Starting phenix.real_space_refine on Mon Oct 13 04:38:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v5h_64789/10_2025/9v5h_64789.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v5h_64789/10_2025/9v5h_64789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v5h_64789/10_2025/9v5h_64789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v5h_64789/10_2025/9v5h_64789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v5h_64789/10_2025/9v5h_64789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v5h_64789/10_2025/9v5h_64789.map" } resolution = 4.0 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= 0.002 sd= 0.029 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 120 5.16 5 C 18906 2.51 5 N 5172 2.21 5 O 5310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 169 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29508 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2213 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2213 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2213 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2213 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2213 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 2213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2213 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 3, 'PTRANS': 13, 'TRANS': 274} Chain breaks: 2 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2705 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 16, 'TRANS': 313} Chain breaks: 1 Chain: "H" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2705 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 16, 'TRANS': 313} Chain breaks: 1 Chain: "I" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2705 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 16, 'TRANS': 313} Chain breaks: 1 Chain: "J" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2705 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 16, 'TRANS': 313} Chain breaks: 1 Chain: "K" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2705 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 16, 'TRANS': 313} Chain breaks: 1 Chain: "L" Number of atoms: 2705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2705 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 16, 'TRANS': 313} Chain breaks: 1 Time building chain proxies: 7.55, per 1000 atoms: 0.26 Number of scatterers: 29508 At special positions: 0 Unit cell: (175.35, 155.4, 115.5, 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 120 16.00 O 5310 8.00 N 5172 7.00 C 18906 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: 2.72 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6924 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 44 sheets defined 43.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 8 through 21 removed outlier: 3.764A pdb=" N GLY A 12 " --> pdb=" O TYR A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 89 through 94 removed outlier: 3.711A pdb=" N LEU A 93 " --> pdb=" O TYR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 123 removed outlier: 3.635A pdb=" N LEU A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASN A 123 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 183 removed outlier: 3.737A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.538A pdb=" N GLY A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.592A pdb=" N PHE A 207 " --> pdb=" O ASP A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 224 removed outlier: 3.602A pdb=" N LEU A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.166A pdb=" N LEU A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 22 Processing helix chain 'B' and resid 44 through 52 Processing helix chain 'B' and resid 64 through 75 removed outlier: 3.538A pdb=" N VAL B 68 " --> pdb=" O HIS B 64 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 75 " --> pdb=" O ILE B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 removed outlier: 3.623A pdb=" N LEU B 93 " --> pdb=" O TYR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.548A pdb=" N TRP B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 183 removed outlier: 3.788A pdb=" N GLN B 175 " --> pdb=" O GLN B 171 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.579A pdb=" N GLY B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.812A pdb=" N ALA B 195 " --> pdb=" O GLU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 213 through 224 removed outlier: 3.757A pdb=" N LEU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 296 removed outlier: 4.417A pdb=" N LEU B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 44 through 52 Processing helix chain 'C' and resid 64 through 75 Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.579A pdb=" N LEU C 93 " --> pdb=" O TYR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 123 removed outlier: 4.506A pdb=" N LEU C 121 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN C 123 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 183 removed outlier: 3.745A pdb=" N GLN C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) Proline residue: C 178 - end of helix Processing helix chain 'C' and resid 191 through 195 removed outlier: 3.567A pdb=" N GLU C 194 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA C 195 " --> pdb=" O GLU C 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 191 through 195' Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 288 through 297 removed outlier: 4.144A pdb=" N LEU C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 44 through 52 removed outlier: 3.779A pdb=" N LEU D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 75 Processing helix chain 'D' and resid 89 through 94 Processing helix chain 'D' and resid 115 through 121 Processing helix chain 'D' and resid 157 through 183 removed outlier: 4.152A pdb=" N GLN D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 202 through 207 Processing helix chain 'D' and resid 213 through 224 Processing helix chain 'D' and resid 288 through 297 removed outlier: 3.924A pdb=" N LEU D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 44 through 53 removed outlier: 4.307A pdb=" N LEU E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 75 Processing helix chain 'E' and resid 89 through 94 removed outlier: 3.563A pdb=" N LEU E 93 " --> pdb=" O TYR E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 122 removed outlier: 4.172A pdb=" N TRP E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 183 removed outlier: 4.004A pdb=" N GLN E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) Proline residue: E 178 - end of helix removed outlier: 3.721A pdb=" N GLY E 183 " --> pdb=" O ALA E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 195 removed outlier: 3.601A pdb=" N ALA E 195 " --> pdb=" O GLU E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 224 removed outlier: 3.777A pdb=" N LEU E 217 " --> pdb=" O PRO E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 297 removed outlier: 4.195A pdb=" N LEU E 292 " --> pdb=" O GLN E 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 22 Processing helix chain 'F' and resid 44 through 53 Processing helix chain 'F' and resid 64 through 75 Processing helix chain 'F' and resid 89 through 94 Processing helix chain 'F' and resid 115 through 123 removed outlier: 3.659A pdb=" N TRP F 119 " --> pdb=" O ALA F 115 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN F 123 " --> pdb=" O TRP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 183 removed outlier: 3.523A pdb=" N GLN F 175 " --> pdb=" O GLN F 171 " (cutoff:3.500A) Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 191 through 195 removed outlier: 3.735A pdb=" N ALA F 195 " --> pdb=" O GLU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 207 removed outlier: 3.637A pdb=" N PHE F 207 " --> pdb=" O ASP F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 224 removed outlier: 3.647A pdb=" N VAL F 224 " --> pdb=" O MET F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 297 Processing helix chain 'G' and resid 325 through 336 Processing helix chain 'G' and resid 350 through 354 Processing helix chain 'G' and resid 373 through 383 Processing helix chain 'G' and resid 394 through 401 removed outlier: 3.677A pdb=" N TYR G 398 " --> pdb=" O THR G 394 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N THR G 399 " --> pdb=" O PRO G 395 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG G 400 " --> pdb=" O ILE G 396 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASN G 401 " --> pdb=" O GLU G 397 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 394 through 401' Processing helix chain 'G' and resid 401 through 423 removed outlier: 3.517A pdb=" N VAL G 405 " --> pdb=" O ASN G 401 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU G 412 " --> pdb=" O LEU G 408 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN G 413 " --> pdb=" O ASP G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 482 removed outlier: 4.085A pdb=" N TYR G 463 " --> pdb=" O PRO G 459 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER G 464 " --> pdb=" O ARG G 460 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU G 479 " --> pdb=" O TRP G 475 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS G 480 " --> pdb=" O ALA G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 522 Processing helix chain 'G' and resid 528 through 531 Processing helix chain 'G' and resid 540 through 553 Processing helix chain 'G' and resid 574 through 586 Processing helix chain 'G' and resid 590 through 594 removed outlier: 3.677A pdb=" N HIS G 593 " --> pdb=" O LEU G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 623 through 631 Processing helix chain 'G' and resid 637 through 652 removed outlier: 4.092A pdb=" N THR G 641 " --> pdb=" O ASP G 637 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 336 Processing helix chain 'H' and resid 350 through 354 Processing helix chain 'H' and resid 355 through 359 removed outlier: 4.090A pdb=" N ASN H 358 " --> pdb=" O ARG H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 373 through 383 Processing helix chain 'H' and resid 394 through 401 removed outlier: 4.297A pdb=" N TYR H 398 " --> pdb=" O THR H 394 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 424 removed outlier: 3.988A pdb=" N VAL H 405 " --> pdb=" O ASN H 