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'TYR:plan': 3, 'ASP:plan': 8, 'GLU:plan': 10, 'ASN:plan1': 5, 'ARG:plan': 4, 'PHE:plan': 2, 'GLN:plan1': 6} Unresolved non-hydrogen planarities: 156 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 Time building chain proxies: 10.19, per 1000 atoms: 0.25 Number of scatterers: 41220 At special positions: 0 Unit cell: (142.429, 184.96, 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 88 16.00 O 7746 8.00 N 7138 7.00 C 26248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10868 Finding SS restraints... Secondary structure from input PDB file: 233 helices and 40 sheets defined 40.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 76 through 83 removed outlier: 3.805A pdb=" N GLU A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'A' and resid 155 through 161 removed outlier: 3.719A pdb=" N VAL A 159 " --> pdb=" O ILE A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 172 through 185 Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 423 through 442 removed outlier: 3.654A pdb=" N GLY A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 464 Processing helix chain 'A' and resid 472 through 488 removed outlier: 4.760A pdb=" N ARG A 485 " --> pdb=" O VAL A 481 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS A 486 " --> pdb=" O LYS A 482 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 487 " --> pdb=" O GLU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 502 through 507 Processing helix chain 'A' and resid 519 through 528 removed outlier: 3.789A pdb=" N ARG A 523 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 539 removed outlier: 4.375A pdb=" N GLY A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 544 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: 3.555A pdb=" N THR D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 233 Processing helix chain 'D' and resid 234 through 242 Processing helix chain 'D' and resid 248 through 269 removed outlier: 4.077A pdb=" N ASN D 252 " --> pdb=" O GLY D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 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: 3.807A pdb=" N LEU D 400 " --> pdb=" O ASP D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 423 through 442 removed outlier: 3.871A pdb=" N SER D 442 " --> pdb=" O SER D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 464 Processing helix chain 'D' and resid 472 through 488 removed outlier: 5.459A pdb=" N ARG D 485 " --> pdb=" O VAL D 481 " (cutoff:3.500A) removed outlier: 6.340A 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: 3.715A 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: 3.748A pdb=" N HIS J 21 " --> pdb=" O SER J 17 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL J 22 " --> pdb=" O LEU J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 41 removed outlier: 3.679A pdb=" N VAL J 40 " --> pdb=" O ALA J 36 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER J 41 " --> pdb=" O GLY J 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 36 through 41' Processing helix chain 'J' and resid 52 through 63 removed outlier: 3.512A pdb=" N SER J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 83 Processing helix chain 'J' and resid 87 through 101 removed outlier: 3.509A pdb=" N ILE J 101 " --> pdb=" O LEU J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 104 through 108 Processing helix chain 'J' and resid 113 through 131 Processing helix chain 'J' and resid 139 through 151 removed outlier: 3.747A pdb=" N LYS J 143 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 166 through 175 removed outlier: 3.511A pdb=" N LEU J 175 " --> pdb=" O ALA J 171 " (cutoff:3.500A) Processing helix chain 'J' and resid 193 through 199 removed outlier: 3.839A pdb=" N GLU J 197 " --> pdb=" O ILE J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 266 removed outlier: 3.748A pdb=" N VAL J 255 " --> pdb=" O MET J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 294 Processing helix chain 'J' and resid 306 through 309 Processing helix chain 'J' and resid 310 through 320 Processing helix chain 'J' and resid 360 through 373 Processing helix chain 'K' and resid 12 through 25 Processing helix chain 'K' and resid 36 through 42 Processing helix chain 'K' and resid 52 through 63 removed outlier: 3.510A pdb=" N SER K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 83 removed outlier: 4.383A pdb=" N THR K 82 " --> pdb=" O ASN K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 87 through 101 removed outlier: 3.552A pdb=" N ILE K 101 " --> pdb=" O LEU K 97 " (cutoff:3.500A) Processing helix chain 'K' and resid 113 through 131 removed outlier: 3.559A pdb=" N ALA K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 150 removed outlier: 3.738A pdb=" N LYS K 143 " --> pdb=" O THR K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 174 Processing helix chain 'K' and resid 193 through 199 removed outlier: 3.967A pdb=" N GLU K 197 " --> pdb=" O ILE K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 266 Processing helix chain 'K' and resid 280 through 294 Processing helix chain 'K' and resid 306 through 309 Processing helix chain 'K' and resid 310 through 320 Processing helix chain 'K' and resid 360 through 373 Processing helix chain 'L' and resid 78 through 83 Processing helix chain 'L' and resid 122 through 130 Processing helix chain 'L' and resid 155 through 161 Processing helix chain 'L' and resid 168 through 171 Processing helix chain 'L' and resid 172 through 185 Processing helix chain 'L' and resid 229 through 233 Processing helix chain 'L' and resid 234 through 243 Processing helix chain 'L' and resid 248 through 269 removed outlier: 3.939A pdb=" N ASN L 252 " --> pdb=" O GLY L 248 " (cutoff:3.500A) Processing helix chain 'L' and resid 288 through 302 removed outlier: 3.559A pdb=" N LEU L 292 " --> pdb=" O SER L 288 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU L 300 " --> pdb=" O LEU L 296 " (cutoff:3.500A) removed outlier: 3.641A 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: 6.597A 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: 4.026A pdb=" N GLY L 539 " --> pdb=" O GLU L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 544 removed outlier: 3.639A pdb=" N LEU L 544 " --> pdb=" O LEU L 541 " (cutoff:3.500A) Processing helix chain 'L' and resid 579 through 586 removed outlier: 3.591A pdb=" N ASN L 586 " --> pdb=" O ALA L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 592 through 603 removed outlier: 4.144A pdb=" N VAL L 596 " --> pdb=" O ASP L 592 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 676 removed outlier: 3.654A pdb=" N HIS L 670 " --> pdb=" O PRO L 666 " (cutoff:3.500A) Processing helix chain 'L' and resid 680 through 687 Processing helix chain 'M' and resid 76 through 83 removed outlier: 3.953A 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: 3.617A 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: 3.902A pdb=" N LEU M 400 " --> pdb=" O ASP M 396 " (cutoff:3.500A) Processing helix chain 'M' and resid 420 through 422 No H-bonds generated for 'chain 'M' and resid 420 through 422' Processing helix chain 'M' and resid 423 through 442 removed outlier: 3.798A pdb=" N SER M 442 " --> pdb=" O SER M 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 464 removed outlier: 3.527A pdb=" N TYR M 464 " --> pdb=" O ALA M 461 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 461 through 464' Processing helix chain 'M' and resid 472 through 484 Processing helix chain 'M' and resid 502 through 508 removed outlier: 3.564A pdb=" N GLN M 508 " --> pdb=" O THR M 504 " (cutoff:3.500A) Processing helix chain 'M' and resid 519 through 529 removed outlier: 3.822A pdb=" N ARG M 523 " --> pdb=" O ASN M 519 " (cutoff:3.500A) Processing helix chain 'M' and resid 534 through 539 Processing helix chain 'M' and resid 540 through 544 removed outlier: 3.619A pdb=" N LEU M 544 " --> pdb=" O LEU M 541 " (cutoff:3.500A) Processing helix chain 'M' and resid 579 through 586 removed outlier: 3.556A pdb=" N ASN M 586 " --> pdb=" O ALA M 582 " (cutoff:3.500A) Processing helix chain 'M' and resid 592 through 603 removed outlier: 4.288A pdb=" N VAL M 596 " --> pdb=" O ASP M 592 " (cutoff:3.500A) Processing helix chain 'M' and resid 666 through 675 removed outlier: 3.647A pdb=" N HIS M 670 " --> pdb=" O PRO M 666 " (cutoff:3.500A) Processing helix chain 'M' and resid 681 through 687 Processing helix chain 'N' and resid 122 through 130 Processing helix chain 'N' and resid 155 through 161 Processing helix chain 'N' and resid 168 through 171 Processing helix chain 'N' and resid 172 through 185 Processing helix chain 'N' and resid 229 through 233 removed outlier: 3.528A pdb=" N ALA N 232 " --> pdb=" O PRO N 229 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 242 Processing helix chain 'N' and resid 248 through 269 Processing helix chain 'N' and resid 289 through 299 Processing helix chain 'N' and resid 360 through 373 Processing helix chain 'N' and resid 376 through 381 Processing helix chain 'N' and resid 396 through 406 removed outlier: 3.583A pdb=" N LEU N 400 " --> pdb=" O ASP N 396 " (cutoff:3.500A) Processing helix chain 'N' and resid 423 through 442 removed outlier: 3.509A pdb=" N SER N 442 " --> pdb=" O SER N 438 " (cutoff:3.500A) Processing helix chain 'N' and resid 461 through 464 Processing helix chain 'N' and resid 471 through 488 removed outlier: 4.069A pdb=" N ASP N 475 " --> pdb=" O GLY N 471 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ARG N 485 " --> pdb=" O VAL N 481 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS N 486 " --> pdb=" O LYS N 482 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR N 487 " --> pdb=" O GLU N 483 " (cutoff:3.500A) Processing helix chain 'N' and resid 497 through 501 Processing helix chain 'N' and resid 502 through 508 Processing helix chain 'N' and resid 519 through 528 removed outlier: 3.581A pdb=" N ARG N 523 " --> pdb=" O ASN N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 534 through 539 Processing helix chain 'N' and resid 540 through 544 removed outlier: 3.643A pdb=" N THR N 543 " --> pdb=" O MET N 540 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU N 544 " --> pdb=" O LEU N 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 540 through 544' Processing helix chain 'N' and resid 579 through 586 removed outlier: 3.998A pdb=" N ASN N 586 " --> pdb=" O ALA N 582 " (cutoff:3.500A) Processing helix chain 'N' and resid 592 through 603 removed outlier: 4.134A pdb=" N VAL N 596 " --> pdb=" O ASP N 592 " (cutoff:3.500A) Processing helix chain 'N' and resid 666 through 676 removed outlier: 3.650A pdb=" N HIS N 670 " --> pdb=" O PRO N 666 " (cutoff:3.500A) Processing helix chain 'N' and resid 681 through 687 Processing helix chain 'O' and resid 73 through 75 No H-bonds generated for 'chain 'O' and resid 73 through 75' Processing helix chain 'O' and resid 78 through 83 Processing helix chain 'O' and resid 122 through 130 Processing helix chain 'O' and resid 155 through 161 Processing helix chain 'O' and resid 168 through 171 Processing helix chain 'O' and resid 172 through 185 removed outlier: 3.520A 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: 3.789A pdb=" N LEU O 292 " --> pdb=" O SER O 288 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU O 300 " --> pdb=" O LEU O 296 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE O 301 " --> pdb=" O TYR O 297 " (cutoff:3.500A) removed outlier: 3.543A 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: 3.783A pdb=" N SER O 442 " --> pdb=" O SER O 438 " (cutoff:3.500A) Processing helix chain 'O' and resid 472 through 488 removed outlier: 5.435A 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: 3.895A pdb=" N GLY O 539 " --> pdb=" O GLU O 535 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 544 removed outlier: 3.568A pdb=" N LEU O 544 " --> pdb=" O LEU O 541 " (cutoff:3.500A) Processing helix chain 'O' and resid 579 through 586 removed outlier: 3.616A pdb=" N ASN O 586 " --> pdb=" O ALA O 582 " (cutoff:3.500A) Processing helix chain 'O' and resid 592 through 603 removed outlier: 3.969A pdb=" N VAL O 596 " --> pdb=" O ASP O 592 " (cutoff:3.500A) Processing helix chain 'O' and resid 666 through 676 removed outlier: 3.806A 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: 3.598A pdb=" N GLN P 15 " --> pdb=" O ASP P 11 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU P 25 " --> pdb=" O HIS P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 41 removed outlier: 3.976A pdb=" N VAL P 40 " --> pdb=" O ALA P 36 " (cutoff:3.500A) removed outlier: 3.847A 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: 4.349A pdb=" N ILE P 76 " --> pdb=" O LEU P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 101 Processing helix chain 'P' and resid 113 through 131 removed outlier: 3.558A pdb=" N ALA P 117 " --> pdb=" O SER P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 151 removed outlier: 4.024A pdb=" N ILE P 151 " --> pdb=" O TRP P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 175 Processing helix chain 'P' and resid 193 through 199 removed outlier: 3.708A pdb=" N GLU P 197 " --> pdb=" O ILE P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 265 Processing helix chain 'P' and resid 281 through 294 Processing helix chain 'P' and resid 306 through 309 Processing helix chain 'P' and resid 310 through 320 Processing helix chain 'P' and resid 356 through 359 Processing helix chain 'P' and resid 360 through 373 Processing helix chain '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 139 through 151 removed outlier: 3.685A pdb=" N ASN Q 149 " --> pdb=" O ALA Q 145 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE Q 151 " --> pdb=" O TRP Q 147 " (cutoff:3.500A) Processing helix chain 'Q' and resid 166 through 175 removed outlier: 3.656A 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: 3.525A 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: 3.621A 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: 3.643A pdb=" N LEU R 175 " --> pdb=" O ALA R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 199 removed outlier: 3.756A pdb=" N ASN R 199 " --> pdb=" O THR R 195 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 265 Processing helix chain 'R' and resid 281 through 