401 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE H 410 " --> pdb=" O PHE H 406 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU H 412 " --> pdb=" O LEU H 408 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ASN H 413 " --> pdb=" O ASP H 409 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU H 414 " --> pdb=" O PHE H 410 " (cutoff:3.500A) Processing helix chain 'H' and resid 432 through 436 removed outlier: 4.087A pdb=" N VAL H 435 " --> pdb=" O THR H 432 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR H 436 " --> pdb=" O SER H 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 432 through 436' Processing helix chain 'H' and resid 461 through 482 removed outlier: 3.636A pdb=" N GLN H 468 " --> pdb=" O SER H 464 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY H 478 " --> pdb=" O ILE H 474 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU H 479 " --> pdb=" O TRP H 475 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS H 480 " --> pdb=" O ALA H 476 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU H 481 " --> pdb=" O TYR H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 509 through 522 Processing helix chain 'H' and resid 528 through 532 removed outlier: 4.194A pdb=" N LYS H 532 " --> pdb=" O ASP H 529 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 553 removed outlier: 4.047A pdb=" N GLY H 543 " --> pdb=" O ASP H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 554 through 557 removed outlier: 3.944A pdb=" N ARG H 557 " --> pdb=" O ALA H 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 554 through 557' Processing helix chain 'H' and resid 574 through 586 Processing helix chain 'H' and resid 587 through 594 removed outlier: 6.318A pdb=" N LEU H 590 " --> pdb=" O LYS H 587 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N HIS H 592 " --> pdb=" O PRO H 589 " (cutoff:3.500A) Processing helix chain 'H' and resid 623 through 631 Processing helix chain 'H' and resid 638 through 652 Processing helix chain 'I' and resid 325 through 336 Processing helix chain 'I' and resid 350 through 354 Processing helix chain 'I' and resid 355 through 359 removed outlier: 3.984A pdb=" N ASN I 358 " --> pdb=" O ARG I 355 " (cutoff:3.500A) Processing helix chain 'I' and resid 373 through 383 Processing helix chain 'I' and resid 396 through 401 removed outlier: 3.506A pdb=" N ASN I 401 " --> pdb=" O GLU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 401 through 409 removed outlier: 3.740A pdb=" N VAL I 405 " --> pdb=" O ASN I 401 " (cutoff:3.500A) Processing helix chain 'I' and resid 410 through 423 Processing helix chain 'I' and resid 432 through 436 removed outlier: 3.948A pdb=" N VAL I 435 " --> pdb=" O THR I 432 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR I 436 " --> pdb=" O SER I 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 432 through 436' Processing helix chain 'I' and resid 461 through 480 removed outlier: 3.626A pdb=" N VAL I 465 " --> pdb=" O TRP I 461 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN I 468 " --> pdb=" O SER I 464 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU I 479 " --> pdb=" O TRP I 475 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS I 480 " --> pdb=" O ALA I 476 " (cutoff:3.500A) Processing helix chain 'I' and resid 509 through 521 Processing helix chain 'I' and resid 528 through 531 Processing helix chain 'I' and resid 540 through 553 Processing helix chain 'I' and resid 554 through 557 removed outlier: 4.129A pdb=" N ARG I 557 " --> pdb=" O ALA I 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 554 through 557' Processing helix chain 'I' and resid 574 through 586 Processing helix chain 'I' and resid 590 through 594 removed outlier: 3.899A pdb=" N HIS I 593 " --> pdb=" O LEU I 590 " (cutoff:3.500A) Processing helix chain 'I' and resid 623 through 630 Processing helix chain 'I' and resid 637 through 652 removed outlier: 3.846A pdb=" N THR I 641 " --> pdb=" O ASP I 637 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 336 Processing helix chain 'J' and resid 350 through 354 Processing helix chain 'J' and resid 373 through 383 Processing helix chain 'J' and resid 396 through 401 removed outlier: 4.078A pdb=" N ASN J 401 " --> pdb=" O GLU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 401 through 410 removed outlier: 3.678A pdb=" N VAL J 405 " --> pdb=" O ASN J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 410 through 424 Processing helix chain 'J' and resid 432 through 436 removed outlier: 3.738A pdb=" N VAL J 435 " --> pdb=" O THR J 432 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR J 436 " --> pdb=" O SER J 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 432 through 436' Processing helix chain 'J' and resid 460 through 482 removed outlier: 4.109A pdb=" N SER J 464 " --> pdb=" O ARG J 460 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER J 466 " --> pdb=" O ILE J 462 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU J 479 " --> pdb=" O TRP J 475 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 521 Processing helix chain 'J' and resid 540 through 552 Processing helix chain 'J' and resid 553 through 557 removed outlier: 3.872A pdb=" N ARG J 557 " --> pdb=" O ALA J 554 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 587 removed outlier: 3.784A pdb=" N LYS J 587 " --> pdb=" O ALA J 583 " (cutoff:3.500A) Processing helix chain 'J' and resid 590 through 594 Processing helix chain 'J' and resid 623 through 631 Processing helix chain 'J' and resid 637 through 652 removed outlier: 4.057A pdb=" N THR J 641 " --> pdb=" O ASP J 637 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 336 Processing helix chain 'K' and resid 373 through 383 Processing helix chain 'K' and resid 394 through 401 removed outlier: 3.782A pdb=" N TYR K 398 " --> pdb=" O THR K 394 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR K 399 " --> pdb=" O PRO K 395 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN K 401 " --> pdb=" O GLU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 401 through 423 removed outlier: 3.758A pdb=" N VAL K 405 " --> pdb=" O ASN K 401 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU K 412 " --> pdb=" O LEU K 408 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ASN K 413 " --> pdb=" O ASP K 409 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR K 423 " --> pdb=" O TYR K 419 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 436 removed outlier: 4.103A pdb=" N VAL K 435 " --> pdb=" O THR K 432 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N TYR K 436 " --> pdb=" O SER K 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 432 through 436' Processing helix chain 'K' and resid 461 through 481 removed outlier: 3.720A pdb=" N VAL K 465 " --> pdb=" O TRP K 461 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU K 479 " --> pdb=" O TRP K 475 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS K 480 " --> pdb=" O ALA K 476 " (cutoff:3.500A) Processing helix chain 'K' and resid 509 through 521 Processing helix chain 'K' and resid 540 through 552 Processing helix chain 'K' and resid 553 through 557 removed outlier: 3.596A pdb=" N ASN K 556 " --> pdb=" O ASN K 553 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG K 557 " --> pdb=" O ALA K 554 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 553 through 557' Processing helix chain 'K' and resid 574 through 586 Processing helix chain 'K' and resid 588 through 594 removed outlier: 3.733A pdb=" N ARG K 591 " --> pdb=" O HIS K 588 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N HIS K 592 " --> pdb=" O PRO K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 623 through 630 removed outlier: 3.521A pdb=" N HIS K 627 " --> pdb=" O ILE K 623 " (cutoff:3.500A) Processing helix chain 'K' and resid 637 through 652 removed outlier: 3.750A pdb=" N THR K 641 " --> pdb=" O ASP K 637 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 336 Processing helix chain 'L' and resid 373 through 383 Processing helix chain 'L' and resid 394 through 401 removed outlier: 3.506A pdb=" N TYR L 398 " --> pdb=" O THR L 394 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR L 399 " --> pdb=" O PRO L 395 " (cutoff:3.500A) Processing helix chain 'L' and resid 401 through 410 removed outlier: 3.718A pdb=" N VAL L 405 " --> pdb=" O ASN L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 410 through 423 Processing helix chain 'L' and resid 459 through 480 removed outlier: 4.264A pdb=" N TYR L 463 " --> pdb=" O PRO L 459 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER L 464 " --> pdb=" O ARG L 460 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER L 466 " --> pdb=" O ILE L 462 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE L 474 " --> pdb=" O LEU L 470 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU L 479 " --> pdb=" O TRP L 475 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS L 480 " --> pdb=" O ALA L 476 " (cutoff:3.500A) Processing helix chain 'L' and resid 509 through 521 Processing helix chain 'L' and resid 540 through 552 Processing helix chain 'L' and resid 573 through 586 removed outlier: 3.673A pdb=" N LEU L 577 " --> pdb=" O SER L 573 " (cutoff:3.500A) Processing helix chain 'L' and resid 588 through 594 removed outlier: 3.907A pdb=" N ARG L 591 " --> pdb=" O HIS L 588 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N HIS L 592 " --> pdb=" O PRO L 589 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N HIS L 593 " --> pdb=" O LEU L 590 " (cutoff:3.500A) Processing helix chain 'L' and resid 623 through 630 removed outlier: 3.714A pdb=" N HIS L 627 " --> pdb=" O ILE L 623 " (cutoff:3.500A) Processing helix chain 'L' and resid 638 through 652 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 5 removed outlier: 7.612A pdb=" N THR A 3 " --> pdb=" O SER A 27 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE A 29 " --> pdb=" O THR A 3 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 5 " --> pdb=" O ILE A 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 82 removed outlier: 6.619A pdb=" N ILE A 79 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N LEU A 103 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER A 81 " --> pdb=" O LEU A 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 235 