294 Processing helix chain 'R' and resid 306 through 309 Processing helix chain 'R' and resid 310 through 320 Processing helix chain 'R' and resid 356 through 359 removed outlier: 3.650A pdb=" N GLY R 359 " --> pdb=" O PHE R 356 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 356 through 359' Processing helix chain 'R' and resid 360 through 373 removed outlier: 3.888A 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: 3.858A pdb=" N ILE S 107 " --> pdb=" O SER S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 113 through 131 Processing helix chain 'S' and resid 139 through 151 removed outlier: 3.607A 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: 4.189A pdb=" N GLU S 197 " --> pdb=" O ILE S 193 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN S 199 " --> pdb=" O THR S 195 " (cutoff:3.500A) Processing helix chain 'S' and resid 251 through 265 Processing helix chain 'S' and resid 280 through 294 removed outlier: 3.941A 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: 3.861A pdb=" N GLN T 15 " --> pdb=" O ASP T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 38 through 42 Processing helix chain 'T' and resid 52 through 64 Processing helix chain 'T' and resid 69 through 83 removed outlier: 4.151A pdb=" N ILE T 75 " --> pdb=" O LEU T 71 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE T 76 " --> pdb=" O LEU T 72 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR T 82 " --> pdb=" O ASN T 78 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 101 removed outlier: 3.514A pdb=" N ILE T 101 " --> pdb=" O LEU T 97 " (cutoff:3.500A) Processing helix chain 'T' and resid 115 through 131 Processing helix chain 'T' and resid 139 through 149 removed outlier: 3.555A 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: 3.760A pdb=" N GLU T 197 " --> pdb=" O ILE T 193 " (cutoff:3.500A) Processing helix chain 'T' and resid 252 through 265 Processing helix chain 'T' and resid 281 through 294 Processing helix chain 'T' and resid 306 through 309 Processing helix chain 'T' and resid 310 through 320 Processing helix chain 'T' and resid 356 through 359 removed outlier: 3.638A 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: 3.711A pdb=" N GLN T 373 " --> pdb=" O GLU T 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 20 removed outlier: 3.573A pdb=" N THR A 16 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A 26 " --> pdb=" O GLN A 18 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 25 through 28 current: chain 'A' and resid 61 through 70 removed outlier: 7.206A pdb=" N ASN A 62 " --> pdb=" O GLU A 97 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLU A 97 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N PHE A 64 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N SER A 91 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N VAL A 70 " --> pdb=" O TRP A 89 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N TRP A 89 " --> pdb=" O VAL A 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 104 through 106 current: chain 'D' and resid 25 through 29 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 25 through 29 current: chain 'D' and resid 61 through 71 removed outlier: 7.068A pdb=" N ASN D 62 " --> pdb=" O GLU D 97 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLU D 97 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N PHE D 64 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER D 91 " --> pdb=" O SER D 68 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL D 70 " --> pdb=" O TRP D 89 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N TRP D 89 " --> pdb=" O VAL D 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 104 through 106 current: chain 'L' and resid 25 through 29 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 25 through 29 current: chain 'L' and resid 61 through 71 removed outlier: 6.990A pdb=" N ASN L 62 " --> pdb=" O GLU L 97 " (cutoff:3.500A) removed outlier: 4.818A 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: 5.137A pdb=" N VAL L 70 " --> pdb=" O TRP L 89 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N TRP L 89 " --> pdb=" O VAL L 70 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 104 through 106 current: chain 'M' and resid 24 through 29 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 24 through 29 current: chain 'M' and resid 61 through 71 removed outlier: 6.898A pdb=" N LEU M 63 " --> pdb=" O GLU M 97 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU M 97 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N GLY M 65 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL M 95 " --> pdb=" O GLY M 65 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N VAL M 67 " --> pdb=" O GLN M 93 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N GLN M 93 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN M 69 " --> pdb=" O SER M 91 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TRP M 89 " --> pdb=" O GLY M 71 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 104 through 106 current: chain 'N' and resid 24 through 28 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 24 through 28 current: chain 'N' and resid 61 through 71 removed outlier: 6.874A pdb=" N LEU N 63 " --> pdb=" O GLU N 97 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLU N 97 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLY N 65 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL N 95 " --> pdb=" O GLY N 65 " (cutoff:3.500A) removed outlier: 5.194A 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) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 104 through 106 current: chain 'O' and resid 25 through 29 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 25 through 29 current: chain 'O' and resid 61 through 71 removed outlier: 7.202A pdb=" N ASN O 62 " --> pdb=" O GLU O 97 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLU O 97 " --> pdb=" O ASN O 62 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N PHE O 64 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL O 95 " --> pdb=" O PHE O 64 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER O 91 " --> pdb=" O SER O 68 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N VAL O 70 " --> pdb=" O TRP O 89 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N TRP O 89 " --> pdb=" O VAL O 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 154 removed outlier: 6.442A pdb=" N ALA A 151 " --> pdb=" O LEU A 140 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA A 164 " --> pdb=" O PHE A 513 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ILE A 195 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N PHE A 414 " --> pdb=" O ILE A 195 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL A 197 " --> pdb=" O PHE A 414 " (cutoff:3.500A) Processing sheet with id=AA3, 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: 7.041A pdb=" N ALA D 164 " --> pdb=" O PHE D 513 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 493 " --> pdb=" O SER D 163 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 456 " --> pdb=" O MET D 492 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N VAL D 494 " --> pdb=" O VAL D 456 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU D 458 " --> pdb=" O VAL D 494 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU D 459 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE D 195 " --> pdb=" O SER D 412 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE D 414 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL D 197 " --> pdb=" O PHE D 414 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N LEU D 224 " --> pdb=" O ALA D 212 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL D 214 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AA5, 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: 6.036A 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: 7.831A 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=AA6, first strand: chain 'J' and resid 43 through 44 Processing sheet with id=AA7, 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=AA8, first strand: chain 'J' and resid 324 through 326 Processing sheet with id=AA9, first strand: chain 'K' and resid 33 through 34 removed outlier: 5.939A 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=AB1, first strand: chain 'K' and resid 43 through 44 Processing sheet with id=AB2, first strand: chain 'K' and resid 183 through 184 removed outlier: 3.748A 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=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 270 through 273 removed outlier: 7.467A 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: 7.360A pdb=" N THR K 273 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ILE K 299 " --> pdb=" O ILE K 324 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N LEU K 326 " --> pdb=" O ILE K 299 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N GLY K 301 " --> pdb=" O LEU K 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.891A pdb=" N TYR L 45 " --> pdb=" O LYS L 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 150 through 153 removed outlier: 6.742A pdb=" N ALA L 151 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET L 560 " --> pdb=" O ILE L 551 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA L 514 " --> pdb=" O ILE L 550 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N ALA L 164 " --> pdb=" O PHE L 513 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL L 456 " --> pdb=" O MET L 492 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N VAL L 494 " --> pdb=" O VAL L 456 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU L 458 " --> pdb=" O VAL L 494 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU L 459 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ILE L 195 " --> pdb=" O SER L 412 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N PHE L 414 " --> pdb=" O ILE L 195 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL L 197 " --> pdb=" O PHE L 414 " (cutoff:3.500A) removed outlier: 8.148A 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=AB6, first strand: chain 'L' and resid 303 through 304 Processing sheet with id=AB7, 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=AB8, 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: 6.657A 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: 7.332A pdb=" N ASP M 415 " --> pdb=" O LYS M 213 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR M 215 " --> pdb=" O ASP M 415 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LEU M 224 " --> pdb=" O ALA M 212 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL M 214 " --> pdb=" O LEU M 224 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 638 through 642 removed outlier: 3.564A pdb=" N SER M 640 " --> pdb=" O GLU M 653 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE M 652 " --> pdb=" O TYR M 660 " (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: 6.532A pdb=" N ALA N 151 " --> pdb=" O LEU N 140 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN N 142 " --> pdb=" O ILE N 563 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 224 through 225 removed outlier: 8.108A pdb=" N LEU N 224 " --> pdb=" O ALA N 212 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL N 214 " --> pdb=" O LEU N 224 " (cutoff:3.500A) removed outlier: 5.500A 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: 6.495A pdb=" N LEU N 454 " --> pdb=" O GLY N 490 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N MET N 492 " --> pdb=" O LEU N 454 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N VAL N 456 " --> pdb=" O MET N 492 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N VAL N 494 " --> pdb=" O VAL N 456 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU N 458 " --> pdb=" O VAL N 494 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ALA N 164 " --> pdb=" O PHE N 513 " (cutoff:3.500A) Processing sheet with id=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: 3.581A pdb=" N GLU O 459 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE O 195 " --> pdb=" O SER O 412 " (cutoff:3.500A) removed outlier: 7.860A 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: 3.620A 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: 3.748A 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: 4.196A 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: 3.602A pdb=" N ILE P 332 " --> pdb=" O LEU P 325 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA P 31 " --> pdb=" O ILE P 272 " (cutoff:3.500A) removed outlier: 8.312A 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: 6.498A 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: 7.588A pdb=" N LEU Q 302 " --> pdb=" O LEU Q 271 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N THR Q 273 " --> pdb=" O LEU Q 302 " (cutoff:3.500A) removed outlier: 6.069A 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: 6.757A pdb=" N ILE Q 30 " --> pdb=" O GLU Q 158 " (cutoff:3.500A) removed outlier: 8.286A 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: 6.018A 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: 3.620A 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: 7.951A pdb=" N PHE S 160 " --> pdb=" O ILE S 30 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE S 32 " --> pdb=" O PHE S 160 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA S 31 " --> pdb=" O ILE S 272 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS S 274 " --> pdb=" O ALA S 31 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ILE S 33 " --> pdb=" O CYS S 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=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: 3.896A pdb=" N VAL S 184 " --> pdb=" O PHE S 190 " (cutoff:3.500A) removed outlier: 3.739A 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: 3.686A pdb=" N ALA T 331 " --> pdb=" O GLY T 338 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ILE T 33 " --> pdb=" O CYS T 274 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE T 32 " --> pdb=" O PHE T 160 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU T 208 " --> pdb=" O PHE T 180 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 217 through 219 1632 hydrogen bonds defined for protein. 4626 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: 9.17 Time building geometry restraints manager: 3.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 13782 1.34 - 1.46: 8658 1.46 - 1.58: 19408 1.58 - 1.70: 0 1.70 - 1.82: 146 Bond restraints: 41994 Sorted by residual: bond pdb=" N GLY N 680 " pdb=" CA GLY N 680 " ideal model delta sigma weight residual 1.447 1.476 -0.029 1.03e-02 9.43e+03 7.77e+00 bond pdb=" N GLU N 677 " pdb=" CA GLU N 677 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.91e+00 bond pdb=" N LYS N 681 " pdb=" CA LYS N 681 " ideal model delta sigma weight residual 1.457 1.489 -0.031 1.29e-02 6.01e+03 5.85e+00 bond pdb=" N SER N 678 " pdb=" CA SER N 678 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.29e-02 6.01e+03 4.96e+00 bond pdb=" C MET S 251 " pdb=" N PRO S 252 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.27e+00 ... (remaining 41989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 56048 1.41 - 2.83: 1046 2.83 - 4.24: 234 4.24 - 5.65: 52 5.65 - 7.07: 16 Bond angle restraints: 57396 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 116.63 110.54 6.09 1.16e+00 7.43e-01 2.75e+01 angle pdb=" C GLU P 111 " pdb=" CA GLU P 111 " pdb=" CB GLU P 111 " ideal model delta sigma weight residual 115.79 109.89 5.90 1.19e+00 7.06e-01 2.46e+01 angle pdb=" N VAL M 217 " pdb=" CA VAL M 217 " pdb=" C VAL M 217 " ideal model delta sigma weight residual 112.96 108.48 4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" N ILE T 115 " pdb=" CA ILE T 115 " pdb=" C ILE T 115 " ideal model delta sigma weight residual 111.90 108.56 3.34 8.10e-01 1.52e+00 1.70e+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 57391 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 23262 17.84 - 35.67: 1424 35.67 - 53.51: 211 53.51 - 71.35: 49 71.35 - 89.19: 14 Dihedral angle restraints: 24960 sinusoidal: 8127 harmonic: 16833 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 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+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 180.00 154.38 25.62 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ILE N 34 " pdb=" C ILE N 34 " pdb=" N SER N 35 " pdb=" CA SER N 35 " ideal model delta harmonic sigma weight residual 180.00 154.76 25.24 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 24957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 4552 0.036 - 0.071: 1596 0.071 - 0.107: 540 0.107 - 0.143: 185 0.143 - 0.178: 9 Chirality restraints: 6882 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 7.96e-01 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.18e-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 7.10e-01 ... (remaining 6879 not shown) Planarity restraints: 7436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE T 83 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+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 4.00e+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 delta sigma weight rms_deltas residual plane pdb=" C VAL L 75 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO L 76 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO L 76 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 76 " -0.023 5.00e-02 4.00e+02 ... (remaining 7433 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 206 2.53 - 3.12: 31561 3.12 - 3.71: 61225 3.71 - 4.31: 78086 4.31 - 4.90: 135558 Nonbonded interactions: 306636 Sorted by model distance: nonbonded pdb=" OD2 ASP M 396 " pdb=" NH2 ARG N 601 " model vdw 1.937 3.120 nonbonded pdb=" OD1 ASP M 396 " pdb=" NH2 ARG N 601 " model vdw 2.039 3.120 nonbonded pdb=" OD1 ASN M 154 " pdb=" OD1 ASP M 156 " model vdw 2.046 3.040 nonbonded pdb=" OE2 GLU A 483 " pdb=" OG SER D 421 " model vdw 2.054 3.040 nonbonded pdb=" CG ASP M 396 " pdb=" NH2 ARG N 601 " model vdw 2.162 3.350 ... (remaining 306631 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 15 or (resid 16 through 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 or (resid 20 through 21 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 22 through 25 and (name N or na \ me CA or name C or name O or name CB )) or resid 26 through 28 or (resid 29 thro \ ugh 47 and (name N or name CA or name C or name O or name CB )) or resid 48 thro \ ugh 51 or (resid 52 and (name N or name CA or name C or name O or name CB )) or \ resid 53 or (resid 54 through 56 and (name N or name CA or name C or name O or n \ ame CB )) or resid 57 or (resid 58 and (name N or name CA or name C or name O or \ name CB )) or resid 59 or (resid 60 and (name N or name CA or name C or name O \ or name CB )) or resid 61 or (resid 62 and (name N or name CA or name C or name \ O or name CB )) or resid 63 or (resid 64 and (name N or name CA or name C or nam \ e O or name CB )) or resid 65 through 67 or (resid 68 and (name N or name CA or \ name C or name O or name CB )) or resid 69 through 74 or (resid 75 and (name N o \ r name CA or name C or name O or name CB )) or resid 87 or (resid 88 through 89 \ and (name N or name CA or name C or name O or name CB )) or resid 90 through 91 \ or (resid 92 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 3 or (resid 94 and (name N or name CA or name C or name O or name CB )) or resid \ 95 through 96 or (resid 97 through 98 and (name N or name CA or name C or name \ O or name CB )) or (resid 99 through 104 and (name N or name CA or name C or nam \ e O or name CB )) or resid 105 or (resid 106 and (name N or name CA or name C or \ name O or name CB )) or resid 107 or (resid 108 through 110 and (name N or name \ CA or name C or name O or name CB )) or resid 111 through 112 or (resid 113 thr \ ough 114 and (name N or name CA or name C or name O or name CB )) or resid 115 o \ r (resid 116 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 17 through 119 or (resid 120 and (name N or name CA or name C or name O or name \ CB )) or resid 121 through 122 or (resid 123 and (name N or name CA or name C or \ name O or name CB )) or resid 124 or (resid 125 through 126 and (name N or name \ CA or name C or name O or name CB )) or resid 127 or (resid 128 through 129 and \ (name N or name CA or name C or name O or name CB )) or resid 130 through 131 o \ r (resid 132 through 136 and (name N or name CA or name C or name O or name CB ) \ ) or resid 137 through 139 or (resid 140 and (name N or name CA or name C or nam \ e O or name CB )) or resid 141 through 144 or (resid 145 and (name N or name CA \ or name C or name O or name CB )) or resid 146 through 147 or (resid 148 and (na \ me N or name CA or name C or name O or name CB )) or resid 149 through 151 or (r \ esid 152 and (name N or name CA or name C or name O or name CB )) or resid 153 o \ r (resid 154 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 55 or (resid 156 through 157 and (name N or name CA or name C or name O or name \ CB )) or resid 158 through 159 or (resid 160 and (name N or name CA or name C or \ name O or name CB )) or resid 161 through 170 or (resid 171 and (name N or name \ CA or name C or name O or name CB )) or resid 172 through 175 or (resid 176 thr \ ough 177 and (name N or name CA or name C or name O or name CB )) or resid 178 t \ hrough 179 or (resid 180 through 181 and (name N or name 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 n \ ame C or name O or name CB )) or resid 185 through 186 or (resid 187 through 190 \ and (name N or name CA or name C or name O or name CB )) or resid 191 through 1 \ 93 or (resid 194 and (name N or name CA or name C or name O or name CB )) or res \ id 195 through 196 or (resid 197 through 199 and (name N or name CA or name C or \ name O or name CB )) or resid 200 through 202 or (resid 203 and (name N or name \ CA or name C or name O or name CB )) or resid 204 through 207 or (resid 208 thr \ ough 209 and (name N or name CA or name C or name O or name CB )) or resid 210 o \ r (resid 211 through 212 and (name N or name CA or name C or name O or name CB ) \ ) or resid 213 through 215 or (resid 216 and (name N or name CA or name C or nam \ e O or name CB )) or resid 217 or (resid 218 and (name N or name CA or name C or \ name O or name CB )) or resid 219 through 228 or (resid 229 and (name N or name \ CA or name C or name O or name CB )) or resid 230 through 232 or (resid 233 thr \ ough 235 and (name N or name CA or name C or name O or name CB )) or resid 236 o \ r (resid 237 through 238 and (name N or name CA or name C or name O or name CB ) \ ) or resid 239 through 242 or (resid 243 and (name N or name CA or name C or nam \ e O or name CB )) or resid 244 through 245 or (resid 246 through 247 and (name N \ or name CA or name 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or name C or name O or n \ ame CB )) or resid 113 through 115 or (resid 116 through 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 or (resid 120 and (name N or \ name CA or name C or name O or name CB )) or resid 121 through 123 or (resid 124 \ and (name N or name CA or name C or name O or name CB )) or resid 125 or (resid \ 126 through 129 and (name N or name CA or name C or name O or name CB )) or res \ id 130 or (resid 131 through 133 and (name N or name CA or name C or name O or n \ ame CB )) or resid 134 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB )) or resid 140 through 146 or (resid 147 and (name N or \ name CA or name C or name O or name CB )) or resid 148 through 150 or (resid 151 \ through 158 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 59 or (resid 160 and (name N or name CA or name C or name O or name CB )) or res \ id 161 through 162 or (resid 163 through 166 and (name N or name CA or name C or \ name O or name CB )) or resid 167 or (resid 168 through 171 and (name N or name \ CA or name C or name O or name CB )) or resid 172 through 185 or (resid 186 thr \ ough 190 and (name N or name CA or name C or name O or name CB )) or resid 191 t \ hrough 196 or (resid 197 and (name N or name CA or name C or name O or name CB ) \ ) or resid 198 through 203 or (resid 204 and (name N or name CA or name C or nam \ e 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 res \ id 217 through 222 or (resid 223 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 (na \ me N or name CA or name C or name O or name CB )) or (resid 234 through 239 and \ (name N or name CA or name C or name O or name CB )) or resid 240 through 245 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 through 256 or (resid 257 through 258 and \ (name N or name CA or name C or name O or name CB )) or resid 259 through 271 o \ r (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 n \ ame C or name O or name CB )) or resid 282 or (resid 283 through 285 and (name N \ or name CA or name C or name O or name CB )) or resid 286 through 303 or (resid \ 304 through 320 and (name N or name CA or name C or name O or name CB )) or res \ id 321 through 322 or (resid 323 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 throug \ h 365 and (name N or name CA or name C or name O or name CB )) or resid 366 thro \ ugh 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 39 or (resid 40 through 47 and (name N or name CA or name C or \ name O or name CB )) or resid 48 or (resid 49 through 50 and (name N or name CA \ or name C or name O or name CB )) or resid 51 or (resid 52 through 54 and (name \ N or name CA or name C or name O or name CB )) or resid 55 or (resid 56 and (nam \ e N or name CA or name C or name O or name CB )) or resid 57 through 58 or (resi \ d 59 through 60 and (name N or name CA or name C or name O or name CB )) or resi \ d 61 or (resid 62 through 63 and (name N or name CA or name C or name O or name \ CB )) or (resid 72 through 78 and (name N or name CA or name C or name O or name \ CB )) or resid 79 or (resid 80 through 83 and (name N or name CA or name C or n \ ame O or name CB )) or resid 84 through 86 or (resid 87 through 91 and (name N o \ r name CA or name C or name O or name CB )) or resid 92 through 93 or (resid 94 \ and (name N or name CA or name C or name O or name CB )) or resid 95 or (resid 9 \ 6 and (name N or name CA or name C or name O or name CB )) or resid 97 through 1 \ 03 or (resid 104 and (name N or name CA or name C or name O or name CB )) or res \ id 105 through 114 or (resid 115 through 118 and (name N or name CA or name C or \ name O or name CB )) or resid 119 or (resid 120 and (name N or name CA or name \ C or name O or name CB )) or resid 121 through 123 or (resid 124 and (name N or \ name CA or name C or name O or name CB )) or resid 125 or (resid 126 through 129 \ and (name N or name CA or name C or name O or name CB )) or resid 130 through 1 \ 31 or (resid 132 through 133 and (name N or name CA or name C or name O or name \ CB )) or resid 134 through 136 or (resid 137 through 139 and (name N or name CA \ or name C or name O or name CB )) or resid 140 through 142 or (resid 143 and (na \ me N or name CA or name C or name O or name CB )) or resid 144 through 146 or (r \ esid 147 and (name N or name CA or name C or name O or name CB )) or resid 148 t \ hrough 150 or (resid 151 through 158 and (name N or name CA or name C or name O \ or name CB )) or resid 159 or (resid 160 and (name N or name CA or name C or nam \ e O or name CB )) or resid 161 through 162 or (resid 163 through 166 and (name N \ or name CA or name C or name O or name CB )) or resid 167 or (resid 168 through \ 171 and (name N or name CA or name C or name O or name CB )) or resid 172 or (r \ esid 173 through 177 and (name N or name CA or name C or name O or name CB )) or \ resid 178 through 185 or (resid 186 through 190 and (name N or name CA or name \ C or name O or name CB )) or resid 191 or (resid 192 and (name N or name CA or n \ ame C or name O or name CB )) or resid 193 through 196 or (resid 197 and (name N \ or name CA or name C or name O or name CB )) or resid 198 through 203 or (resid \ 204 and (name N or name CA or name C or name O or name CB )) or resid 205 throu \ gh 206 or (resid 207 and (name N or name CA or name C or name O or name CB )) or \ resid 208 through 209 or (resid 210 through 211 and (name N or name CA or name \ C or name O or name CB )) or resid 212 through 214 or (resid 215 through 216 and \ (name N or name CA or name C or name O or name CB )) or resid 217 or (resid 218 \ through 226 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 27 through 229 or (resid 230 and (name