removed outlier: 3.598A pdb=" N ALA A 231 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL A 242 " --> pdb=" O GLY A 279 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLY A 279 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N SER A 244 " --> pdb=" O VAL A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 3 Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 7 removed outlier: 5.951A pdb=" N ARG B 134 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ILE B 144 " --> pdb=" O ARG B 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.810A pdb=" N ALA B 231 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR B 278 " --> pdb=" O TRP B 243 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER B 245 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 276 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 247 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 274 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 231 through 235 removed outlier: 3.810A pdb=" N ALA B 231 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N THR B 278 " --> pdb=" O TRP B 243 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER B 245 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE B 276 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL B 247 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU B 274 " --> pdb=" O VAL B 247 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 25 through 30 removed outlier: 8.068A pdb=" N VAL C 5 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE C 29 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ALA C 7 " --> pdb=" O ILE C 29 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL C 78 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 4 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE C 80 " --> pdb=" O VAL C 4 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE C 82 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ARG C 134 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE C 144 " --> pdb=" O ARG C 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 231 through 235 removed outlier: 4.232A pdb=" N ALA C 231 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N THR C 278 " --> pdb=" O TRP C 243 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N SER C 245 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ILE C 276 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 247 " --> pdb=" O LEU C 274 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU C 274 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 57 removed outlier: 7.808A pdb=" N TYR D 57 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE D 29 " --> pdb=" O TYR D 57 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL D 5 " --> pdb=" O SER D 27 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ILE D 29 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ALA D 7 " --> pdb=" O ILE D 29 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL D 78 " --> pdb=" O LYS D 2 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL D 4 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N PHE D 80 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE D 79 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LEU D 103 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N SER D 81 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N ARG D 134 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ILE D 144 " --> pdb=" O ARG D 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 231 through 235 removed outlier: 4.116A pdb=" N ALA D 231 " --> pdb=" O VAL D 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 246 through 248 Processing sheet with id=AB4, first strand: chain 'E' and resid 3 through 5 removed outlier: 6.753A pdb=" N THR E 3 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N PHE E 30 " --> pdb=" O THR E 3 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL E 5 " --> pdb=" O PHE E 30 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N TYR E 57 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ILE E 29 " --> pdb=" O TYR E 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.361A pdb=" N ILE E 79 " --> pdb=" O PHE E 101 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N LEU E 103 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER E 81 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA E 146 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG E 134 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE E 144 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 231 through 235 removed outlier: 4.101A pdb=" N ALA E 231 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL E 242 " --> pdb=" O GLY E 279 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY E 279 " --> pdb=" O VAL E 242 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N SER E 244 " --> pdb=" O VAL E 277 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL E 277 " --> pdb=" O SER E 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 3 through 5 removed outlier: 7.635A pdb=" N THR F 3 " --> pdb=" O SER F 27 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE F 29 " --> pdb=" O THR F 3 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N VAL F 5 " --> pdb=" O ILE F 29 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.663A pdb=" N ILE F 79 " --> pdb=" O PHE F 101 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N LEU F 103 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N SER F 81 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ARG F 134 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE F 144 " --> pdb=" O ARG F 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.833A pdb=" N ALA F 231 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE F 240 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA F 281 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL F 242 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY F 279 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER F 244 " --> pdb=" O VAL F 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 231 through 235 removed outlier: 3.833A pdb=" N ALA F 231 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N PHE F 240 " --> pdb=" O ALA F 281 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA F 281 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL F 242 " --> pdb=" O GLY F 279 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLY F 279 " --> pdb=" O VAL F 242 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N SER F 244 " --> pdb=" O VAL F 277 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 362 through 365 removed outlier: 6.633A pdb=" N VAL G 343 " --> pdb=" O HIS G 363 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL G 365 " --> pdb=" O VAL G 343 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLY G 345 " --> pdb=" O VAL G 365 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR G 344 " --> pdb=" O VAL G 318 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE G 320 " --> pdb=" O TYR G 344 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LEU G 346 " --> pdb=" O ILE G 320 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 427 through 430 removed outlier: 6.905A pdb=" N ILE G 427 " --> pdb=" O THR G 486 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE G 488 " --> pdb=" O ILE G 427 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N PHE G 429 " --> pdb=" O PHE G 488 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ILE G 563 " --> pdb=" O PHE G 485 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU G 487 " --> pdb=" O ILE G 563 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 493 through 494 Processing sheet with id=AC5, first strand: chain 'G' and resid 525 through 527 removed outlier: 5.388A pdb=" N ILE G 525 " --> pdb=" O ARG G 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 534 through 536 Processing sheet with id=AC7, first strand: chain 'H' and resid 362 through 365 removed outlier: 6.885A pdb=" N VAL H 343 " --> pdb=" O HIS H 363 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL H 365 " --> pdb=" O VAL H 343 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY H 345 " --> pdb=" O VAL H 365 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR H 344 " --> pdb=" O VAL H 318 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ILE H 320 " --> pdb=" O TYR H 344 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU H 346 " --> pdb=" O ILE H 320 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE H 428 " --> pdb=" O VAL H 386 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N ILE H 427 " --> pdb=" O THR H 486 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE H 488 " --> pdb=" O ILE H 427 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE H 429 " --> pdb=" O PHE H 488 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE H 565 " --> pdb=" O ARG H 489 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 525 through 527 removed outlier: 5.805A pdb=" N ILE H 525 " --> pdb=" O ARG H 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'H' and resid 534 through 535 Processing sheet with id=AD1, first strand: chain 'I' and resid 362 through 366 removed outlier: 3.537A pdb=" N TYR I 344 " --> pdb=" O VAL I 318 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE I 320 " --> pdb=" O TYR I 344 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU I 346 " --> pdb=" O ILE I 320 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG I 317 " --> pdb=" O VAL I 385 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N LEU I 387 " --> pdb=" O ARG I 317 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU I 319 " --> pdb=" O LEU I 387 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL I 386 " --> pdb=" O ARG I 426 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE I 428 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ILE I 427 " --> pdb=" O THR I 486 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N PHE I 488 " --> pdb=" O ILE I 427 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE I 429 " --> pdb=" O PHE I 488 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE I 485 " --> pdb=" O GLU I 561 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE I 563 " --> pdb=" O PHE I 485 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LEU I 