N or name CA or name C or name O or name \ CB )) or resid 231 or (resid 232 through 233 and (name N or name CA or name C or \ name O or name CB )) or (resid 234 through 239 and (name N or name CA or name C \ or name O or name CB )) or resid 240 through 242 or (resid 243 through 251 and \ (name N or name CA or name C or name O or name CB )) or resid 252 or (resid 253 \ through 254 and (name N or name CA or name C or name O or name CB )) or resid 25 \ 5 or (resid 256 through 258 and (name N or name CA or name C or name O or name C \ B )) or resid 259 through 263 or (resid 264 through 266 and (name N or name CA o \ r name C or name O or name CB )) or resid 267 through 269 or (resid 270 and (nam \ e N or name CA or name C or name O or name CB )) or resid 271 or (resid 272 thro \ ugh 273 and (name N or name CA or name C or name O or name CB )) or resid 274 th \ rough 277 or (resid 278 through 281 and (name N or name CA or name C or name O o \ r name CB )) or resid 282 or (resid 283 through 285 and (name N or name CA or na \ me C or name O or name CB )) or resid 286 through 288 or (resid 289 and (name N \ or name CA or name C or name O or name CB )) or resid 290 through 291 or (resid \ 292 and (name N or name CA or name C or name O or name CB )) or resid 293 or (re \ sid 294 and (name N or name CA or name C or name O or name CB )) or resid 295 or \ (resid 296 through 299 and (name N or name CA or name C or name O or name CB )) \ or resid 300 through 302 or (resid 303 through 320 and (name N or name CA or na \ me C or name O or name CB )) or resid 321 or (resid 322 through 333 and (name N \ or name CA or name C or name O or name CB )) or resid 334 or (resid 335 through \ 337 and (name N or name CA or name C or name O or name CB )) or resid 338 or res \ id 359 or (resid 360 through 365 and (name N or name CA or name C or name O or n \ ame CB )) or resid 366 or (resid 367 through 371 and (name N or name CA or name \ C or name O or name CB )) or resid 372 or (resid 373 and (name N or name CA or n \ ame C or name O or name CB )))) } 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 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 570 or (resid 57 \ 1 and (name N or name CA or name C or name O or name CB )) or resid 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: 7.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 36.100 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 41994 Z= 0.114 Angle : 0.514 7.067 57396 Z= 0.282 Chirality : 0.043 0.178 6882 Planarity : 0.003 0.065 7436 Dihedral : 12.099 89.186 14092 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.35 % Favored : 94.51 % Rotamer: Outliers : 0.03 % Allowed : 0.69 % Favored : 99.28 % 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: -0.23 (0.12), residues: 5761 helix: 1.44 (0.12), residues: 2055 sheet: -0.88 (0.19), residues: 786 loop : -1.12 (0.11), residues: 2920 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 0.017 0.001 PHE Q 367 TRP 0.012 0.001 TRP T 147 HIS 0.005 0.001 HIS M 162 Details of bonding type rmsd covalent geometry : bond 0.00222 (41994) covalent geometry : angle 0.51440 (57396) hydrogen bonds : bond 0.18048 ( 1632) hydrogen bonds : angle 6.78653 ( 4626) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1021 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 1020 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 ARG cc_start: 0.6938 (mtt90) cc_final: 0.6654 (mtt-85) REVERT: A 66 ILE cc_start: 0.7864 (mt) cc_final: 0.7484 (pt) REVERT: A 123 GLU cc_start: 0.5486 (pp20) cc_final: 0.5274 (tm-30) REVERT: A 136 LYS cc_start: 0.7909 (mtmm) cc_final: 0.7194 (tptt) REVERT: A 154 ASN cc_start: 0.6132 (t0) cc_final: 0.5494 (t0) REVERT: A 156 ASP cc_start: 0.7457 (m-30) cc_final: 0.6674 (m-30) REVERT: A 215 TYR cc_start: 0.3507 (m-80) cc_final: 0.3158 (t80) REVERT: D 290 HIS cc_start: 0.8715 (m-70) cc_final: 0.8010 (m170) REVERT: D 296 LEU cc_start: 0.8533 (mm) cc_final: 0.7878 (tp) REVERT: J 162 THR cc_start: 0.7574 (p) cc_final: 0.7352 (p) REVERT: J 257 MET cc_start: 0.8766 (mmm) cc_final: 0.8495 (tmm) REVERT: J 258 ASP cc_start: 0.8995 (m-30) cc_final: 0.8598 (m-30) REVERT: J 259 GLN cc_start: 0.8889 (mm110) cc_final: 0.8539 (mm-40) REVERT: K 181 ASP cc_start: 0.7603 (p0) cc_final: 0.7331 (p0) REVERT: K 195 THR cc_start: 0.7185 (p) cc_final: 0.6908 (p) REVERT: N 464 TYR cc_start: 0.6716 (m-80) cc_final: 0.6343 (m-80) REVERT: O 613 ASN cc_start: 0.8067 (m-40) cc_final: 0.7797 (t0) REVERT: P 21 HIS cc_start: 0.7467 (t-90) cc_final: 0.7067 (t-90) REVERT: P 156 GLN cc_start: 0.8074 (pm20) cc_final: 0.7863 (pm20) REVERT: P 278 TYR cc_start: 0.8611 (m-80) cc_final: 0.8350 (m-80) REVERT: Q 19 LEU cc_start: 0.9186 (tp) cc_final: 0.8723 (pp) REVERT: Q 26 ASP cc_start: 0.5933 (p0) cc_final: 0.4946 (p0) REVERT: Q 156 GLN cc_start: 0.5971 (pm20) cc_final: 0.5399 (pm20) REVERT: Q 168 MET cc_start: 0.6159 (mpp) cc_final: 0.5226 (tpt) REVERT: Q 203 SER cc_start: 0.8037 (p) cc_final: 0.7798 (m) REVERT: Q 257 MET cc_start: 0.6674 (mmp) cc_final: 0.6381 (ppp) REVERT: Q 258 ASP cc_start: 0.7578 (p0) cc_final: 0.5941 (p0) REVERT: Q 276 TYR cc_start: 0.3662 (t80) cc_final: 0.3056 (t80) REVERT: Q 278 TYR cc_start: 0.6710 (m-80) cc_final: 0.6077 (m-10) REVERT: Q 284 ASN cc_start: 0.8350 (m-40) cc_final: 0.7746 (m-40) REVERT: Q 314 LYS cc_start: 0.7161 (mttp) cc_final: 0.6536 (mmmt) REVERT: R 26 ASP cc_start: 0.7901 (p0) cc_final: 0.7334 (m-30) REVERT: R 84 PRO cc_start: 0.6516 (Cg_endo) cc_final: 0.6120 (Cg_exo) REVERT: R 153 ARG cc_start: 0.7012 (mtm-85) cc_final: 0.5892 (mtp180) REVERT: R 156 GLN cc_start: 0.5659 (tp-100) cc_final: 0.4759 (pm20) REVERT: R 168 MET cc_start: 0.7802 (mmm) cc_final: 0.7600 (tpp) REVERT: R 208 LEU cc_start: 0.8719 (tt) cc_final: 0.8263 (tt) REVERT: R 292 GLN cc_start: 0.8455 (tt0) cc_final: 0.8174 (tt0) REVERT: S 211 LEU cc_start: 0.8678 (mp) cc_final: 0.8439 (mm) REVERT: S 253 TYR cc_start: 0.8111 (t80) cc_final: 0.7656 (t80) REVERT: S 306 VAL cc_start: 0.7753 (p) cc_final: 0.7031 (m) REVERT: T 164 TYR cc_start: 0.7682 (m-80) cc_final: 0.7299 (m-80) REVERT: T 169 GLU cc_start: 0.7590 (mp0) cc_final: 0.7347 (mp0) REVERT: T 176 ASN cc_start: 0.8395 (m-40) cc_final: 0.8077 (t0) REVERT: T 276 TYR cc_start: 0.8916 (t80) cc_final: 0.8389 (t80) outliers start: 1 outliers final: 0 residues processed: 1020 average time/residue: 0.2314 time to fit residues: 376.6742 Evaluate side-chains 542 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 394 optimal weight: 1.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 265 optimal weight: 2.9990 chunk 523 optimal weight: 2.9990 chunk 497 optimal weight: 20.0000 chunk 414 optimal weight: 4.9990 chunk 310 optimal weight: 0.5980 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 0.0040 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN J 78 ASN J 239 HIS K 176 ASN L 110 GLN N 182 GLN ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 HIS Q 149 ASN Q 309 ASN ** R 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 311 GLN ** S 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.155466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.103725 restraints weight = 84159.804| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 3.97 r_work: 0.3165 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 41994 Z= 0.140 Angle : 0.565 11.417 57396 Z= 0.289 Chirality : 0.045 0.218 6882 Planarity : 0.004 0.059 7436 Dihedral : 3.769 29.862 6152 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.76 % Favored : 94.13 % Rotamer: Outliers : 2.10 % Allowed : 10.36 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.11), residues: 5761 helix: 1.48 (0.12), residues: 2075 sheet: -0.73 (0.20), residues: 778 loop : -1.15 (0.11), residues: 2908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG Q 228 TYR 0.024 0.001 TYR J 276 PHE 0.016 0.001 PHE S 32 TRP 0.027 0.001 TRP Q 227 HIS 0.008 0.001 HIS S 239 Details of bonding type rmsd covalent geometry : bond 0.00328 (41994) covalent geometry : angle 0.56475 (57396) hydrogen bonds : bond 0.03868 ( 1632) hydrogen bonds : angle 5.06695 ( 4626) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 593 time to evaluate : 1.616 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: A 66 ILE cc_start: 0.7207 (mt) cc_final: 0.6812 (pt) REVERT: A 109 SER cc_start: 0.7864 (t) cc_final: 0.7442 (m) REVERT: A 123 GLU cc_start: 0.5214 (pp20) cc_final: 0.4957 (tp30) REVERT: A 136 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7710 (mmtt) REVERT: D 14 ILE cc_start: 0.8480 (mm) cc_final: 0.8202 (mt) REVERT: D 237 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8123 (pt0) REVERT: D 260 GLU cc_start: 0.8747 (tt0) cc_final: 0.8321 (tp30) REVERT: D 290 HIS cc_start: 0.8788 (m-70) cc_final: 0.8027 (m170) REVERT: J 96 ARG cc_start: 0.7724 (mtt-85) cc_final: 0.7266 (ptp-110) REVERT: J 170 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7336 (tm-30) REVERT: J 198 GLU cc_start: 0.7256 (mp0) cc_final: 0.6812 (mt-10) REVERT: K 123 CYS cc_start: 0.9327 (m) cc_final: 0.9077 (p) REVERT: M 272 GLU cc_start: 0.6959 (pm20) cc_final: 0.6754 (pm20) REVERT: M 334 VAL cc_start: 0.8016 (t) cc_final: 0.7805 (t) REVERT: N 105 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7004 (mp0) REVERT: N 162 HIS cc_start: 0.7899 (m-70) cc_final: 0.7694 (m-70) REVERT: O 14 ILE cc_start: 0.9076 (mm) cc_final: 0.8830 (mm) REVERT: O 459 GLU cc_start: 0.8386 (mm-30) cc_final: 0.8068 (mm-30) REVERT: O 492 MET cc_start: 0.9086 (ttt) cc_final: 0.8816 (ttt) REVERT: O 602 GLN cc_start: 0.8535 (mt0) cc_final: 0.8333 (mt0) REVERT: O 613 ASN cc_start: 0.8404 (m-40) cc_final: 0.7960 (t0) REVERT: P 99 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7447 (mp10) REVERT: P 126 ILE cc_start: 0.8680 (tp) cc_final: 0.8355 (pt) REVERT: P 156 GLN cc_start: 0.8165 (pm20) cc_final: 0.7881 (pm20) REVERT: P 219 LEU cc_start: 0.8640 (tp) cc_final: 0.8427 (pp) REVERT: Q 19 LEU cc_start: 0.9175 (tp) cc_final: 0.8918 (pp) REVERT: Q 26 ASP cc_start: 0.5900 (p0) cc_final: 0.4997 (p0) REVERT: Q 167 LEU cc_start: 0.6434 (OUTLIER) cc_final: 0.6232 (tp) REVERT: Q 168 MET cc_start: 0.6266 (mpp) cc_final: 0.5284 (tpt) REVERT: Q 203 SER cc_start: 0.8091 (p) cc_final: 0.7571 (m) REVERT: Q 207 LYS cc_start: 0.5557 (OUTLIER) cc_final: 0.4929 (ptpp) REVERT: Q 228 ARG cc_start: 0.4569 (OUTLIER) cc_final: 0.4034 (ptt90) REVERT: Q 257 MET cc_start: 0.7147 (mmp) cc_final: 0.6178 (ppp) REVERT: Q 258 ASP cc_start: 0.7527 (p0) cc_final: 0.6089 (p0) REVERT: Q 276 TYR cc_start: 0.3469 (t80) cc_final: 0.3181 (t80) REVERT: Q 278 TYR cc_start: 0.7063 (m-80) cc_final: 0.6179 (m-80) REVERT: Q 284 ASN cc_start: 0.8458 (m-40) cc_final: 0.7764 (m-40) REVERT: R 26 ASP cc_start: 0.8143 (p0) cc_final: 0.7530 (m-30) REVERT: R 153 ARG cc_start: 0.6870 (mtm-85) cc_final: 0.5753 (mtp180) REVERT: R 156 GLN cc_start: 0.5212 (tp-100) cc_final: 0.4655 (pm20) REVERT: R 205 TRP cc_start: 0.6090 (m100) cc_final: 0.5799 (m100) REVERT: R 279 LYS cc_start: 0.6994 (ptpt) cc_final: 0.6456 (mmmt) REVERT: R 292 GLN cc_start: 0.8569 (tt0) cc_final: 0.8253 (tt0) REVERT: S 77 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8859 (pm20) REVERT: S 119 GLU cc_start: 0.9173 (mm-30) cc_final: 0.8911 (mm-30) REVERT: T 9 TYR cc_start: 0.8246 (m-80) cc_final: 0.7886 (m-10) REVERT: T 164 TYR cc_start: 0.7976 (m-80) cc_final: 0.7459 (m-80) REVERT: T 168 MET cc_start: 0.8353 (mmm) cc_final: 0.7841 (mmm) REVERT: T 176 ASN cc_start: 0.8415 (m-40) cc_final: 0.8089 (t0) REVERT: T 276 TYR cc_start: 0.8974 (t80) cc_final: 0.8612 (t80) outliers start: 79 outliers final: 50 residues processed: 639 average time/residue: 0.2162 time to fit residues: 225.8044 Evaluate side-chains 545 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 490 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain D residue 235 CYS Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 668 THR Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 554 GLU Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain N residue 28 VAL Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 196 ILE Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain O residue 577 ASP Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 99 GLN Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain Q residue 162 THR Chi-restraints excluded: chain Q residue 167 LEU Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 207 LYS Chi-restraints excluded: chain Q residue 228 ARG Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 264 LEU Chi-restraints excluded: chain Q residue 271 LEU Chi-restraints excluded: chain Q residue 273 THR Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 GLN Chi-restraints excluded: chain S residue 163 ASN Chi-restraints excluded: chain T residue 38 CYS Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 161 THR Chi-restraints excluded: chain T residue 184 VAL Chi-restraints excluded: chain T residue 273 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 550 optimal weight: 7.9990 chunk 249 optimal weight: 8.9990 chunk 390 optimal weight: 0.9980 chunk 141 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 201 optimal weight: 3.9990 chunk 194 optimal weight: 0.5980 chunk 207 optimal weight: 2.9990 chunk 565 optimal weight: 9.9990 chunk 527 optimal weight: 7.9990 chunk 535 optimal weight: 0.4980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 110 GLN M 49 GLN ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 309 ASN Q 14 GLN Q 149 ASN Q 176 ASN Q 259 GLN R 21 HIS ** R 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 21 HIS ** S 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 309 ASN T 156 GLN T 212 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.152344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.099275 restraints weight = 83392.710| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.43 r_work: 0.3118 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 41994 Z= 0.174 Angle : 0.562 9.728 57396 Z= 0.288 Chirality : 0.045 0.188 6882 Planarity : 0.004 0.045 7436 Dihedral : 3.892 33.178 6152 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.76 % Favored : 94.15 % Rotamer: Outliers : 2.97 % Allowed : 11.34 % Favored : 85.69 % 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: -0.22 (0.11), residues: 5761 helix: 1.42 (0.12), residues: 2084 sheet: -0.79 (0.20), residues: 767 loop : -1.15 (0.11), residues: 2910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 96 TYR 0.023 0.001 TYR D 60 PHE 0.022 0.001 PHE S 361 TRP 0.029 0.001 TRP Q 340 HIS 0.015 0.001 HIS S 21 Details of bonding type rmsd covalent geometry : bond 0.00416 (41994) covalent geometry : angle 0.56196 (57396) hydrogen bonds : bond 0.03682 ( 1632) hydrogen bonds : angle 4.69986 ( 4626) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 526 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.7497 (mt) cc_final: 0.7149 (pt) REVERT: A 109 SER cc_start: 0.8056 (t) cc_final: 0.7511 (m) REVERT: A 110 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7162 (mm110) REVERT: A 136 LYS cc_start: 0.8271 (mtmm) cc_final: 0.7793 (tptt) REVERT: A 519 ASN cc_start: 0.3726 (p0) cc_final: 0.3323 (p0) REVERT: D 14 ILE cc_start: 0.8644 (mm) cc_final: 0.8407 (mt) REVERT: D 243 PHE cc_start: 0.8150 (m-80) cc_final: 0.7905 (m-80) REVERT: J 96 ARG cc_start: 0.7895 (mtt-85) cc_final: 0.7577 (mtt180) REVERT: J 170 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7557 (tm-30) REVERT: J 239 HIS cc_start: 0.4914 (t70) cc_final: 0.4158 (t70) REVERT: J 259 GLN cc_start: 0.8382 (mm-40) cc_final: 0.8166 (mt0) REVERT: J 278 TYR cc_start: 0.7084 (m-80) cc_final: 0.6440 (m-80) REVERT: K 198 GLU cc_start: 0.8408 (pm20) cc_final: 0.8197 (pm20) REVERT: M 483 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: N 502 ASP cc_start: 0.8061 (t0) cc_final: 0.7716 (t70) REVERT: O 14 ILE cc_start: 0.9063 (mm) cc_final: 0.8838 (mm) REVERT: O 39 PHE cc_start: 0.8410 (m-80) cc_final: 0.8044 (m-80) REVERT: O 41 ASP cc_start: 0.8019 (t0) cc_final: 0.7687 (t70) REVERT: O 459 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8004 (mm-30) REVERT: O 492 MET cc_start: 0.9080 (ttt) cc_final: 0.8689 (ttt) REVERT: O 691 TYR cc_start: 0.8374 (m-80) cc_final: 0.7931 (m-80) REVERT: P 74 LYS cc_start: 0.5271 (pttp) cc_final: 0.4661 (pptt) REVERT: P 99 GLN cc_start: 0.7759 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: P 126 ILE cc_start: 0.8681 (tp) cc_final: 0.8358 (pt) REVERT: P 156 GLN cc_start: 0.8102 (pm20) cc_final: 0.7814 (pm20) REVERT: Q 26 ASP cc_start: 0.6158 (p0) cc_final: 0.5337 (p0) REVERT: Q 168 MET cc_start: 0.6069 (mpp) cc_final: 0.5051 (tpt) REVERT: Q 169 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7282 (tt0) REVERT: Q 176 ASN cc_start: 0.9237 (t0) cc_final: 0.8918 (p0) REVERT: Q 179 TYR cc_start: 0.7754 (p90) cc_final: 0.6708 (p90) REVERT: Q 207 LYS cc_start: 0.5509 (OUTLIER) cc_final: 0.4905 (ptpp) REVERT: Q 228 ARG cc_start: 0.4999 (OUTLIER) cc_final: 0.4442 (ptt90) REVERT: Q 256 MET cc_start: 0.3861 (mmp) cc_final: 0.3600 (mmt) REVERT: Q 257 MET cc_start: 0.6936 (mmp) cc_final: 0.6209 (ppp) REVERT: Q 258 ASP cc_start: 0.7444 (p0) cc_final: 0.5900 (p0) REVERT: Q 276 TYR cc_start: 0.3658 (t80) cc_final: 0.3448 (t80) REVERT: Q 278 TYR cc_start: 0.7581 (m-80) cc_final: 0.6414 (m-80) REVERT: Q 284 ASN cc_start: 0.8469 (m-40) cc_final: 0.7756 (m-40) REVERT: R 26 ASP cc_start: 0.8227 (p0) cc_final: 0.7356 (m-30) REVERT: R 153 ARG cc_start: 0.6993 (mtm-85) cc_final: 0.5384 (mtt90) REVERT: R 156 GLN cc_start: 0.5202 (tp-100) cc_final: 0.4633 (pm20) REVERT: R 217 TRP cc_start: 0.5451 (m-10) cc_final: 0.5171 (m-10) REVERT: R 279 LYS cc_start: 0.7162 (ptpt) cc_final: 0.6585 (mmmt) REVERT: R 292 GLN cc_start: 0.8639 (tt0) cc_final: 0.8383 (tt0) REVERT: T 168 MET cc_start: 0.8227 (mmm) cc_final: 0.7705 (mmm) REVERT: T 176 ASN cc_start: 0.8320 (m-40) cc_final: 0.8042 (t0) REVERT: T 198 GLU cc_start: 0.7228 (pp20) cc_final: 0.7006 (pp20) outliers start: 112 outliers final: 71 residues processed: 597 average time/residue: 0.2289 time to fit residues: 222.4128 Evaluate side-chains 539 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 464 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 235 CYS Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 554 GLU Chi-restraints excluded: chain L residue 589 VAL Chi-restraints excluded: chain L residue 668 THR Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 407 SER Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 486 LYS Chi-restraints excluded: chain M residue 552 ILE Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 411 ILE Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 335 VAL Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 99 GLN Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 368 LEU Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 149 ASN Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 207 LYS Chi-restraints excluded: chain Q residue 228 ARG Chi-restraints excluded: chain Q residue 264 LEU Chi-restraints excluded: chain Q residue 273 THR Chi-restraints excluded: chain Q residue 370 GLU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 211 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 163 ASN Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 38 CYS Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 161 THR Chi-restraints excluded: chain T residue 184 VAL Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 355 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 369 optimal weight: 0.8980 chunk 498 optimal weight: 9.9990 chunk 276 optimal weight: 3.9990 chunk 144 optimal weight: 40.0000 chunk 134 optimal weight: 9.9990 chunk 61 optimal weight: 0.0050 chunk 63 optimal weight: 20.0000 chunk 117 optimal weight: 30.0000 chunk 190 optimal weight: 10.0000 chunk 229 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 overall best weight: 1.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 GLN J 239 HIS J 309 ASN M 87 HIS ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 GLN ** S 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.151255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.097831 restraints weight = 83079.780| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.48 r_work: 0.3091 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 41994 Z= 0.171 Angle : 0.544 8.428 57396 Z= 0.279 Chirality : 0.045 0.198 6882 Planarity : 0.004 0.040 7436 Dihedral : 3.903 32.388 6152 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.92 % Favored : 94.01 % Rotamer: Outliers : 3.03 % Allowed : 13.17 % Favored : 83.80 % 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: -0.21 (0.11), residues: 5761 helix: 1.47 (0.12), residues: 2076 sheet: -0.85 (0.19), residues: 782 loop : -1.13 (0.11), residues: 2903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 26 TYR 0.026 0.001 TYR J 276 PHE 0.014 0.001 PHE M 513 TRP 0.025 0.001 TRP Q 147 HIS 0.011 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00414 (41994) covalent geometry : angle 0.54415 (57396) hydrogen bonds : bond 0.03402 ( 1632) hydrogen bonds : angle 4.52652 ( 4626) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 489 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.7461 (mt) cc_final: 0.7142 (pt) REVERT: A 109 SER cc_start: 0.8141 (t) cc_final: 0.7781 (m) REVERT: A 110 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7127 (mm110) REVERT: A 123 GLU cc_start: 0.4929 (tm-30) cc_final: 0.4681 (tm-30) REVERT: A 136 LYS cc_start: 0.8326 (mtmm) cc_final: 0.8002 (ttpt) REVERT: A 163 SER cc_start: 0.4501 (OUTLIER) cc_final: 0.4242 (p) REVERT: A 419 MET cc_start: 0.5467 (mpp) cc_final: 0.5204 (mpp) REVERT: A 519 ASN cc_start: 0.3965 (p0) cc_final: 0.3584 (p0) REVERT: D 243 PHE cc_start: 0.8175 (m-80) cc_final: 0.7943 (m-80) REVERT: D 256 ASP cc_start: 0.8447 (m-30) cc_final: 0.7985 (p0) REVERT: D 290 HIS cc_start: 0.8797 (m170) cc_final: 0.8312 (m170) REVERT: J 170 GLN cc_start: 0.7772 (tm-30) cc_final: 0.7503 (tm-30) REVERT: J 259 GLN cc_start: 0.8492 (mm-40) cc_final: 0.8243 (mt0) REVERT: J 278 TYR cc_start: 0.7175 (m-80) cc_final: 0.6517 (m-80) REVERT: K 28 ARG cc_start: 0.3729 (tpm170) cc_final: 0.3386 (mmm-85) REVERT: K 123 CYS cc_start: 0.9293 (m) cc_final: 0.8767 (p) REVERT: K 124 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8148 (mm-30) REVERT: K 168 MET cc_start: 0.7714 (tpp) cc_final: 0.7328 (tpp) REVERT: K 172 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7671 (mt) REVERT: L 268 ARG cc_start: 0.7907 (tmt170) cc_final: 0.7561 (tmt170) REVERT: M 483 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: N 162 HIS cc_start: 0.8098 (m-70) cc_final: 0.7710 (m-70) REVERT: O 39 PHE cc_start: 0.8487 (m-80) cc_final: 0.8077 (m-80) REVERT: O 41 ASP cc_start: 0.8073 (t0) cc_final: 0.7709 (t70) REVERT: O 459 GLU cc_start: 0.8375 (mm-30) cc_final: 0.7958 (mm-30) REVERT: O 492 MET cc_start: 0.9081 (ttt) cc_final: 0.8714 (ttt) REVERT: O 691 TYR cc_start: 0.8424 (m-80) cc_final: 0.7872 (m-80) REVERT: P 74 LYS cc_start: 0.5277 (pttp) cc_final: 0.4668 (pptt) REVERT: P 156 GLN cc_start: 0.8044 (pm20) cc_final: 0.7754 (pm20) REVERT: Q 26 ASP cc_start: 0.6313 (p0) cc_final: 0.5336 (p0) REVERT: Q 155 HIS cc_start: 0.8048 (m170) cc_final: 0.7410 (m90) REVERT: Q 168 MET cc_start: 0.6155 (mpp) cc_final: 0.5198 (tpt) REVERT: Q 169 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7183 (tt0) REVERT: Q 179 TYR cc_start: 0.7797 (p90) cc_final: 0.6713 (p90) REVERT: Q 207 LYS cc_start: 0.5228 (OUTLIER) cc_final: 0.4726 (ptpp) REVERT: Q 257 MET cc_start: 0.7211 (mmp) cc_final: 0.6666 (ppp) REVERT: Q 258 ASP cc_start: 0.7660 (p0) cc_final: 0.6942 (p0) REVERT: Q 261 LYS cc_start: 0.8582 (pttt) cc_final: 0.7776 (mmtt) REVERT: Q 278 TYR cc_start: 0.7836 (m-80) cc_final: 0.6536 (m-80) REVERT: Q 284 ASN cc_start: 0.8534 (m-40) cc_final: 0.7866 (m-40) REVERT: R 26 ASP cc_start: 0.8330 (p0) cc_final: 0.7526 (m-30) REVERT: R 153 ARG cc_start: 0.6969 (mtm-85) cc_final: 0.5451 (mtt90) REVERT: R 217 TRP cc_start: 0.5616 (m-10) cc_final: 0.5381 (m-10) REVERT: R 316 MET cc_start: 0.7334 (mmm) cc_final: 0.7037 (tpp) REVERT: R 354 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.5564 (pp) REVERT: T 176 ASN cc_start: 0.8346 (m-40) cc_final: 0.7985 (t0) REVERT: T 241 SER cc_start: 0.7035 (t) cc_final: 0.6726 (m) REVERT: T 289 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8788 (mp10) outliers start: 114 outliers final: 84 residues processed: 578 average time/residue: 0.2236 time to fit residues: 212.6909 Evaluate side-chains 545 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 455 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 172 LEU Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 503 SER Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 589 VAL Chi-restraints excluded: chain L residue 668 THR Chi-restraints excluded: chain M residue 155 ILE Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 335 VAL Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 407 SER Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 552 ILE Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 411 ILE Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 155 HIS Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 270 ILE Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 13 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 207 LYS Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 271 LEU Chi-restraints excluded: chain Q residue 273 THR Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain R residue 354 LEU Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 163 ASN Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 38 CYS Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 155 HIS Chi-restraints excluded: chain T residue 161 THR Chi-restraints excluded: chain T residue 184 VAL Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 273 THR Chi-restraints excluded: chain T residue 289 GLN Chi-restraints excluded: chain T residue 355 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 396 optimal weight: 2.9990 chunk 365 optimal weight: 0.9990 chunk 429 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 410 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 222 optimal weight: 6.9990 chunk 381 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 542 optimal weight: 50.0000 chunk 438 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS L 49 GLN L 87 HIS L 290 HIS ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 HIS O 508 GLN O 613 ASN Q 149 ASN Q 170 GLN ** R 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 292 GLN ** S 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.147028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.094206 restraints weight = 83397.094| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.73 r_work: 0.2988 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.175 41994 Z= 0.377 Angle : 0.731 11.183 57396 Z= 0.377 Chirality : 0.051 0.203 6882 Planarity : 0.005 0.058 7436 Dihedral : 4.844 35.184 6152 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.85 % Favored : 92.05 % Rotamer: Outliers : 4.22 % Allowed : 14.21 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.11), residues: 5761 helix: 0.98 (0.12), residues: 2077 sheet: -1.43 (0.19), residues: 761 loop : -1.32 (0.11), residues: 2923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 298 TYR 0.031 0.002 TYR L 111 PHE 0.022 0.002 PHE M 513 TRP 0.026 0.002 TRP Q 147 HIS 0.014 0.002 HIS N 162 Details of bonding type rmsd covalent geometry : bond 0.00921 (41994) covalent geometry : angle 0.73053 (57396) hydrogen bonds : bond 0.04860 ( 1632) hydrogen bonds : angle 4.90638 ( 4626) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 456 time to evaluate : 1.