487 " --> pdb=" O ILE I 563 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N ILE I 565 " --> pdb=" O LEU I 487 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ARG I 489 " --> pdb=" O ILE I 565 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 493 through 494 Processing sheet with id=AD3, first strand: chain 'I' and resid 525 through 527 removed outlier: 5.796A pdb=" N ILE I 525 " --> pdb=" O ARG I 601 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'I' and resid 534 through 535 Processing sheet with id=AD5, first strand: chain 'J' and resid 362 through 366 removed outlier: 3.797A pdb=" N TYR J 344 " --> pdb=" O VAL J 318 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE J 320 " --> pdb=" O TYR J 344 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU J 346 " --> pdb=" O ILE J 320 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL J 386 " --> pdb=" O ARG J 426 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE J 428 " --> pdb=" O VAL J 386 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE J 427 " --> pdb=" O THR J 486 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N PHE J 488 " --> pdb=" O ILE J 427 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N PHE J 429 " --> pdb=" O PHE J 488 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE J 563 " --> pdb=" O PHE J 485 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N LEU J 487 " --> pdb=" O ILE J 563 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE J 565 " --> pdb=" O LEU J 487 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ARG J 489 " --> pdb=" O ILE J 565 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 493 through 494 Processing sheet with id=AD7, first strand: chain 'J' and resid 526 through 528 Processing sheet with id=AD8, first strand: chain 'J' and resid 534 through 536 Processing sheet with id=AD9, first strand: chain 'K' and resid 362 through 365 removed outlier: 3.509A pdb=" N TYR K 344 " --> pdb=" O VAL K 318 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE K 320 " --> pdb=" O TYR K 344 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU K 346 " --> pdb=" O ILE K 320 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ARG K 317 " --> pdb=" O VAL K 385 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU K 387 " --> pdb=" O ARG K 317 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU K 319 " --> pdb=" O LEU K 387 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL K 386 " --> pdb=" O ARG K 426 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE K 428 " --> pdb=" O VAL K 386 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE K 427 " --> pdb=" O THR K 486 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N PHE K 488 " --> pdb=" O ILE K 427 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE K 429 " --> pdb=" O PHE K 488 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ILE K 563 " --> pdb=" O PHE K 485 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU K 487 " --> pdb=" O ILE K 563 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 493 through 494 Processing sheet with id=AE2, first strand: chain 'K' and resid 525 through 528 removed outlier: 5.436A pdb=" N ILE K 525 " --> pdb=" O ARG K 601 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL K 603 " --> pdb=" O ILE K 525 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU K 527 " --> pdb=" O VAL K 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'K' and resid 534 through 536 Processing sheet with id=AE4, first strand: chain 'L' and resid 362 through 365 removed outlier: 6.630A pdb=" N VAL L 343 " --> pdb=" O HIS L 363 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N VAL L 365 " --> pdb=" O VAL L 343 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY L 345 " --> pdb=" O VAL L 365 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE L 320 " --> pdb=" O TYR L 344 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU L 346 " --> pdb=" O ILE L 320 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 427 through 430 removed outlier: 6.666A pdb=" N ILE L 427 " --> pdb=" O THR L 486 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N PHE L 488 " --> pdb=" O ILE L 427 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE L 429 " --> pdb=" O PHE L 488 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N PHE L 485 " --> pdb=" O GLU L 561 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N ILE L 563 " --> pdb=" O PHE L 485 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU L 487 " --> pdb=" O ILE L 563 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N ILE L 565 " --> pdb=" O LEU L 487 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ARG L 489 " --> pdb=" O ILE L 565 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'L' and resid 493 through 494 Processing sheet with id=AE7, first strand: chain 'L' and resid 525 through 528 Processing sheet with id=AE8, first strand: chain 'L' and resid 535 through 536 1148 hydrogen bonds defined for protein. 3240 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: 5.38 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6252 1.33 - 1.45: 7057 1.45 - 1.58: 16745 1.58 - 1.70: 0 1.70 - 1.82: 180 Bond restraints: 30234 Sorted by residual: bond pdb=" CB GLN J 533 " pdb=" CG GLN J 533 " ideal model delta sigma weight residual 1.520 1.462 0.058 3.00e-02 1.11e+03 3.73e+00 bond pdb=" CA ASN F 102 " pdb=" CB ASN F 102 " ideal model delta sigma weight residual 1.531 1.558 -0.027 1.52e-02 4.33e+03 3.19e+00 bond pdb=" CB VAL B 247 " pdb=" CG2 VAL B 247 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.16e+00 bond pdb=" CA PHE G 485 " pdb=" CB PHE G 485 " ideal model delta sigma weight residual 1.532 1.562 -0.030 1.74e-02 3.30e+03 2.88e+00 bond pdb=" CA MET L 638 " pdb=" C MET L 638 " ideal model delta sigma weight residual 1.521 1.537 -0.017 9.90e-03 1.02e+04 2.80e+00 ... (remaining 30229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 40603 3.91 - 7.82: 403 7.82 - 11.73: 55 11.73 - 15.65: 7 15.65 - 19.56: 2 Bond angle restraints: 41070 Sorted by residual: angle pdb=" CB ARG G 355 " pdb=" CG ARG G 355 " pdb=" CD ARG G 355 " ideal model delta sigma weight residual 111.30 124.82 -13.52 2.30e+00 1.89e-01 3.46e+01 angle pdb=" C ASN G 401 " pdb=" CA ASN G 401 " pdb=" CB ASN G 401 " ideal model delta sigma weight residual 111.15 118.27 -7.12 1.24e+00 6.50e-01 3.30e+01 angle pdb=" CA LEU L 590 " pdb=" CB LEU L 590 " pdb=" CG LEU L 590 " ideal model delta sigma weight residual 116.30 135.86 -19.56 3.50e+00 8.16e-02 3.12e+01 angle pdb=" N GLY B 113 " pdb=" CA GLY B 113 " pdb=" C GLY B 113 " ideal model delta sigma weight residual 111.56 116.87 -5.31 1.01e+00 9.80e-01 2.76e+01 angle pdb=" CA LEU H 590 " pdb=" CB LEU H 590 " pdb=" CG LEU H 590 " ideal model delta sigma weight residual 116.30 134.55 -18.25 3.50e+00 8.16e-02 2.72e+01 ... (remaining 41065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 15216 17.98 - 35.96: 2093 35.96 - 53.93: 508 53.93 - 71.91: 69 71.91 - 89.89: 12 Dihedral angle restraints: 17898 sinusoidal: 7158 harmonic: 10740 Sorted by residual: dihedral pdb=" CA ARG C 114 " pdb=" C ARG C 114 " pdb=" N ALA C 115 " pdb=" CA ALA C 115 " ideal model delta harmonic sigma weight residual 180.00 147.90 32.10 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA PHE C 198 " pdb=" C PHE C 198 " pdb=" N GLY C 199 " pdb=" CA GLY C 199 " ideal model delta harmonic sigma weight residual -180.00 -149.91 -30.09 0 5.00e+00 4.00e-02 3.62e+01 dihedral pdb=" CA ASP I 637 " pdb=" C ASP I 637 " pdb=" N MET I 638 " pdb=" CA MET I 638 " ideal model delta harmonic sigma weight residual -180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 17895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3272 0.051 - 0.102: 988 0.102 - 0.152: 255 0.152 - 0.203: 25 0.203 - 0.254: 8 Chirality restraints: 4548 Sorted by residual: chirality pdb=" CB ILE G 562 " pdb=" CA ILE G 562 " pdb=" CG1 ILE G 562 " pdb=" CG2 ILE G 562 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU K 387 " pdb=" CB LEU K 387 " pdb=" CD1 LEU K 387 " pdb=" CD2 LEU K 387 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR B 176 " pdb=" CA THR B 176 " pdb=" OG1 THR B 176 " pdb=" CG2 THR B 176 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 4545 not shown) Planarity restraints: 5322 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP K 375 " -0.042 2.00e-02 2.50e+03 3.91e-02 3.83e+01 pdb=" CG TRP K 375 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 TRP K 375 " -0.046 2.00e-02 2.50e+03 pdb=" CD2 TRP K 375 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP K 375 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP K 375 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP K 375 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 375 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 375 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP K 375 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 423 " 0.023 2.00e-02 2.50e+03 3.12e-02 1.95e+01 pdb=" CG TYR L 423 " -0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR L 423 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR L 423 " 0.026 2.00e-02 2.50e+03 pdb=" CE1 TYR L 423 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR L 423 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR L 423 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 423 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G 632 " 0.022 2.00e-02 2.50e+03 2.73e-02 1.86e+01 pdb=" CG TRP G 632 " -0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP G 632 " 0.039 2.00e-02 2.50e+03 pdb=" CD2 TRP G 632 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP G 632 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP G 632 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 632 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 632 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 632 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP G 632 " 0.002 2.00e-02 2.50e+03 ... (remaining 5319 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 10716 2.87 - 3.38: 30478 3.38 - 3.88: 48337 3.88 - 4.39: 53720 4.39 - 4.90: 84998 Nonbonded interactions: 228249 Sorted by model distance: nonbonded pdb=" O ASN G 401 " pdb=" OD1 ASN G 401 " model vdw 2.358 3.040 nonbonded pdb=" O GLU I 640 " pdb=" OD1 ASP I 643 " model vdw 2.383 3.040 nonbonded pdb=" O SER C 75 " pdb=" OG SER C 75 " model vdw 2.392 3.040 nonbonded pdb=" O ASP G 539 " pdb=" OD1 ASP G 542 " model vdw 2.402 3.040 nonbonded pdb=" O ASP A 90 " pdb=" OE1 GLN A 94 " model vdw 2.427 3.040 ... (remaining 228244 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.220 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30234 Z= 0.193 Angle : 1.022 19.558 41070 Z= 0.546 Chirality : 0.052 0.254 4548 Planarity : 0.006 0.064 5322 Dihedral : 16.841 89.888 10974 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 2.21 % Allowed : 37.14 % Favored : 60.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.42 (0.13), residues: 3666 helix: -0.72 (0.14), residues: 1349 sheet: -0.32 (0.24), residues: 484 loop : -1.22 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG H 460 TYR 0.076 0.002 TYR L 423 PHE 0.032 0.002 PHE E 207 TRP 0.106 0.004 TRP K 375 HIS 0.024 0.001 HIS L 363 Details of bonding type rmsd covalent geometry : bond 0.00398 (30234) covalent geometry : angle 1.02185 (41070) hydrogen bonds : bond 0.15132 ( 1130) hydrogen bonds : angle 7.80012 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 1079 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 11 MET cc_start: 0.7468 (pmm) cc_final: 0.7023 (pmm) REVERT: A 64 HIS cc_start: 0.4716 (m-70) cc_final: 0.4512 (m-70) REVERT: A 70 ARG cc_start: 0.8097 (mtm110) cc_final: 0.7293 (mtm-85) REVERT: A 74 LEU cc_start: 0.5433 (OUTLIER) cc_final: 0.4450 (tp) REVERT: A 84 TYR cc_start: 0.5754 (t80) cc_final: 0.4878 (t80) REVERT: A 159 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.6779 (mm) REVERT: A 164 LYS cc_start: 0.8428 (mttt) cc_final: 0.8106 (mtmm) REVERT: A 175 GLN cc_start: 0.8372 (pp30) cc_final: 0.8073 (pm20) REVERT: A 211 HIS cc_start: 0.6461 (m-70) cc_final: 0.6248 (m-70) REVERT: A 246 ARG cc_start: 0.7406 (pmt-80) cc_final: 0.6766 (pmt-80) REVERT: B 13 CYS cc_start: 0.8011 (m) cc_final: 0.7525 (m) REVERT: B 91 GLU cc_start: 0.7452 (tp30) cc_final: 0.6660 (tp30) REVERT: B 110 LYS cc_start: 0.6190 (tmtt) cc_final: 0.5853 (ttmm) REVERT: B 172 LEU cc_start: 0.8211 (tt) cc_final: 0.7937 (pp) REVERT: B 215 SER cc_start: 0.8299 (p) cc_final: 0.7723 (t) REVERT: C 13 CYS cc_start: 0.7976 (m) cc_final: 0.7576 (m) REVERT: C 119 TRP cc_start: 0.5833 (m100) cc_final: 0.5443 (m-10) REVERT: D 1 MET cc_start: 0.6975 (tpp) cc_final: 0.6442 (ptp) REVERT: D 9 HIS cc_start: 0.7221 (t-90) cc_final: 0.6980 (t-170) REVERT: D 13 CYS cc_start: 0.8188 (m) cc_final: 0.7489 (m) REVERT: D 20 LEU cc_start: 0.8349 (tp) cc_final: 0.7921 (pp) REVERT: D 94 GLN cc_start: 0.7830 (pt0) cc_final: 0.7250 (pt0) REVERT: D 103 LEU cc_start: 0.7838 (tp) cc_final: 0.7474 (tp) REVERT: D 172 LEU cc_start: 0.8794 (tp) cc_final: 0.8524 (tt) REVERT: D 175 GLN cc_start: 0.8478 (pm20) cc_final: 0.8248 (pm20) REVERT: D 177 LEU cc_start: 0.8057 (mt) cc_final: 0.7820 (pp) REVERT: D 275 GLU cc_start: 0.5143 (mm-30) cc_final: 0.4817 (mm-30) REVERT: E 159 ILE cc_start: 0.7866 (tp) cc_final: 0.7108 (mm) REVERT: E 163 HIS cc_start: 0.7487 (m-70) cc_final: 0.7196 (m-70) REVERT: E 171 GLN cc_start: 0.8272 (pp30) cc_final: 0.8045 (pp30) REVERT: E 175 GLN cc_start: 0.8309 (pm20) cc_final: 0.7882 (pm20) REVERT: E 239 LYS cc_start: 0.5762 (tppt) cc_final: 0.5477 (tptp) REVERT: F 17 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8048 (mm-30) REVERT: F 84 TYR cc_start: 0.4518 (t80) cc_final: 0.4048 (t80) REVERT: F 220 MET cc_start: 0.7222 (mmp) cc_final: 0.6670 (mmp) REVERT: G 321 LEU cc_start: 0.8549 (mp) cc_final: 0.8155 (pp) REVERT: G 373 SER cc_start: 0.6011 (p) cc_final: 0.5741 (t) REVERT: G 403 LEU cc_start: 0.7257 (mp) cc_final: 0.6187 (mm) REVERT: G 415 ARG cc_start: 0.7316 (mtp180) cc_final: 0.7042 (mtt180) REVERT: G 428 ILE cc_start: 0.7088 (mt) cc_final: 0.6530 (mt) REVERT: G 467 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7680 (mmmt) REVERT: G 479 GLU cc_start: 0.7863 (mp0) cc_final: 0.7578 (mp0) REVERT: G 486 THR cc_start: 0.7272 (p) cc_final: 0.6987 (p) REVERT: G 510 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6405 (mpt-90) REVERT: G 527 LEU cc_start: 0.8573 (mp) cc_final: 0.8290 (pp) REVERT: G 542 ASP cc_start: 0.7906 (p0) cc_final: 0.7641 (p0) REVERT: G 570 ASN cc_start: 0.7548 (t0) cc_final: 0.6782 (p0) REVERT: G 647 ASP cc_start: 0.8215 (t0) cc_final: 0.7861 (t70) REVERT: H 378 TYR cc_start: 0.7362 (t80) cc_final: 0.7160 (t80) REVERT: H 467 LYS cc_start: 0.8037 (mmmt) cc_final: 0.7754 (mmmt) REVERT: H 486 THR cc_start: 0.7452 (m) cc_final: 0.6904 (p) REVERT: H 498 LEU cc_start: 0.6705 (mt) cc_final: 0.6454 (pp) REVERT: H 534 LYS cc_start: 0.4338 (OUTLIER) cc_final: 0.2944 (pptt) REVERT: H 545 GLU cc_start: 0.6555 (mm-30) cc_final: 0.6139 (mm-30) REVERT: H 548 TYR cc_start: 0.6724 (t80) cc_final: 0.6515 (t80) REVERT: H 619 ARG cc_start: 0.4315 (ptp90) cc_final: 0.3270 (ppt170) REVERT: H 632 TRP cc_start: 0.6939 (t60) cc_final: 0.6714 (t60) REVERT: I 353 ILE cc_start: 0.8141 (tp) cc_final: 0.7929 (pt) REVERT: I 467 LYS cc_start: 0.8030 (mmmt) cc_final: 0.7294 (mmmt) REVERT: I 542 ASP cc_start: 0.7191 (OUTLIER) cc_final: 0.6550 (t0) REVERT: I 570 ASN cc_start: 0.7669 (m-40) cc_final: 0.7349 (p0) REVERT: I 576 GLU cc_start: 0.8025 (pt0) cc_final: 0.7383 (pm20) REVERT: I 577 LEU cc_start: 0.9057 (mt) cc_final: 0.8418 (pp) REVERT: I 637 ASP cc_start: 0.5310 (t0) cc_final: 0.4649 (t0) REVERT: J 327 ILE cc_start: 0.7889 (pt) cc_final: 0.7052 (mt) REVERT: J 365 VAL cc_start: 0.6735 (t) cc_final: 0.6441 (t) REVERT: J 381 LYS cc_start: 0.7128 (tppt) cc_final: 0.6826 (tppt) REVERT: J 403 LEU cc_start: 0.7728 (mt) cc_final: 0.7294 (mp) REVERT: J 407 GLU cc_start: 0.7440 (mt-10) cc_final: 0.7117 (mp0) REVERT: J 408 LEU cc_start: 0.7905 (tp) cc_final: 0.7010 (pp) REVERT: J 411 GLU cc_start: 0.6450 (pm20) cc_final: 0.5750 (pm20) REVERT: J 412 GLU cc_start: 0.6716 (mm-30) cc_final: 0.5974 (mm-30) REVERT: J 438 MET cc_start: -0.2333 (mtm) cc_final: -0.3061 (mtm) REVERT: J 486 THR cc_start: 0.7320 (m) cc_final: 0.6555 (p) REVERT: J 492 ASN cc_start: 0.7978 (t0) cc_final: 0.7566 (t0) REVERT: J 570 ASN cc_start: 0.7823 (t0) cc_final: 0.6091 (p0) REVERT: J 576 GLU cc_start: 0.7820 (pt0) cc_final: 0.7617 (pm20) REVERT: K 377 GLU cc_start: 0.6440 (tp30) cc_final: 0.5857 (mm-30) REVERT: K 411 GLU cc_start: 0.6573 (tp30) cc_final: 0.6213 (tp30) REVERT: K 412 GLU cc_start: 0.7505 (mp0) cc_final: 0.6916 (mp0) REVERT: K 415 ARG cc_start: 0.7355 (mtp180) cc_final: 0.7095 (mtp180) REVERT: K 427 ILE cc_start: 0.6455 (tt) cc_final: 0.6082 (mm) REVERT: K 438 MET cc_start: -0.0546 (mtm) cc_final: -0.1097 (mtm) REVERT: K 467 LYS cc_start: 0.7909 (mmmt) cc_final: 0.7209 (mmmt) REVERT: K 594 PHE cc_start: 0.6072 (m-80) cc_final: 0.5751 (m-80) REVERT: L 467 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7554 (mmmt) REVERT: L 472 ARG cc_start: 0.7615 (mmt180) cc_final: 0.7099 (mmt180) REVERT: L 485 PHE cc_start: 0.5720 (p90) cc_final: 0.5470 (p90) REVERT: L 512 ILE cc_start: 0.7512 (tp) cc_final: 0.7062 (mm) REVERT: L 515 LEU cc_start: 0.8597 (mt) cc_final: 0.8328 (mt) REVERT: L 562 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8170 (mm) REVERT: L 570 ASN cc_start: 0.8060 (m-40) cc_final: 0.7804 (t0) REVERT: L 576 GLU cc_start: 0.8545 (mp0) cc_final: 0.8252 (pm20) REVERT: L 633 GLU cc_start: 0.7017 (tm-30) cc_final: 0.6641 (tm-30) outliers start: 69 outliers final: 49 residues processed: 1110 average time/residue: 0.2051 time to fit residues: 351.4808 Evaluate side-chains 1081 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 1026 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain F residue 45 VAL Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 329 ASN Chi-restraints excluded: chain G residue 387 LEU Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 510 ARG Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 631 ASP Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 649 PHE Chi-restraints excluded: chain I residue 405 VAL Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 462 ILE Chi-restraints excluded: chain I residue 494 MET Chi-restraints excluded: chain I residue 541 ARG Chi-restraints excluded: chain I residue 542 ASP Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 633 GLU Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 335 LEU Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 474 ILE Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain K residue 408 LEU Chi-restraints excluded: chain K residue 422 LYS Chi-restraints excluded: chain K residue 638 MET Chi-restraints excluded: chain L residue 407 GLU Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 644 GLU Chi-restraints excluded: chain L residue 649 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN B 211 HIS C 32 HIS C 64 HIS D 133 HIS ** D 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 GLN ** D 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 468 GLN ** J 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN K 570 ASN ** K 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 639 GLN L 329 ASN ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 553 ASN ** L 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.156510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.123509 restraints weight = 74919.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.126885 restraints weight = 55552.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.129454 restraints weight = 44099.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.131455 restraints weight = 36664.