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ASP cc_start: 0.7838 (t0) cc_final: 0.7621 (t0) REVERT: A 66 ILE cc_start: 0.7482 (mt) cc_final: 0.7146 (pt) REVERT: A 110 GLN cc_start: 0.8070 (mm-40) cc_final: 0.7436 (mm110) REVERT: A 136 LYS cc_start: 0.8371 (mtmm) cc_final: 0.7909 (ttpt) REVERT: A 163 SER cc_start: 0.4715 (OUTLIER) cc_final: 0.4477 (p) REVERT: A 419 MET cc_start: 0.5085 (mpp) cc_final: 0.4798 (ppp) REVERT: A 458 LEU cc_start: 0.7328 (tt) cc_final: 0.7003 (mp) REVERT: A 519 ASN cc_start: 0.4620 (p0) cc_final: 0.4229 (p0) REVERT: D 256 ASP cc_start: 0.8682 (m-30) cc_final: 0.8061 (p0) REVERT: J 170 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7485 (tm-30) REVERT: J 239 HIS cc_start: 0.5222 (t-90) cc_final: 0.4608 (t70) REVERT: J 259 GLN cc_start: 0.8385 (mm-40) cc_final: 0.8045 (mm-40) REVERT: K 226 ILE cc_start: 0.7312 (tp) cc_final: 0.7070 (pt) REVERT: L 268 ARG cc_start: 0.8093 (tmt170) cc_final: 0.7819 (tmt170) REVERT: M 60 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7874 (t80) REVERT: M 211 LYS cc_start: 0.7913 (mttt) cc_final: 0.7447 (mptt) REVERT: M 370 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9035 (mp) REVERT: M 483 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8247 (mp0) REVERT: M 486 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8859 (tttp) REVERT: O 41 ASP cc_start: 0.8435 (t0) cc_final: 0.8152 (t70) REVERT: O 492 MET cc_start: 0.9242 (ttt) cc_final: 0.8897 (ttt) REVERT: O 662 TYR cc_start: 0.8613 (m-80) cc_final: 0.8252 (m-80) REVERT: O 691 TYR cc_start: 0.8490 (m-80) cc_final: 0.7768 (m-80) REVERT: P 156 GLN cc_start: 0.8027 (pm20) cc_final: 0.7770 (pm20) REVERT: Q 26 ASP cc_start: 0.6499 (p0) cc_final: 0.5964 (p0) REVERT: Q 158 GLU cc_start: 0.6202 (OUTLIER) cc_final: 0.5620 (mm-30) REVERT: Q 164 TYR cc_start: 0.5535 (p90) cc_final: 0.5232 (p90) REVERT: Q 169 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6930 (tt0) REVERT: Q 179 TYR cc_start: 0.7916 (p90) cc_final: 0.6548 (p90) REVERT: Q 181 ASP cc_start: 0.6986 (p0) cc_final: 0.5969 (p0) REVERT: Q 228 ARG cc_start: 0.5724 (OUTLIER) cc_final: 0.5145 (ptt90) REVERT: Q 257 MET cc_start: 0.7342 (mmp) cc_final: 0.6508 (ppp) REVERT: Q 258 ASP cc_start: 0.7442 (p0) cc_final: 0.5978 (p0) REVERT: Q 278 TYR cc_start: 0.8273 (m-80) cc_final: 0.7332 (m-80) REVERT: Q 284 ASN cc_start: 0.8493 (m-40) cc_final: 0.7944 (m-40) REVERT: Q 314 LYS cc_start: 0.6505 (mmtp) cc_final: 0.6288 (mmtt) REVERT: Q 369 GLU cc_start: 0.8680 (tp30) cc_final: 0.8246 (tt0) REVERT: R 153 ARG cc_start: 0.7261 (mtm-85) cc_final: 0.5482 (mmt90) REVERT: R 217 TRP cc_start: 0.5665 (m-10) cc_final: 0.5405 (m-10) REVERT: R 292 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: R 330 ARG cc_start: 0.8248 (mtp180) cc_final: 0.7922 (mmm-85) REVERT: T 176 ASN cc_start: 0.8310 (m-40) cc_final: 0.7882 (t0) REVERT: T 241 SER cc_start: 0.7550 (t) cc_final: 0.7298 (m) REVERT: T 258 ASP cc_start: 0.8902 (t0) cc_final: 0.8466 (t0) outliers start: 159 outliers final: 106 residues processed: 586 average time/residue: 0.2316 time to fit residues: 222.4237 Evaluate side-chains 544 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 430 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 474 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 169 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 142 HIS Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 195 THR Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 VAL Chi-restraints excluded: chain L residue 668 THR Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 235 CYS Chi-restraints excluded: chain M residue 236 ASP Chi-restraints excluded: chain M residue 241 VAL Chi-restraints excluded: chain M residue 249 SER Chi-restraints excluded: chain M residue 335 VAL Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 486 LYS Chi-restraints excluded: chain M residue 552 ILE Chi-restraints excluded: chain M residue 577 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 411 ILE Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain O residue 40 VAL Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 236 ASP Chi-restraints excluded: chain O residue 334 VAL Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 270 ILE Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 161 THR Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 207 LYS Chi-restraints excluded: chain Q residue 228 ARG Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 264 LEU Chi-restraints excluded: chain Q residue 271 LEU Chi-restraints excluded: chain Q residue 273 THR Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 292 GLN Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 163 ASN Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 38 CYS Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 155 HIS Chi-restraints excluded: chain T residue 161 THR Chi-restraints excluded: chain T residue 164 TYR Chi-restraints excluded: chain T residue 184 VAL Chi-restraints excluded: chain T residue 230 THR Chi-restraints excluded: chain T residue 270 ILE Chi-restraints excluded: chain T residue 273 THR Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain T residue 371 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 225 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 245 optimal weight: 0.4980 chunk 168 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 134 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 454 optimal weight: 0.8980 chunk 548 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS J 199 ASN K 199 ASN ** L 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 HIS R 155 HIS ** R 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.150162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.097714 restraints weight = 82909.040| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 3.70 r_work: 0.3054 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 41994 Z= 0.129 Angle : 0.539 12.849 57396 Z= 0.277 Chirality : 0.044 0.187 6882 Planarity : 0.004 0.056 7436 Dihedral : 4.158 31.277 6152 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.52 % Favored : 94.41 % Rotamer: Outliers : 2.84 % Allowed : 15.77 % Favored : 81.39 % 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: -0.41 (0.11), residues: 5761 helix: 1.31 (0.12), residues: 2072 sheet: -1.17 (0.20), residues: 741 loop : -1.20 (0.11), residues: 2948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG T 194 TYR 0.026 0.001 TYR J 278 PHE 0.029 0.001 PHE T 367 TRP 0.030 0.001 TRP S 147 HIS 0.009 0.001 HIS N 670 Details of bonding type rmsd covalent geometry : bond 0.00308 (41994) covalent geometry : angle 0.53911 (57396) hydrogen bonds : bond 0.03162 ( 1632) hydrogen bonds : angle 4.48765 ( 4626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 486 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.7422 (mt) cc_final: 0.7103 (pt) REVERT: A 110 GLN cc_start: 0.7825 (mm-40) cc_final: 0.7397 (mm110) REVERT: A 136 LYS cc_start: 0.8348 (mtmm) cc_final: 0.7910 (ttpt) REVERT: A 163 SER cc_start: 0.4699 (OUTLIER) cc_final: 0.4498 (p) REVERT: A 458 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6990 (mp) REVERT: A 519 ASN cc_start: 0.4676 (p0) cc_final: 0.4290 (p0) REVERT: D 256 ASP cc_start: 0.8562 (m-30) cc_final: 0.8036 (p0) REVERT: D 290 HIS cc_start: 0.8638 (m-70) cc_final: 0.8166 (m170) REVERT: D 460 GLU cc_start: 0.8558 (tt0) cc_final: 0.8283 (tm-30) REVERT: J 170 GLN cc_start: 0.7802 (tm-30) cc_final: 0.7531 (tm-30) REVERT: J 239 HIS cc_start: 0.5316 (t-90) cc_final: 0.4645 (t70) REVERT: J 259 GLN cc_start: 0.8512 (mm-40) cc_final: 0.8190 (mm-40) REVERT: J 271 LEU cc_start: 0.6559 (tp) cc_final: 0.5463 (mp) REVERT: J 278 TYR cc_start: 0.6798 (m-80) cc_final: 0.5971 (m-80) REVERT: K 28 ARG cc_start: 0.4085 (tpm170) cc_final: 0.3671 (mmm-85) REVERT: K 123 CYS cc_start: 0.9308 (m) cc_final: 0.8888 (p) REVERT: K 226 ILE cc_start: 0.7170 (tp) cc_final: 0.6937 (pt) REVERT: L 84 PRO cc_start: 0.8944 (Cg_endo) cc_final: 0.8709 (Cg_exo) REVERT: L 268 ARG cc_start: 0.7958 (tmt170) cc_final: 0.7670 (tmt170) REVERT: M 60 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7895 (t80) REVERT: M 211 LYS cc_start: 0.7921 (mttt) cc_final: 0.7346 (mptt) REVERT: M 483 GLU cc_start: 0.8888 (OUTLIER) cc_final: 0.8197 (mp0) REVERT: M 486 LYS cc_start: 0.9107 (ptmt) cc_final: 0.8802 (tttp) REVERT: N 661 GLN cc_start: 0.8043 (mt0) cc_final: 0.7550 (tt0) REVERT: O 41 ASP cc_start: 0.8332 (t0) cc_final: 0.7963 (t70) REVERT: O 492 MET cc_start: 0.9226 (ttt) cc_final: 0.8885 (ttt) REVERT: O 691 TYR cc_start: 0.8529 (m-80) cc_final: 0.7779 (m-80) REVERT: P 74 LYS cc_start: 0.4942 (pttp) cc_final: 0.4314 (ptmt) REVERT: P 156 GLN cc_start: 0.7969 (pm20) cc_final: 0.7726 (pm20) REVERT: Q 26 ASP cc_start: 0.6525 (p0) cc_final: 0.5876 (p0) REVERT: Q 158 GLU cc_start: 0.5682 (OUTLIER) cc_final: 0.5213 (mm-30) REVERT: Q 164 TYR cc_start: 0.5606 (p90) cc_final: 0.5354 (p90) REVERT: Q 169 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7140 (tt0) REVERT: Q 179 TYR cc_start: 0.7843 (p90) cc_final: 0.6614 (p90) REVERT: Q 181 ASP cc_start: 0.6920 (p0) cc_final: 0.5794 (p0) REVERT: Q 207 LYS cc_start: 0.4839 (OUTLIER) cc_final: 0.4466 (ptpp) REVERT: Q 228 ARG cc_start: 0.5995 (OUTLIER) cc_final: 0.5491 (ptt90) REVERT: Q 257 MET cc_start: 0.7360 (mmp) cc_final: 0.6750 (ppp) REVERT: Q 258 ASP cc_start: 0.7800 (p0) cc_final: 0.7135 (p0) REVERT: Q 261 LYS cc_start: 0.8575 (pttt) cc_final: 0.7811 (mmtt) REVERT: R 97 LEU cc_start: 0.5786 (OUTLIER) cc_final: 0.5396 (pp) REVERT: R 153 ARG cc_start: 0.7061 (mtm-85) cc_final: 0.5284 (mmt180) REVERT: R 217 TRP cc_start: 0.5713 (m-10) cc_final: 0.5479 (m-10) REVERT: S 77 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8814 (pm20) REVERT: S 119 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8710 (mm-30) REVERT: S 259 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8293 (mm-40) REVERT: T 176 ASN cc_start: 0.8302 (m-40) cc_final: 0.7968 (t0) REVERT: T 192 ASP cc_start: 0.8537 (t0) cc_final: 0.8154 (t0) REVERT: T 241 SER cc_start: 0.7222 (t) cc_final: 0.6937 (m) REVERT: T 276 TYR cc_start: 0.9030 (t80) cc_final: 0.8630 (t80) outliers start: 107 outliers final: 79 residues processed: 568 average time/residue: 0.2323 time to fit residues: 215.7021 Evaluate side-chains 540 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 452 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 492 MET Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 169 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 196 ILE Chi-restraints excluded: chain K residue 360 ASP Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 554 GLU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 552 ILE Chi-restraints excluded: chain M residue 577 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 411 ILE Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 236 ASP Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 139 THR Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 270 ILE Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain Q residue 149 ASN Chi-restraints excluded: chain Q residue 156 GLN Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 207 LYS Chi-restraints excluded: chain Q residue 228 ARG Chi-restraints excluded: chain Q residue 264 LEU Chi-restraints excluded: chain Q residue 271 LEU Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 97 LEU Chi-restraints excluded: chain R residue 155 HIS Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 77 GLN Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 163 ASN Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 38 CYS Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 155 HIS Chi-restraints excluded: chain T residue 164 TYR Chi-restraints excluded: chain T residue 355 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 272 optimal weight: 3.9990 chunk 483 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 372 optimal weight: 0.0970 chunk 32 optimal weight: 7.9990 chunk 409 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 230 optimal weight: 7.9990 chunk 279 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 ASN L 49 GLN ** L 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 170 GLN Q 284 ASN R 292 GLN ** S 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 311 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.148822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.095837 restraints weight = 83279.551| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 3.45 r_work: 0.3052 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 41994 Z= 0.196 Angle : 0.574 13.028 57396 Z= 0.294 Chirality : 0.045 0.200 6882 Planarity : 0.004 0.048 7436 Dihedral : 4.181 33.071 6152 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.87 % Favored : 93.04 % Rotamer: Outliers : 3.27 % Allowed : 16.17 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.11), residues: 5761 helix: 1.35 (0.12), residues: 2069 sheet: -1.22 (0.19), residues: 776 loop : -1.20 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG S 58 TYR 0.023 0.001 TYR D 60 PHE 0.025 0.001 PHE T 367 TRP 0.027 0.001 TRP Q 147 HIS 0.027 0.001 HIS R 155 Details of bonding type rmsd covalent geometry : bond 0.00478 (41994) covalent geometry : angle 0.57374 (57396) hydrogen bonds : bond 0.03507 ( 1632) hydrogen bonds : angle 4.50636 ( 4626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 450 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.7572 (mt) cc_final: 0.7235 (pt) REVERT: A 110 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7348 (mm110) REVERT: A 136 LYS cc_start: 0.8389 (mtmm) cc_final: 0.7955 (ttpt) REVERT: A 163 SER cc_start: 0.4615 (OUTLIER) cc_final: 0.4275 (p) REVERT: A 419 MET cc_start: 0.5467 (mpp) cc_final: 0.5139 (mpp) REVERT: A 458 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7023 (mp) REVERT: A 459 GLU cc_start: 0.4679 (tp30) cc_final: 0.4466 (tp30) REVERT: A 508 GLN cc_start: 0.8295 (mt0) cc_final: 0.8082 (mp10) REVERT: A 519 ASN cc_start: 0.4572 (p0) cc_final: 0.4165 (p0) REVERT: D 256 ASP cc_start: 0.8575 (m-30) cc_final: 0.8052 (p0) REVERT: J 170 GLN cc_start: 0.7874 (tm-30) cc_final: 0.7594 (tm-30) REVERT: J 239 HIS cc_start: 0.5281 (t-90) cc_final: 0.4609 (t70) REVERT: J 259 GLN cc_start: 0.8449 (mm-40) cc_final: 0.8146 (mm-40) REVERT: J 271 LEU cc_start: 0.6514 (tp) cc_final: 0.5412 (mp) REVERT: K 168 MET cc_start: 0.7465 (tpp) cc_final: 0.7192 (tpp) REVERT: K 226 ILE cc_start: 0.7138 (tp) cc_final: 0.6895 (pt) REVERT: L 84 PRO cc_start: 0.9072 (Cg_endo) cc_final: 0.8843 (Cg_exo) REVERT: L 268 ARG cc_start: 0.7966 (tmt170) cc_final: 0.7678 (tmt170) REVERT: M 60 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7858 (t80) REVERT: M 211 LYS cc_start: 0.7951 (mttt) cc_final: 0.7408 (mptt) REVERT: M 370 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8880 (mp) REVERT: M 483 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8168 (mp0) REVERT: M 486 LYS cc_start: 0.9072 (ptmt) cc_final: 0.8756 (tttp) REVERT: N 661 GLN cc_start: 0.8168 (mt0) cc_final: 0.7595 (tt0) REVERT: O 41 ASP cc_start: 0.8368 (t0) cc_final: 0.8053 (t70) REVERT: O 492 MET cc_start: 0.9171 (ttt) cc_final: 0.8828 (ttt) REVERT: O 691 TYR cc_start: 0.8568 (m-80) cc_final: 0.7779 (m-80) REVERT: O 692 ARG cc_start: 0.7196 (ttm110) cc_final: 0.6866 (ttm-80) REVERT: P 74 LYS cc_start: 0.4962 (pttp) cc_final: 0.4344 (ptmt) REVERT: Q 26 ASP cc_start: 0.6709 (p0) cc_final: 0.6125 (p0) REVERT: Q 158 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5647 (mm-30) REVERT: Q 164 TYR cc_start: 0.5588 (p90) cc_final: 0.5380 (p90) REVERT: Q 169 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7030 (tt0) REVERT: Q 179 TYR cc_start: 0.7893 (p90) cc_final: 0.6561 (p90) REVERT: Q 181 ASP cc_start: 0.7070 (p0) cc_final: 0.6016 (p0) REVERT: Q 228 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5615 (ptt90) REVERT: Q 257 MET cc_start: 0.7425 (mmp) cc_final: 0.6564 (ppp) REVERT: Q 258 ASP cc_start: 0.7812 (p0) cc_final: 0.6682 (p0) REVERT: R 153 ARG cc_start: 0.7075 (mtm-85) cc_final: 0.6822 (mtt90) REVERT: R 330 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7814 (mmm-85) REVERT: S 119 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8733 (mm-30) REVERT: S 259 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8377 (mm-40) REVERT: T 176 ASN cc_start: 0.8265 (m-40) cc_final: 0.7919 (t0) REVERT: T 192 ASP cc_start: 0.8514 (t0) cc_final: 0.8160 (t0) REVERT: T 241 SER cc_start: 0.7603 (t) cc_final: 0.7382 (m) REVERT: T 276 TYR cc_start: 0.9033 (t80) cc_final: 0.8656 (t80) outliers start: 123 outliers final: 98 residues processed: 545 average time/residue: 0.2121 time to fit residues: 190.7876 Evaluate side-chains 541 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 436 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 19 LEU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 169 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain K residue 15 GLN Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 142 HIS Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 554 GLU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 668 THR Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 335 VAL Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 552 ILE Chi-restraints excluded: chain M residue 577 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 411 ILE Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 236 ASP Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 270 ILE Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain Q residue 149 ASN Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 184 VAL Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 207 LYS Chi-restraints excluded: chain Q residue 228 ARG Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 264 LEU Chi-restraints excluded: chain Q residue 271 LEU Chi-restraints excluded: chain Q residue 273 THR Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 163 ASN Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 38 CYS Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 155 HIS Chi-restraints excluded: chain T residue 161 THR Chi-restraints excluded: chain T residue 164 TYR Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain T residue 371 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 343 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 452 optimal weight: 20.0000 chunk 429 optimal weight: 4.9990 chunk 125 optimal weight: 7.9990 chunk 285 optimal weight: 2.9990 chunk 296 optimal weight: 10.0000 chunk 507 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 386 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS J 239 HIS K 15 GLN K 199 ASN ** L 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 ASN ** S 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.147177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.094245 restraints weight = 82874.355| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 3.64 r_work: 0.3006 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.5057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.142 41994 Z= 0.287 Angle : 0.650 12.761 57396 Z= 0.335 Chirality : 0.048 0.233 6882 Planarity : 0.005 0.054 7436 Dihedral : 4.589 34.104 6152 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.72 % Favored : 92.14 % Rotamer: Outliers : 3.56 % Allowed : 16.12 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.11), residues: 5761 helix: 1.18 (0.12), residues: 2061 sheet: -1.45 (0.19), residues: 774 loop : -1.35 (0.11), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG O 571 TYR 0.027 0.002 TYR D 60 PHE 0.021 0.002 PHE L 513 TRP 0.028 0.002 TRP R 147 HIS 0.012 0.002 HIS O 162 Details of bonding type rmsd covalent geometry : bond 0.00704 (41994) covalent geometry : angle 0.65017 (57396) hydrogen bonds : bond 0.04159 ( 1632) hydrogen bonds : angle 4.68543 ( 4626) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 437 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.7412 (mt) cc_final: 0.7058 (pt) REVERT: A 110 GLN cc_start: 0.7964 (mm-40) cc_final: 0.7307 (mm110) REVERT: A 136 LYS cc_start: 0.8365 (mtmm) cc_final: 0.7900 (ttpt) REVERT: A 163 SER cc_start: 0.4719 (OUTLIER) cc_final: 0.4197 (p) REVERT: A 419 MET cc_start: 0.5209 (mpp) cc_final: 0.4992 (mpp) REVERT: A 458 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7047 (mp) REVERT: A 482 LYS cc_start: 0.7446 (tppt) cc_final: 0.6592 (ttmt) REVERT: A 508 GLN cc_start: 0.8352 (mt0) cc_final: 0.8130 (mp10) REVERT: A 519 ASN cc_start: 0.4898 (p0) cc_final: 0.4522 (p0) REVERT: D 256 ASP cc_start: 0.8645 (m-30) cc_final: 0.8048 (p0) REVERT: D 290 HIS cc_start: 0.8641 (OUTLIER) cc_final: 0.8253 (m90) REVERT: J 170 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7579 (tm-30) REVERT: J 239 HIS cc_start: 0.5235 (t70) cc_final: 0.4283 (t70) REVERT: J 259 GLN cc_start: 0.8480 (mm-40) cc_final: 0.8141 (mm-40) REVERT: L 84 PRO cc_start: 0.9003 (Cg_endo) cc_final: 0.8695 (Cg_exo) REVERT: L 268 ARG cc_start: 0.8091 (tmt170) cc_final: 0.7763 (tmt170) REVERT: M 60 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8135 (t80) REVERT: M 370 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.8887 (mp) REVERT: M 483 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8155 (mp0) REVERT: M 486 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8919 (tttp) REVERT: O 41 ASP cc_start: 0.8447 (t0) cc_final: 0.8131 (t70) REVERT: O 78 LYS cc_start: 0.9251 (mtmm) cc_final: 0.8979 (mtmm) REVERT: O 492 MET cc_start: 0.9275 (ttt) cc_final: 0.8913 (ttt) REVERT: O 691 TYR cc_start: 0.8591 (m-80) cc_final: 0.7734 (m-80) REVERT: O 692 ARG cc_start: 0.7131 (ttm110) cc_final: 0.6792 (ttm-80) REVERT: P 74 LYS cc_start: 0.4763 (pttp) cc_final: 0.4218 (ptmt) REVERT: P 97 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8974 (pp) REVERT: Q 26 ASP cc_start: 0.6778 (p0) cc_final: 0.6254 (p0) REVERT: Q 154 GLU cc_start: 0.6123 (pm20) cc_final: 0.5912 (pm20) REVERT: Q 158 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5521 (mm-30) REVERT: Q 169 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7026 (tt0) REVERT: Q 176 ASN cc_start: 0.9244 (t0) cc_final: 0.8853 (p0) REVERT: Q 179 TYR cc_start: 0.8034 (p90) cc_final: 0.6790 (p90) REVERT: Q 181 ASP cc_start: 0.7147 (p0) cc_final: 0.6218 (p0) REVERT: Q 228 ARG cc_start: 0.6134 (OUTLIER) cc_final: 0.5626 (ptt90) REVERT: Q 256 MET cc_start: 0.3566 (mmt) cc_final: 0.3357 (mmt) REVERT: Q 257 MET cc_start: 0.7527 (mmp) cc_final: 0.6803 (ppp) REVERT: Q 258 ASP cc_start: 0.7904 (p0) cc_final: 0.7303 (p0) REVERT: Q 261 LYS cc_start: 0.8600 (pttt) cc_final: 0.7820 (mmtt) REVERT: Q 278 TYR cc_start: 0.8123 (m-80) cc_final: 0.7702 (m-80) REVERT: R 153 ARG cc_start: 0.7278 (mtm-85) cc_final: 0.6991 (mtt90) REVERT: R 330 ARG cc_start: 0.8192 (mmm-85) cc_final: 0.7718 (mmm-85) REVERT: S 119 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8770 (mm-30) REVERT: T 176 ASN cc_start: 0.8386 (m-40) cc_final: 0.8035 (t0) REVERT: T 192 ASP cc_start: 0.8651 (t0) cc_final: 0.8325 (t0) REVERT: T 241 SER cc_start: 0.7581 (t) cc_final: 0.7347 (m) REVERT: T 258 ASP cc_start: 0.8850 (t0) cc_final: 0.8420 (t0) outliers start: 134 outliers final: 107 residues processed: 542 average time/residue: 0.2172 time to fit residues: 194.7928 Evaluate side-chains 537 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 420 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 290 HIS Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 169 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain K residue 15 GLN Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 142 HIS Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 554 GLU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 589 VAL Chi-restraints excluded: chain L residue 668 THR Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 50 ILE Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 335 VAL Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 486 LYS Chi-restraints excluded: chain M residue 552 ILE Chi-restraints excluded: chain M residue 577 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 411 ILE Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 236 ASP Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 270 ILE Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain Q residue 149 ASN Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 184 VAL Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 207 LYS Chi-restraints excluded: chain Q residue 228 ARG Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 264 LEU Chi-restraints excluded: chain Q residue 271 LEU Chi-restraints excluded: chain Q residue 273 THR Chi-restraints excluded: chain R residue 21 HIS Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 163 ASN Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 38 CYS Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 155 HIS Chi-restraints excluded: chain T residue 161 THR Chi-restraints excluded: chain T residue 164 TYR Chi-restraints excluded: chain T residue 355 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 139 optimal weight: 20.0000 chunk 512 optimal weight: 6.9990 chunk 69 optimal weight: 9.9990 chunk 452 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 163 optimal weight: 0.0270 chunk 318 optimal weight: 40.0000 chunk 114 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 347 optimal weight: 0.8980 chunk 515 optimal weight: 5.9990 overall best weight: 2.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN D 290 HIS K 199 ASN ** L 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 309 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.147919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.096216 restraints weight = 82792.741| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.61 r_work: 0.3060 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2930 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 41994 Z= 0.204 Angle : 0.601 13.211 57396 Z= 0.307 Chirality : 0.046 0.192 6882 Planarity : 0.004 0.054 7436 Dihedral : 4.392 32.898 6152 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.89 % Favored : 93.02 % Rotamer: Outliers : 3.48 % Allowed : 16.36 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.11), residues: 5761 helix: 1.27 (0.12), residues: 2062 sheet: -1.37 (0.19), residues: 780 loop : -1.31 (0.11), residues: 2919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 194 TYR 0.034 0.001 TYR J 278 PHE 0.024 0.001 PHE T 367 TRP 0.031 0.002 TRP R 217 HIS 0.015 0.001 HIS D 290 Details of bonding type rmsd covalent geometry : bond 0.00499 (41994) covalent geometry : angle 0.60132 (57396) hydrogen bonds : bond 0.03581 ( 1632) hydrogen bonds : angle 4.58311 ( 4626) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 435 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.7538 (mt) cc_final: 0.7186 (pt) REVERT: A 69 GLN cc_start: 0.8844 (mt0) cc_final: 0.8433 (mp10) REVERT: A 110 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7443 (mm110) REVERT: A 136 LYS cc_start: 0.8403 (mtmm) cc_final: 0.7926 (ttpt) REVERT: A 419 MET cc_start: 0.5412 (mpp) cc_final: 0.5209 (mpp) REVERT: A 458 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7003 (mp) REVERT: D 256 ASP cc_start: 0.8649 (m-30) cc_final: 0.8073 (p0) REVERT: D 460 GLU cc_start: 0.8733 (tt0) cc_final: 0.8381 (tm-30) REVERT: J 170 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7587 (tm-30) REVERT: J 239 HIS cc_start: 0.5083 (t70) cc_final: 0.4444 (t70) REVERT: J 259 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8233 (mm-40) REVERT: J 271 LEU cc_start: 0.6539 (tp) cc_final: 0.5410 (mp) REVERT: J 276 TYR cc_start: 0.4720 (t80) cc_final: 0.4384 (t80) REVERT: L 84 PRO cc_start: 0.9000 (Cg_endo) cc_final: 0.8678 (Cg_exo) REVERT: L 268 ARG cc_start: 0.8300 (tmt170) cc_final: 0.7971 (tmt170) REVERT: M 60 TYR cc_start: 0.8852 (OUTLIER) cc_final: 0.8367 (t80) REVERT: M 370 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8894 (mp) REVERT: M 483 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8357 (mp0) REVERT: M 486 LYS cc_start: 0.9174 (ptmt) cc_final: 0.8836 (tttp) REVERT: O 41 ASP cc_start: 0.8534 (t0) cc_final: 0.8229 (t70) REVERT: O 78 LYS cc_start: 0.9250 (mtmm) cc_final: 0.9028 (mtmm) REVERT: O 492 MET cc_start: 0.9306 (ttt) cc_final: 0.8985 (ttt) REVERT: O 691 TYR cc_start: 0.8667 (m-80) cc_final: 0.7995 (m-80) REVERT: O 692 ARG cc_start: 0.7243 (ttm110) cc_final: 0.6912 (ttm-80) REVERT: P 97 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8941 (pp) REVERT: Q 26 ASP cc_start: 0.6859 (p0) cc_final: 0.6316 (p0) REVERT: Q 154 GLU cc_start: 0.6121 (pm20) cc_final: 0.5911 (pm20) REVERT: Q 158 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.5626 (mm-30) REVERT: Q 164 TYR cc_start: 0.5178 (p90) cc_final: 0.4889 (p90) REVERT: Q 169 GLU cc_start: 0.7593 (mt-10) cc_final: 0.6971 (tt0) REVERT: Q 179 TYR cc_start: 0.8075 (p90) cc_final: 0.6608 (p90) REVERT: Q 181 ASP cc_start: 0.7219 (p0) cc_final: 0.6288 (p0) REVERT: Q 228 ARG cc_start: 0.6052 (OUTLIER) cc_final: 0.5508 (ptt90) REVERT: Q 257 MET cc_start: 0.7478 (mmp) cc_final: 0.6581 (ppp) REVERT: Q 258 ASP cc_start: 0.7964 (p0) cc_final: 0.7047 (p0) REVERT: Q 278 TYR cc_start: 0.8130 (m-80) cc_final: 0.7713 (m-80) REVERT: R 153 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6789 (mtt90) REVERT: S 58 ARG cc_start: 0.8915 (ptp-110) cc_final: 0.8706 (tpt90) REVERT: T 168 MET cc_start: 0.8506 (mmm) cc_final: 0.7898 (mmm) REVERT: T 176 