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.132865 restraints weight = 31609.031| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30234 Z= 0.146 Angle : 0.773 15.403 41070 Z= 0.389 Chirality : 0.048 0.219 4548 Planarity : 0.005 0.075 5322 Dihedral : 7.027 58.630 4163 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.53 % Favored : 95.44 % Rotamer: Outliers : 5.15 % Allowed : 28.02 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.09 (0.13), residues: 3666 helix: -0.30 (0.14), residues: 1367 sheet: -0.34 (0.24), residues: 485 loop : -1.10 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 415 TYR 0.026 0.001 TYR J 423 PHE 0.018 0.002 PHE H 488 TRP 0.037 0.002 TRP K 375 HIS 0.020 0.001 HIS A 163 Details of bonding type rmsd covalent geometry : bond 0.00310 (30234) covalent geometry : angle 0.77293 (41070) hydrogen bonds : bond 0.05046 ( 1130) hydrogen bonds : angle 6.16003 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 1051 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 HIS cc_start: 0.7783 (m90) cc_final: 0.7558 (m90) REVERT: A 17 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8425 (mm-30) REVERT: A 74 LEU cc_start: 0.5027 (OUTLIER) cc_final: 0.4332 (tp) REVERT: A 159 ILE cc_start: 0.8414 (mt) cc_final: 0.8073 (mm) REVERT: A 163 HIS cc_start: 0.8513 (m-70) cc_final: 0.8156 (m-70) REVERT: A 215 SER cc_start: 0.8439 (p) cc_final: 0.8153 (t) REVERT: A 275 GLU cc_start: 0.7148 (tp30) cc_final: 0.6140 (pm20) REVERT: B 13 CYS cc_start: 0.7927 (m) cc_final: 0.7581 (m) REVERT: B 70 ARG cc_start: 0.8705 (mpp80) cc_final: 0.8464 (mpp80) REVERT: B 110 LYS cc_start: 0.6376 (tmtt) cc_final: 0.6077 (ttmm) REVERT: B 119 TRP cc_start: 0.6740 (OUTLIER) cc_final: 0.6521 (t60) REVERT: B 134 ARG cc_start: 0.5811 (tpt-90) cc_final: 0.5390 (tpt-90) REVERT: B 163 HIS cc_start: 0.8786 (m-70) cc_final: 0.8410 (m-70) REVERT: B 172 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7708 (pp) REVERT: B 175 GLN cc_start: 0.8221 (pm20) cc_final: 0.7931 (pm20) REVERT: B 215 SER cc_start: 0.8263 (p) cc_final: 0.7897 (t) REVERT: B 298 LEU cc_start: 0.6392 (tp) cc_final: 0.5988 (mt) REVERT: C 13 CYS cc_start: 0.8339 (m) cc_final: 0.7810 (m) REVERT: C 119 TRP cc_start: 0.6884 (m100) cc_final: 0.6355 (m-10) REVERT: C 164 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8135 (mtmm) REVERT: C 175 GLN cc_start: 0.8466 (pm20) cc_final: 0.7875 (pm20) REVERT: C 239 LYS cc_start: 0.7893 (mmmt) cc_final: 0.7615 (tmtt) REVERT: D 1 MET cc_start: 0.7310 (tpp) cc_final: 0.6343 (ptp) REVERT: D 9 HIS cc_start: 0.7690 (t-90) cc_final: 0.7420 (t-90) REVERT: D 13 CYS cc_start: 0.8617 (m) cc_final: 0.8099 (m) REVERT: D 17 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8315 (mm-30) REVERT: D 24 TYR cc_start: 0.5197 (m-80) cc_final: 0.4087 (m-80) REVERT: D 83 TYR cc_start: 0.6796 (m-80) cc_final: 0.6277 (m-80) REVERT: D 84 TYR cc_start: 0.6516 (t80) cc_final: 0.6219 (t80) REVERT: D 94 GLN cc_start: 0.7692 (pt0) cc_final: 0.7171 (pt0) REVERT: D 101 PHE cc_start: 0.7887 (m-80) cc_final: 0.7599 (m-80) REVERT: D 175 GLN cc_start: 0.8464 (pm20) cc_final: 0.8215 (pm20) REVERT: D 177 LEU cc_start: 0.8104 (mt) cc_final: 0.7901 (pp) REVERT: E 9 HIS cc_start: 0.7042 (t70) cc_final: 0.6821 (t70) REVERT: E 51 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8073 (mt-10) REVERT: E 70 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8293 (mtm-85) REVERT: E 159 ILE cc_start: 0.8330 (tp) cc_final: 0.7606 (mm) REVERT: E 163 HIS cc_start: 0.8533 (m-70) cc_final: 0.7941 (m-70) REVERT: E 170 ARG cc_start: 0.7965 (tpp-160) cc_final: 0.7664 (tpp-160) REVERT: E 171 GLN cc_start: 0.8528 (pp30) cc_final: 0.8297 (pp30) REVERT: E 175 GLN cc_start: 0.8192 (pm20) cc_final: 0.7700 (pm20) REVERT: E 220 MET cc_start: 0.7666 (mmt) cc_final: 0.7441 (mmt) REVERT: F 70 ARG cc_start: 0.9011 (mmt90) cc_final: 0.8704 (mmm-85) REVERT: F 84 TYR cc_start: 0.5729 (t80) cc_final: 0.5362 (t80) REVERT: F 117 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5299 (mt) REVERT: F 220 MET cc_start: 0.7539 (mmp) cc_final: 0.7195 (mmp) REVERT: F 280 GLN cc_start: 0.6394 (OUTLIER) cc_final: 0.4861 (pp30) REVERT: G 327 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7358 (mp) REVERT: G 330 HIS cc_start: 0.8246 (m90) cc_final: 0.8019 (m90) REVERT: G 331 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8569 (tp) REVERT: G 334 ARG cc_start: 0.8077 (tpp-160) cc_final: 0.7366 (tpp-160) REVERT: G 338 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.4247 (mp0) REVERT: G 339 ASP cc_start: 0.8089 (p0) cc_final: 0.7300 (p0) REVERT: G 357 LEU cc_start: 0.7999 (mt) cc_final: 0.7694 (pp) REVERT: G 379 HIS cc_start: 0.7449 (m-70) cc_final: 0.6771 (m-70) REVERT: G 415 ARG cc_start: 0.8245 (mtp180) cc_final: 0.8018 (mtt180) REVERT: G 466 SER cc_start: 0.8543 (m) cc_final: 0.8258 (p) REVERT: G 467 LYS cc_start: 0.8414 (mmmt) cc_final: 0.7629 (mmmt) REVERT: G 479 GLU cc_start: 0.8139 (mp0) cc_final: 0.7890 (mp0) REVERT: G 480 LYS cc_start: 0.7422 (mptt) cc_final: 0.6952 (mptt) REVERT: G 486 THR cc_start: 0.7586 (p) cc_final: 0.7327 (p) REVERT: G 527 LEU cc_start: 0.8698 (mp) cc_final: 0.8398 (pp) REVERT: G 637 ASP cc_start: 0.6105 (m-30) cc_final: 0.5691 (t70) REVERT: H 320 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8189 (pt) REVERT: H 327 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7672 (pt) REVERT: H 356 PHE cc_start: 0.8097 (m-10) cc_final: 0.6950 (m-80) REVERT: H 428 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7415 (mm) REVERT: H 467 LYS cc_start: 0.8511 (mmmt) cc_final: 0.7740 (mmmt) REVERT: H 486 THR cc_start: 0.7755 (m) cc_final: 0.7370 (t) REVERT: H 488 PHE cc_start: 0.7550 (p90) cc_final: 0.7300 (p90) REVERT: H 545 GLU cc_start: 0.7638 (mm-30) cc_final: 0.6941 (mm-30) REVERT: H 561 GLU cc_start: 0.5792 (mp0) cc_final: 0.5554 (mp0) REVERT: H 588 HIS cc_start: 0.7897 (t70) cc_final: 0.7695 (t70) REVERT: H 633 GLU cc_start: 0.8354 (mp0) cc_final: 0.8134 (mp0) REVERT: I 353 ILE cc_start: 0.8600 (tp) cc_final: 0.8184 (pt) REVERT: I 467 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7241 (mmmt) REVERT: I 469 LEU cc_start: 0.9081 (tp) cc_final: 0.8844 (mm) REVERT: I 492 ASN cc_start: 0.7331 (t0) cc_final: 0.6910 (t0) REVERT: I 542 ASP cc_start: 0.7523 (m-30) cc_final: 0.6846 (t70) REVERT: I 570 ASN cc_start: 0.8206 (m-40) cc_final: 0.7211 (p0) REVERT: I 575 GLU cc_start: 0.8625 (tt0) cc_final: 0.7984 (mt-10) REVERT: I 576 GLU cc_start: 0.8237 (pt0) cc_final: 0.7963 (pt0) REVERT: I 594 PHE cc_start: 0.6881 (t80) cc_final: 0.6673 (t80) REVERT: I 628 ARG cc_start: 0.8474 (ptm-80) cc_final: 0.8165 (ptm-80) REVERT: J 334 ARG cc_start: 0.7708 (tmt170) cc_final: 0.7415 (tmt170) REVERT: J 365 VAL cc_start: 0.6755 (t) cc_final: 0.6478 (t) REVERT: J 404 ARG cc_start: 0.8061 (tpt170) cc_final: 0.7805 (tpt170) REVERT: J 407 GLU cc_start: 0.8371 (mt-10) cc_final: 0.7932 (mp0) REVERT: J 411 GLU cc_start: 0.7396 (pm20) cc_final: 0.7118 (pm20) REVERT: J 438 MET cc_start: -0.2245 (mtm) cc_final: -0.2631 (mtm) REVERT: J 461 TRP cc_start: 0.6837 (m-90) cc_final: 0.6431 (m-90) REVERT: J 486 THR cc_start: 0.7419 (m) cc_final: 0.6595 (p) REVERT: J 488 PHE cc_start: 0.7677 (p90) cc_final: 0.7299 (p90) REVERT: J 492 ASN cc_start: 0.7966 (t0) cc_final: 0.7314 (t0) REVERT: J 576 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: J 639 GLN cc_start: 0.8441 (pm20) cc_final: 0.8169 (pm20) REVERT: K 406 PHE cc_start: 0.7893 (t80) cc_final: 0.6684 (t80) REVERT: K 415 ARG cc_start: 0.8328 (mtp180) cc_final: 0.8083 (mtp180) REVERT: K 438 MET cc_start: -0.1062 (mtm) cc_final: -0.1298 (mtm) REVERT: K 466 SER cc_start: 0.8568 (m) cc_final: 0.8257 (p) REVERT: K 467 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7398 (mmmt) REVERT: K 472 ARG cc_start: 0.8545 (mtt180) cc_final: 0.8288 (mtt180) REVERT: K 475 TRP cc_start: 0.8150 (t-100) cc_final: 0.7941 (t60) REVERT: K 488 PHE cc_start: 0.7732 (p90) cc_final: 0.7213 (p90) REVERT: K 491 PHE cc_start: 0.6399 (m-80) cc_final: 0.5590 (m-10) REVERT: K 492 ASN cc_start: 0.7416 (t0) cc_final: 0.6958 (p0) REVERT: K 590 LEU cc_start: 0.8562 (tt) cc_final: 0.7984 (mm) REVERT: K 594 PHE cc_start: 0.7044 (m-80) cc_final: 0.6769 (m-80) REVERT: K 638 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7782 (pmm) REVERT: L 372 HIS cc_start: 0.6980 (m90) cc_final: 0.6664 (m90) REVERT: L 427 ILE cc_start: 0.6263 (OUTLIER) cc_final: 0.5870 (pt) REVERT: L 467 LYS cc_start: 0.8424 (mmmt) cc_final: 0.7673 (mmmt) REVERT: L 470 LEU cc_start: 0.9018 (tt) cc_final: 0.8654 (mt) REVERT: L 472 ARG cc_start: 0.8400 (mmt180) cc_final: 0.7418 (mmt90) REVERT: L 477 TYR cc_start: 0.6781 (m-10) cc_final: 0.6516 (m-10) REVERT: L 480 LYS cc_start: 0.6172 (OUTLIER) cc_final: 0.4818 (pptt) REVERT: L 488 PHE cc_start: 0.7873 (p90) cc_final: 0.7496 (p90) REVERT: L 492 ASN cc_start: 0.6877 (t0) cc_final: 0.6590 (t0) REVERT: L 510 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7779 (mmp80) REVERT: L 512 ILE cc_start: 0.8029 (tp) cc_final: 0.7551 (pt) REVERT: L 515 LEU cc_start: 0.8689 (mt) cc_final: 0.8445 (mt) REVERT: L 576 GLU cc_start: 0.8701 (mp0) cc_final: 0.8500 (pm20) outliers start: 161 outliers final: 98 residues processed: 1129 average time/residue: 0.1986 time to fit residues: 346.9927 Evaluate side-chains 1125 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 1012 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 119 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 152 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 241 THR Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 377 GLU Chi-restraints excluded: chain G residue 382 LYS Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 463 TYR Chi-restraints excluded: chain G residue 489 ARG Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 630 LEU Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 398 TYR Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 456 VAL Chi-restraints excluded: chain H residue 463 TYR Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 648 PHE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 410 PHE Chi-restraints excluded: chain I residue 411 GLU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 463 TYR Chi-restraints excluded: chain I residue 465 VAL Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 633 GLU Chi-restraints excluded: chain I residue 641 THR Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 335 LEU Chi-restraints excluded: chain J residue 383 CYS Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 494 MET Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 576 GLU Chi-restraints excluded: chain J residue 631 ASP Chi-restraints excluded: chain J residue 649 PHE Chi-restraints excluded: chain K residue 383 CYS Chi-restraints excluded: chain K residue 428 ILE Chi-restraints excluded: chain K residue 494 MET Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 638 MET Chi-restraints excluded: chain K residue 648 PHE Chi-restraints excluded: chain L residue 373 SER Chi-restraints excluded: chain L residue 380 VAL Chi-restraints excluded: chain L residue 413 ASN Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 427 ILE Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 463 TYR Chi-restraints excluded: chain L residue 480 LYS Chi-restraints excluded: chain L residue 494 MET Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 585 PHE Chi-restraints excluded: chain L residue 644 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 133 optimal weight: 0.0470 chunk 169 optimal weight: 9.9990 chunk 191 optimal weight: 0.6980 chunk 323 optimal weight: 2.9990 chunk 334 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 313 optimal weight: 7.9990 chunk 143 optimal weight: 0.0980 chunk 138 optimal weight: 1.9990 chunk 265 optimal weight: 0.2980 overall best weight: 0.4280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 HIS B 73 GLN B 102 ASN B 171 GLN B 211 HIS C 64 HIS D 147 GLN D 171 GLN D 218 HIS ** D 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 533 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 570 ASN ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 627 HIS ** J 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 518 ASN ** K 588 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 639 GLN ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 588 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.157040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.124299 restraints weight = 74011.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.127706 restraints weight = 54590.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.130344 restraints weight = 43061.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.132352 restraints weight = 35737.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.133841 restraints weight = 30727.300| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30234 Z= 0.132 Angle : 0.737 13.891 41070 Z= 0.365 Chirality : 0.047 0.210 4548 Planarity : 0.004 0.065 5322 Dihedral : 5.912 58.527 4094 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 5.25 % Allowed : 27.35 % Favored : 67.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.14), residues: 3666 helix: -0.19 (0.14), residues: 1377 sheet: -0.24 (0.24), residues: 498 loop : -1.04 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 489 TYR 0.028 0.001 TYR J 423 PHE 0.019 0.001 PHE H 429 TRP 0.039 0.002 TRP G 493 HIS 0.015 0.001 HIS J 588 Details of bonding type rmsd covalent geometry : bond 0.00289 (30234) covalent geometry : angle 0.73731 (41070) hydrogen bonds : bond 0.04477 ( 1130) hydrogen bonds : angle 5.75971 ( 3240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1252 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 1088 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 PHE cc_start: 0.7014 (m-80) cc_final: 0.6790 (t80) REVERT: A 9 HIS cc_start: 0.7820 (m90) cc_final: 0.7603 (m90) REVERT: A 70 ARG cc_start: 0.8301 (mtm110) cc_final: 0.7847 (mtm110) REVERT: A 74 LEU cc_start: 0.5182 (OUTLIER) cc_final: 0.4535 (tp) REVERT: A 159 ILE cc_start: 0.8412 (mt) cc_final: 0.7791 (mm) REVERT: A 163 HIS cc_start: 0.8606 (m-70) cc_final: 0.8043 (m-70) REVERT: A 175 GLN cc_start: 0.8406 (pm20) cc_final: 0.8055 (pm20) REVERT: A 215 SER cc_start: 0.8454 (p) cc_final: 0.8177 (t) REVERT: A 242 VAL cc_start: 0.7483 (t) cc_final: 0.7065 (m) REVERT: B 13 CYS cc_start: 0.8009 (m) cc_final: 0.7682 (m) REVERT: B 119 TRP cc_start: 0.6773 (OUTLIER) cc_final: 0.5841 (t60) REVERT: B 134 ARG cc_start: 0.5859 (tpt-90) cc_final: 0.5489 (tpt-90) REVERT: B 163 HIS cc_start: 0.8791 (m-70) cc_final: 0.8209 (m-70) REVERT: B 175 GLN cc_start: 0.8260 (pm20) cc_final: 0.7924 (pm20) REVERT: B 215 SER cc_start: 0.8293 (p) cc_final: 0.7942 (t) REVERT: B 287 MET cc_start: 0.4387 (tmm) cc_final: 0.3967 (tmm) REVERT: B 298 LEU cc_start: 0.6564 (tp) cc_final: 0.6095 (mt) REVERT: C 13 CYS cc_start: 0.8335 (m) cc_final: 0.7802 (m) REVERT: C 17 GLU cc_start: 0.8590 (mm-30) cc_final: 0.8354 (mm-30) REVERT: C 119 TRP cc_start: 0.6863 (m100) cc_final: 0.6317 (m-10) REVERT: C 164 LYS cc_start: 0.8656 (mtmm) cc_final: 0.7973 (mtmm) REVERT: C 239 LYS cc_start: 0.7887 (mmmt) cc_final: 0.7631 (tmtt) REVERT: D 1 MET cc_start: 0.7273 (tpp) cc_final: 0.6356 (ptp) REVERT: D 9 HIS cc_start: 0.7695 (t-90) cc_final: 0.7374 (t-170) REVERT: D 13 CYS cc_start: 0.8517 (m) cc_final: 0.7956 (m) REVERT: D 17 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8254 (mm-30) REVERT: D 45 VAL cc_start: 0.7907 (t) cc_final: 0.7626 (m) REVERT: D 48 LEU cc_start: 0.7371 (mp) cc_final: 0.6836 (mt) REVERT: D 80 PHE cc_start: 0.7333 (m-80) cc_final: 0.7119 (m-10) REVERT: D 83 TYR cc_start: 0.6759 (m-80) cc_final: 0.6195 (m-80) REVERT: D 84 TYR cc_start: 0.6575 (t80) cc_final: 0.6220 (t80) REVERT: D 164 LYS cc_start: 0.8839 (mmmm) cc_final: 0.8453 (mmmm) REVERT: D 167 HIS cc_start: 0.8449 (m90) cc_final: 0.8018 (m90) REVERT: D 175 GLN cc_start: 0.8500 (pm20) cc_final: 0.8229 (pm20) REVERT: D 226 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6144 (t70) REVERT: E 17 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8156 (pt0) REVERT: E 51 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8050 (mt-10) REVERT: E 67 TRP cc_start: 0.7549 (m100) cc_final: 0.7289 (m100) REVERT: E 70 ARG cc_start: 0.8560 (ttm-80) cc_final: 0.8257 (ttm110) REVERT: E 102 ASN cc_start: 0.6106 (t0) cc_final: 0.5823 (t0) REVERT: E 132 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6805 (mm) REVERT: E 159 ILE cc_start: 0.8414 (tp) cc_final: 0.7700 (mm) REVERT: E 163 HIS cc_start: 0.8563 (m-70) cc_final: 0.7963 (m-70) REVERT: E 170 ARG cc_start: 0.8059 (tpp-160) cc_final: 0.7358 (tpp80) REVERT: E 175 GLN cc_start: 0.8228 (pm20) cc_final: 0.7638 (pm20) REVERT: E 239 LYS cc_start: 0.5743 (OUTLIER) cc_final: 0.5431 (tptp) REVERT: F 84 TYR cc_start: 0.5888 (t80) cc_final: 0.5467 (t80) REVERT: F 175 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7489 (mm-40) REVERT: F 220 MET cc_start: 0.7520 (mmp) cc_final: 0.7114 (mmp) REVERT: F 280 GLN cc_start: 0.6372 (OUTLIER) cc_final: 0.4819 (pp30) REVERT: G 327 ILE cc_start: 0.8347 (OUTLIER) cc_final: 0.7380 (mp) REVERT: G 331 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8539 (tp) REVERT: G 338 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.5371 (mm-30) REVERT: G 339 ASP cc_start: 0.8003 (p0) cc_final: 0.7603 (p0) REVERT: G 382 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.7161 (pttp) REVERT: G 415 ARG cc_start: 0.8250 (mtp180) cc_final: 0.8030 (mtt180) REVERT: G 466 SER cc_start: 0.8509 (m) cc_final: 0.8248 (p) REVERT: G 467 LYS cc_start: 0.8392 (mmmt) cc_final: 0.7655 (mmmt) REVERT: G 468 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7992 (tm-30) REVERT: G 475 TRP cc_start: 0.8202 (t-100) cc_final: 0.7843 (t60) REVERT: G 480 LYS cc_start: 0.7543 (mptt) cc_final: 0.7247 (mptt) REVERT: G 486 THR cc_start: 0.7545 (p) cc_final: 0.7279 (p) REVERT: G 527 LEU cc_start: 0.8665 (mp) cc_final: 0.8349 (pp) REVERT: G 542 ASP cc_start: 0.8426 (p0) cc_final: 0.7910 (m-30) REVERT: G 564 ASN cc_start: 0.8366 (m110) cc_final: 0.6796 (t0) REVERT: G 632 TRP cc_start: 0.8178 (t-100) cc_final: 0.7929 (t-100) REVERT: G 654 ASP cc_start: 0.2895 (OUTLIER) cc_final: 0.2259 (p0) REVERT: H 320 ILE cc_start: 0.8567 (OUTLIER) cc_final: 0.8221 (pt) REVERT: H 378 TYR cc_start: 0.8290 (t80) cc_final: 0.8032 (t80) REVERT: H 467 LYS cc_start: 0.8441 (mmmt) cc_final: 0.7685 (mmmt) REVERT: H 472 ARG cc_start: 0.8563 (mmm160) cc_final: 0.8198 (mmt180) REVERT: H 475 TRP cc_start: 0.8138 (t60) cc_final: 0.7743 (t60) REVERT: H 486 THR cc_start: 0.7720 (m) cc_final: 0.7298 (t) REVERT: H 488 PHE cc_start: 0.7590 (p90) cc_final: 0.7293 (p90) REVERT: I 346 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7407 (tt) REVERT: I 353 ILE cc_start: 0.8620 (tp) cc_final: 0.8223 (pt) REVERT: I 373 SER cc_start: 0.6619 (OUTLIER) cc_final: 0.6263 (p) REVERT: I 467 LYS cc_start: 0.7980 (mmmt) cc_final: 0.7161 (mmmt) REVERT: I 472 ARG cc_start: 0.8292 (mmt180) cc_final: 0.8013 (mmt180) REVERT: I 492 ASN cc_start: 0.7397 (t0) cc_final: 0.7042 (t0) REVERT: I 542 ASP cc_start: 0.7559 (m-30) cc_final: 0.6787 (t70) REVERT: I 594 PHE cc_start: 0.6942 (t80) cc_final: 0.6735 (t80) REVERT: I 636 ILE cc_start: 0.7549 (mm) cc_final: 0.7343 (mt) REVERT: I 637 ASP cc_start: 0.5963 (t0) cc_final: 0.5664 (t0) REVERT: I 654 ASP cc_start: 0.3299 (OUTLIER) cc_final: 0.2712 (p0) REVERT: J 327 ILE cc_start: 0.8185 (pt) cc_final: 0.7675 (mp) REVERT: J 404 ARG cc_start: 0.8119 (tpt170) cc_final: 0.7649 (tpt170) REVERT: J 407 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8181 (mm-30) REVERT: J 412 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7010 (mp0) REVERT: J 415 ARG cc_start: 0.8331 (mtp180) cc_final: 0.7913 (mtp180) REVERT: J 429 PHE cc_start: 0.7926 (t80) cc_final: 0.7580 (t80) REVERT: J 475 TRP cc_start: 0.7915 (t60) cc_final: 0.7628 (t60) REVERT: J 486 THR cc_start: 0.7384 (m) cc_final: 0.6563 (p) REVERT: J 488 PHE cc_start: 0.7679 (p90) cc_final: 0.7304 (p90) REVERT: J 492 ASN cc_start: 0.7759 (t0) cc_final: 0.7175 (t0) REVERT: J 637 ASP cc_start: 0.5826 (t0) cc_final: 0.5518 (t0) REVERT: K 438 MET cc_start: -0.1102 (mtm) cc_final: -0.1313 (mtm) REVERT: K 466 SER cc_start: 0.8632 (m) cc_final: 0.8284 (p) REVERT: K 467 LYS cc_start: 0.8165 (mmmt) cc_final: 0.7371 (mmmt) REVERT: K 472 ARG cc_start: 0.8632 (mtt180) cc_final: 0.8074 (mmm160) REVERT: K 480 LYS cc_start: 0.8236 (OUTLIER) cc_final: 0.7962 (ttpp) REVERT: K 488 PHE cc_start: 0.7820 (p90) cc_final: 0.7344 (p90) REVERT: K 492 ASN cc_start: 0.7201 (t0) cc_final: 0.6881 (t0) REVERT: K 493 TRP cc_start: 0.7697 (m-10) cc_final: 0.7132 (m100) REVERT: K 549 ARG cc_start: 0.7630 (ptm160) cc_final: 0.7159 (mtm180) REVERT: K 570 ASN cc_start: 0.8148 (m110) cc_final: 0.7928 (p0) REVERT: K 590 LEU cc_start: 0.8627 (tt) cc_final: 0.8068 (mp) REVERT: L 344 TYR cc_start: 0.5606 (m-80) cc_final: 0.5322 (m-10) REVERT: L 355 ARG cc_start: 0.7823 (mmp80) cc_final: 0.7598 (mmp80) REVERT: L 368 ASP cc_start: 0.7024 (t0) cc_final: 0.6780 (t0) REVERT: L 372 HIS cc_start: 0.6992 (m90) cc_final: 0.6580 (m90) REVERT: L 427 ILE cc_start: 0.6326 (OUTLIER) cc_final: 0.5910 (pt) REVERT: L 467 LYS cc_start: 0.8409 (mmmt) cc_final: 0.7581 (mmmt) REVERT: L 470 LEU cc_start: 0.9048 (tt) cc_final: 0.8674 (mt) REVERT: L 472 