ASN cc_start: 0.8408 (m-40) cc_final: 0.8085 (t0) REVERT: T 192 ASP cc_start: 0.8725 (t0) cc_final: 0.8415 (t0) REVERT: T 241 SER cc_start: 0.7599 (t) cc_final: 0.7367 (m) REVERT: T 258 ASP cc_start: 0.8970 (t0) cc_final: 0.8580 (t0) outliers start: 131 outliers final: 115 residues processed: 535 average time/residue: 0.2233 time to fit residues: 197.2373 Evaluate side-chains 542 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 420 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 454 LEU Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain D residue 530 VAL Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 169 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 255 VAL Chi-restraints excluded: chain J residue 272 ILE Chi-restraints excluded: chain K residue 23 LEU Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain K residue 142 HIS Chi-restraints excluded: chain K residue 184 VAL Chi-restraints excluded: chain K residue 198 GLU Chi-restraints excluded: chain L residue 148 SER Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 279 LEU Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 427 LEU Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 554 GLU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 668 THR Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 169 THR Chi-restraints excluded: chain M residue 335 VAL Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 419 MET Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 552 ILE Chi-restraints excluded: chain M residue 577 ASP Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 158 LEU Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 411 ILE Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain N residue 670 HIS Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 61 ILE Chi-restraints excluded: chain O residue 120 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 149 ILE Chi-restraints excluded: chain O residue 236 ASP Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 40 VAL Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 270 ILE Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain Q residue 156 GLN Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 184 VAL Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 196 ILE Chi-restraints excluded: chain Q residue 207 LYS Chi-restraints excluded: chain Q residue 228 ARG Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 264 LEU Chi-restraints excluded: chain Q residue 271 LEU Chi-restraints excluded: chain Q residue 273 THR Chi-restraints excluded: chain R residue 21 HIS Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 80 LYS Chi-restraints excluded: chain R residue 148 ILE Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 205 TRP Chi-restraints excluded: chain R residue 298 LEU Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 163 ASN Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 38 CYS Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 155 HIS Chi-restraints excluded: chain T residue 161 THR Chi-restraints excluded: chain T residue 164 TYR Chi-restraints excluded: chain T residue 184 VAL Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain T residue 371 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 66 optimal weight: 0.3980 chunk 363 optimal weight: 1.9990 chunk 103 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 346 optimal weight: 20.0000 chunk 433 optimal weight: 3.9990 chunk 202 optimal weight: 0.9990 chunk 251 optimal weight: 0.9990 chunk 490 optimal weight: 10.0000 chunk 274 optimal weight: 2.9990 chunk 233 optimal weight: 0.7980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS J 282 HIS K 15 GLN K 199 ASN L 602 GLN ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 GLN Q 176 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.149772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.098181 restraints weight = 82375.867| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.28 r_work: 0.3080 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 41994 Z= 0.120 Angle : 0.553 13.845 57396 Z= 0.283 Chirality : 0.044 0.194 6882 Planarity : 0.004 0.049 7436 Dihedral : 4.049 30.608 6152 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.92 % Favored : 93.99 % Rotamer: Outliers : 2.81 % Allowed : 17.05 % Favored : 80.14 % 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: -0.35 (0.11), residues: 5761 helix: 1.43 (0.12), residues: 2062 sheet: -1.16 (0.19), residues: 759 loop : -1.20 (0.11), residues: 2940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG T 194 TYR 0.031 0.001 TYR J 278 PHE 0.027 0.001 PHE T 367 TRP 0.034 0.001 TRP R 147 HIS 0.010 0.001 HIS N 670 Details of bonding type rmsd covalent geometry : bond 0.00281 (41994) covalent geometry : angle 0.55295 (57396) hydrogen bonds : bond 0.02984 ( 1632) hydrogen bonds : angle 4.39546 ( 4626) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11522 Ramachandran restraints generated. 5761 Oldfield, 0 Emsley, 5761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 459 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 ILE cc_start: 0.7552 (mt) cc_final: 0.7216 (pt) REVERT: A 69 GLN cc_start: 0.8872 (mt0) cc_final: 0.8440 (mp10) REVERT: A 110 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7004 (mm-40) REVERT: A 136 LYS cc_start: 0.8418 (mtmm) cc_final: 0.7980 (ttpt) REVERT: A 419 MET cc_start: 0.5518 (mpp) cc_final: 0.5181 (mpp) REVERT: A 458 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7079 (mp) REVERT: A 491 MET cc_start: 0.6316 (tmm) cc_final: 0.5824 (tmm) REVERT: D 80 LEU cc_start: 0.8895 (tp) cc_final: 0.8655 (tt) REVERT: D 237 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7416 (pm20) REVERT: D 256 ASP cc_start: 0.8512 (m-30) cc_final: 0.8024 (p0) REVERT: D 459 GLU cc_start: 0.8815 (tp30) cc_final: 0.8180 (tt0) REVERT: D 460 GLU cc_start: 0.8520 (tt0) cc_final: 0.8243 (tm-30) REVERT: J 170 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7627 (tm-30) REVERT: J 239 HIS cc_start: 0.5130 (t70) cc_final: 0.4611 (t-90) REVERT: J 259 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8178 (mm-40) REVERT: J 271 LEU cc_start: 0.6652 (tp) cc_final: 0.5594 (mp) REVERT: J 278 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.6214 (m-80) REVERT: K 123 CYS cc_start: 0.9274 (m) cc_final: 0.8745 (p) REVERT: K 286 VAL cc_start: 0.8280 (t) cc_final: 0.7900 (p) REVERT: L 84 PRO cc_start: 0.8910 (Cg_endo) cc_final: 0.8639 (Cg_exo) REVERT: M 60 TYR cc_start: 0.8590 (OUTLIER) cc_final: 0.8120 (t80) REVERT: M 483 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8124 (mp0) REVERT: M 486 LYS cc_start: 0.8969 (ptmt) cc_final: 0.8584 (tttp) REVERT: N 433 ARG cc_start: 0.9239 (ttp80) cc_final: 0.8977 (ttp80) REVERT: N 661 GLN cc_start: 0.8049 (mt0) cc_final: 0.7310 (tt0) REVERT: O 41 ASP cc_start: 0.8350 (t0) cc_final: 0.8054 (t70) REVERT: O 78 LYS cc_start: 0.9027 (mtmm) cc_final: 0.8783 (mtmm) REVERT: O 492 MET cc_start: 0.9040 (ttt) cc_final: 0.8713 (ttt) REVERT: O 691 TYR cc_start: 0.8663 (m-80) cc_final: 0.8042 (m-80) REVERT: P 97 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8909 (pp) REVERT: P 99 GLN cc_start: 0.7881 (pm20) cc_final: 0.7365 (pm20) REVERT: Q 26 ASP cc_start: 0.6849 (p0) cc_final: 0.6343 (p0) REVERT: Q 154 GLU cc_start: 0.6114 (pm20) cc_final: 0.5879 (pm20) REVERT: Q 158 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5859 (mm-30) REVERT: Q 164 TYR cc_start: 0.5076 (p90) cc_final: 0.4759 (p90) REVERT: Q 168 MET cc_start: 0.6317 (mpp) cc_final: 0.5316 (tpt) REVERT: Q 169 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7181 (tt0) REVERT: Q 176 ASN cc_start: 0.9197 (t0) cc_final: 0.8919 (t0) REVERT: Q 179 TYR cc_start: 0.8043 (p90) cc_final: 0.6714 (p90) REVERT: Q 181 ASP cc_start: 0.7424 (p0) cc_final: 0.6508 (p0) REVERT: Q 228 ARG cc_start: 0.6108 (OUTLIER) cc_final: 0.5708 (ptt90) REVERT: Q 257 MET cc_start: 0.7543 (mmp) cc_final: 0.6848 (ppp) REVERT: Q 258 ASP cc_start: 0.8042 (p0) cc_final: 0.7540 (p0) REVERT: Q 261 LYS cc_start: 0.8459 (pttt) cc_final: 0.7657 (mmtp) REVERT: Q 278 TYR cc_start: 0.8025 (m-80) cc_final: 0.7698 (m-80) REVERT: R 153 ARG cc_start: 0.7109 (mtm-85) cc_final: 0.6761 (mtt90) REVERT: R 316 MET cc_start: 0.7556 (mmm) cc_final: 0.7222 (tpp) REVERT: T 176 ASN cc_start: 0.8331 (m-40) cc_final: 0.8009 (t0) REVERT: T 192 ASP cc_start: 0.8599 (t0) cc_final: 0.8389 (t0) outliers start: 106 outliers final: 86 residues processed: 533 average time/residue: 0.2136 time to fit residues: 189.0282 Evaluate side-chains 531 residues out of total 5146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 437 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 18 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 454 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 502 ASP Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain D residue 113 THR Chi-restraints excluded: chain D residue 237 GLU Chi-restraints excluded: chain D residue 335 VAL Chi-restraints excluded: chain D residue 437 ASP Chi-restraints excluded: chain D residue 472 ILE Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain J residue 162 THR Chi-restraints excluded: chain J residue 169 GLU Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 208 LEU Chi-restraints excluded: chain J residue 210 LYS Chi-restraints excluded: chain J residue 278 TYR Chi-restraints excluded: chain K residue 15 GLN Chi-restraints excluded: chain K residue 53 VAL Chi-restraints excluded: chain K residue 100 GLN Chi-restraints excluded: chain L residue 168 SER Chi-restraints excluded: chain L residue 196 ILE Chi-restraints excluded: chain L residue 281 VAL Chi-restraints excluded: chain L residue 335 VAL Chi-restraints excluded: chain L residue 530 VAL Chi-restraints excluded: chain L residue 554 GLU Chi-restraints excluded: chain L residue 580 VAL Chi-restraints excluded: chain L residue 670 HIS Chi-restraints excluded: chain M residue 60 TYR Chi-restraints excluded: chain M residue 146 VAL Chi-restraints excluded: chain M residue 335 VAL Chi-restraints excluded: chain M residue 370 LEU Chi-restraints excluded: chain M residue 389 LEU Chi-restraints excluded: chain M residue 483 GLU Chi-restraints excluded: chain M residue 552 ILE Chi-restraints excluded: chain M residue 668 THR Chi-restraints excluded: chain N residue 90 ILE Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 411 ILE Chi-restraints excluded: chain N residue 412 SER Chi-restraints excluded: chain N residue 457 VAL Chi-restraints excluded: chain N residue 530 VAL Chi-restraints excluded: chain N residue 551 ILE Chi-restraints excluded: chain O residue 47 ILE Chi-restraints excluded: chain O residue 146 VAL Chi-restraints excluded: chain O residue 236 ASP Chi-restraints excluded: chain O residue 562 THR Chi-restraints excluded: chain O residue 576 LEU Chi-restraints excluded: chain O residue 581 THR Chi-restraints excluded: chain P residue 13 THR Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 97 LEU Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain P residue 132 VAL Chi-restraints excluded: chain P residue 162 THR Chi-restraints excluded: chain P residue 195 THR Chi-restraints excluded: chain P residue 270 ILE Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 23 LEU Chi-restraints excluded: chain Q residue 139 THR Chi-restraints excluded: chain Q residue 156 GLN Chi-restraints excluded: chain Q residue 158 GLU Chi-restraints excluded: chain Q residue 184 VAL Chi-restraints excluded: chain Q residue 193 ILE Chi-restraints excluded: chain Q residue 207 LYS Chi-restraints excluded: chain Q residue 228 ARG Chi-restraints excluded: chain Q residue 241 SER Chi-restraints excluded: chain Q residue 264 LEU Chi-restraints excluded: chain Q residue 271 LEU Chi-restraints excluded: chain Q residue 273 THR Chi-restraints excluded: chain R residue 30 ILE Chi-restraints excluded: chain R residue 56 LEU Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 157 VAL Chi-restraints excluded: chain R residue 184 VAL Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain R residue 198 GLU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 44 HIS Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 88 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 163 ASN Chi-restraints excluded: chain S residue 198 GLU Chi-restraints excluded: chain T residue 38 CYS Chi-restraints excluded: chain T residue 87 THR Chi-restraints excluded: chain T residue 130 VAL Chi-restraints excluded: chain T residue 155 HIS Chi-restraints excluded: chain T residue 164 TYR Chi-restraints excluded: chain T residue 355 PHE Chi-restraints excluded: chain T residue 371 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 579 random chunks: chunk 479 optimal weight: 5.9990 chunk 441 optimal weight: 5.9990 chunk 343 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 318 optimal weight: 50.0000 chunk 495 optimal weight: 0.0370 chunk 32 optimal weight: 9.9990 chunk 353 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 9.9990 chunk 418 optimal weight: 9.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 HIS K 15 GLN K 199 ASN ** N 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.149557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.097334 restraints weight = 83559.314| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.53 r_work: 0.3063 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.314 41994 Z= 0.242 Angle : 0.708 59.195 57396 Z= 0.395 Chirality : 0.046 0.657 6882 Planarity : 0.004 0.133 7436 Dihedral : 4.062 30.891 6152 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 2.73 % Allowed : 17.26 % Favored : 80.01 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.11), residues: 5761 helix: 1.40 (0.12), residues: 2063 sheet: -1.16 (0.19), residues: 769 loop : -1.20 (0.11), residues: 2929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 268 TYR 0.030 0.001 TYR J 278 PHE 0.037 0.001 PHE K 180 TRP 0.030 0.002 TRP R 147 HIS 0.019 0.001 HIS Q 363 Details of bonding type rmsd covalent geometry : bond 0.00528 (41994) covalent geometry : angle 0.70762 (57396) hydrogen bonds : bond 0.03094 ( 1632) hydrogen bonds : angle 4.40627 ( 4626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12825.11 seconds wall clock time: 218 minutes 34.53 seconds (13114.53 seconds total)