ARG cc_start: 0.8527 (mmt180) cc_final: 0.7563 (mmm160) REVERT: L 488 PHE cc_start: 0.7991 (p90) cc_final: 0.7672 (p90) REVERT: L 491 PHE cc_start: 0.7145 (m-10) cc_final: 0.6926 (m-80) REVERT: L 510 ARG cc_start: 0.7967 (mmm160) cc_final: 0.7765 (mmp80) REVERT: L 512 ILE cc_start: 0.8066 (tp) cc_final: 0.7608 (mm) REVERT: L 515 LEU cc_start: 0.8681 (mt) cc_final: 0.8433 (mt) REVERT: L 558 CYS cc_start: 0.5078 (OUTLIER) cc_final: 0.4518 (p) REVERT: L 576 GLU cc_start: 0.8733 (mp0) cc_final: 0.8439 (pm20) outliers start: 164 outliers final: 93 residues processed: 1164 average time/residue: 0.2028 time to fit residues: 367.2396 Evaluate side-chains 1119 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 1007 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 119 TRP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 197 CYS Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain F residue 11 MET Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 329 ASN Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 377 GLU Chi-restraints excluded: chain G residue 382 LYS Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 489 ARG Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 654 ASP Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 456 VAL Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain H residue 648 PHE Chi-restraints excluded: chain H residue 649 PHE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 346 LEU Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 377 GLU Chi-restraints excluded: chain I residue 410 PHE Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 463 TYR Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 633 GLU Chi-restraints excluded: chain I residue 641 THR Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 335 LEU Chi-restraints excluded: chain J residue 383 CYS Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 494 MET Chi-restraints excluded: chain J residue 649 PHE Chi-restraints excluded: chain K residue 383 CYS Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 465 VAL Chi-restraints excluded: chain K residue 480 LYS Chi-restraints excluded: chain K residue 648 PHE Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 427 ILE Chi-restraints excluded: chain L residue 463 TYR Chi-restraints excluded: chain L residue 469 LEU Chi-restraints excluded: chain L residue 487 LEU Chi-restraints excluded: chain L residue 558 CYS Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 585 PHE Chi-restraints excluded: chain L residue 638 MET Chi-restraints excluded: chain L residue 644 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 72 optimal weight: 3.9990 chunk 17 optimal weight: 0.0670 chunk 364 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 276 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 0.5980 chunk 289 optimal weight: 0.9980 chunk 324 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 171 GLN B 211 HIS ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS D 218 HIS E 9 HIS ** E 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 291 GLN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 ASN ** G 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 627 HIS ** I 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN K 329 ASN K 340 HIS K 588 HIS L 329 ASN ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.156717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.123600 restraints weight = 73854.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.127054 restraints weight = 54296.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.129682 restraints weight = 42901.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.131656 restraints weight = 35579.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.133208 restraints weight = 30666.661| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30234 Z= 0.131 Angle : 0.726 14.140 41070 Z= 0.362 Chirality : 0.047 0.234 4548 Planarity : 0.004 0.068 5322 Dihedral : 5.729 59.753 4085 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.64 % Rotamer: Outliers : 6.24 % Allowed : 27.13 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.14), residues: 3666 helix: -0.24 (0.14), residues: 1395 sheet: -0.24 (0.24), residues: 520 loop : -0.98 (0.14), residues: 1751 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 52 TYR 0.026 0.001 TYR J 423 PHE 0.020 0.001 PHE I 648 TRP 0.044 0.002 TRP I 493 HIS 0.028 0.001 HIS H 627 Details of bonding type rmsd covalent geometry : bond 0.00283 (30234) covalent geometry : angle 0.72621 (41070) hydrogen bonds : bond 0.04183 ( 1130) hydrogen bonds : angle 5.58808 ( 3240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 1074 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 6 PHE cc_start: 0.7121 (m-80) cc_final: 0.6907 (t80) REVERT: A 9 HIS cc_start: 0.7856 (m90) cc_final: 0.7631 (m90) REVERT: A 64 HIS cc_start: 0.5608 (m-70) cc_final: 0.5372 (m90) REVERT: A 70 ARG cc_start: 0.8290 (mtm110) cc_final: 0.7861 (mtm110) REVERT: A 74 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.4724 (tp) REVERT: A 103 LEU cc_start: 0.7556 (pp) cc_final: 0.7306 (mm) REVERT: A 159 ILE cc_start: 0.8530 (mt) cc_final: 0.7812 (mm) REVERT: A 163 HIS cc_start: 0.8639 (m-70) cc_final: 0.8061 (m-70) REVERT: A 171 GLN cc_start: 0.8613 (pp30) cc_final: 0.8110 (pp30) REVERT: A 175 GLN cc_start: 0.8432 (pm20) cc_final: 0.7521 (pm20) REVERT: A 215 SER cc_start: 0.8431 (p) cc_final: 0.8165 (t) REVERT: A 240 PHE cc_start: 0.7509 (p90) cc_final: 0.7147 (p90) REVERT: B 13 CYS cc_start: 0.8006 (m) cc_final: 0.7675 (m) REVERT: B 14 LEU cc_start: 0.7295 (mm) cc_final: 0.7087 (pp) REVERT: B 91 GLU cc_start: 0.8026 (tp30) cc_final: 0.7298 (tp30) REVERT: B 163 HIS cc_start: 0.8815 (m-70) cc_final: 0.8423 (m-70) REVERT: B 175 GLN cc_start: 0.8301 (pm20) cc_final: 0.7802 (pm20) REVERT: B 211 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7572 (p90) REVERT: B 215 SER cc_start: 0.8324 (p) cc_final: 0.7982 (t) REVERT: B 298 LEU cc_start: 0.6603 (tp) cc_final: 0.6158 (mt) REVERT: C 13 CYS cc_start: 0.8340 (m) cc_final: 0.7805 (m) REVERT: C 17 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8377 (mm-30) REVERT: C 70 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7802 (mtm-85) REVERT: C 119 TRP cc_start: 0.6923 (m100) cc_final: 0.6536 (m-10) REVERT: C 164 LYS cc_start: 0.8660 (mtmm) cc_final: 0.8327 (mtmm) REVERT: C 175 GLN cc_start: 0.8514 (pm20) cc_final: 0.8147 (pm20) REVERT: C 239 LYS cc_start: 0.7844 (mmmt) cc_final: 0.7611 (tmtt) REVERT: D 1 MET cc_start: 0.7150 (tpp) cc_final: 0.6325 (ptp) REVERT: D 9 HIS cc_start: 0.7707 (t-90) cc_final: 0.7377 (t-170) REVERT: D 13 CYS cc_start: 0.8563 (m) cc_final: 0.7969 (m) REVERT: D 17 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8261 (mm-30) REVERT: D 48 LEU cc_start: 0.7525 (OUTLIER) cc_final: 0.7318 (mt) REVERT: D 83 TYR cc_start: 0.6825 (m-80) cc_final: 0.6225 (m-80) REVERT: D 84 TYR cc_start: 0.6687 (t80) cc_final: 0.6303 (t80) REVERT: D 102 ASN cc_start: 0.6999 (t0) cc_final: 0.6786 (t0) REVERT: D 164 LYS cc_start: 0.8847 (mmmm) cc_final: 0.8561 (mmmm) REVERT: D 167 HIS cc_start: 0.8414 (m90) cc_final: 0.8153 (m90) REVERT: D 170 ARG cc_start: 0.8104 (ptt-90) cc_final: 0.7721 (ptp90) REVERT: D 175 GLN cc_start: 0.8509 (pm20) cc_final: 0.8201 (pm20) REVERT: D 177 LEU cc_start: 0.8143 (mt) cc_final: 0.7923 (pp) REVERT: D 218 HIS cc_start: 0.8283 (t-90) cc_final: 0.7921 (t70) REVERT: D 222 ARG cc_start: 0.7681 (mtt-85) cc_final: 0.7376 (tpt-90) REVERT: D 226 ASP cc_start: 0.6830 (OUTLIER) cc_final: 0.6093 (t70) REVERT: E 1 MET cc_start: 0.6907 (mtt) cc_final: 0.6277 (ptt) REVERT: E 5 VAL cc_start: 0.5617 (OUTLIER) cc_final: 0.5379 (m) REVERT: E 17 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: E 67 TRP cc_start: 0.7571 (m100) cc_final: 0.7294 (m100) REVERT: E 69 GLU cc_start: 0.8290 (tm-30) cc_final: 0.7917 (pp20) REVERT: E 70 ARG cc_start: 0.8562 (ttm-80) cc_final: 0.8175 (ttm110) REVERT: E 102 ASN cc_start: 0.6101 (t0) cc_final: 0.5789 (t0) REVERT: E 104 HIS cc_start: 0.6817 (t-90) cc_final: 0.6349 (t70) REVERT: E 132 LEU cc_start: 0.6991 (OUTLIER) cc_final: 0.6669 (mm) REVERT: E 159 ILE cc_start: 0.8414 (tp) cc_final: 0.7712 (mm) REVERT: E 163 HIS cc_start: 0.8582 (m-70) cc_final: 0.7988 (m-70) REVERT: E 170 ARG cc_start: 0.8053 (tpp-160) cc_final: 0.7212 (tpp80) REVERT: E 175 GLN cc_start: 0.8180 (pm20) cc_final: 0.7479 (pm20) REVERT: E 220 MET cc_start: 0.7714 (mmt) cc_final: 0.7510 (mmt) REVERT: E 239 LYS cc_start: 0.5809 (OUTLIER) cc_final: 0.5607 (tptp) REVERT: F 84 TYR cc_start: 0.5956 (t80) cc_final: 0.5626 (t80) REVERT: F 93 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7656 (pp) REVERT: F 161 LEU cc_start: 0.8638 (pp) cc_final: 0.8364 (mt) REVERT: F 175 GLN cc_start: 0.7937 (tm-30) cc_final: 0.7471 (mm-40) REVERT: F 213 PRO cc_start: 0.8280 (Cg_exo) cc_final: 0.8064 (Cg_endo) REVERT: F 220 MET cc_start: 0.7576 (mmp) cc_final: 0.7154 (mmp) REVERT: F 280 GLN cc_start: 0.6371 (OUTLIER) cc_final: 0.4807 (pp30) REVERT: G 327 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7453 (mp) REVERT: G 382 LYS cc_start: 0.7825 (ptmm) cc_final: 0.7141 (pttm) REVERT: G 411 GLU cc_start: 0.7310 (mp0) cc_final: 0.7080 (mp0) REVERT: G 415 ARG cc_start: 0.8487 (mtt180) cc_final: 0.8082 (mtt180) REVERT: G 428 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7727 (mm) REVERT: G 466 SER cc_start: 0.8560 (m) cc_final: 0.8293 (p) REVERT: G 467 LYS cc_start: 0.8399 (mmmt) cc_final: 0.7671 (mmmt) REVERT: G 468 GLN cc_start: 0.8210 (tm-30) cc_final: 0.7992 (tm-30) REVERT: G 475 TRP cc_start: 0.8184 (t-100) cc_final: 0.7982 (t60) REVERT: G 486 THR cc_start: 0.7608 (p) cc_final: 0.7272 (p) REVERT: G 542 ASP cc_start: 0.8389 (p0) cc_final: 0.7857 (m-30) REVERT: G 564 ASN cc_start: 0.8333 (m110) cc_final: 0.6826 (t0) REVERT: G 654 ASP cc_start: 0.2896 (OUTLIER) cc_final: 0.2264 (p0) REVERT: H 320 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8351 (pt) REVERT: H 327 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7857 (pt) REVERT: H 346 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.7134 (tt) REVERT: H 379 HIS cc_start: 0.7638 (m90) cc_final: 0.7238 (m90) REVERT: H 428 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7420 (mm) REVERT: H 438 MET cc_start: 0.0295 (mtm) cc_final: 0.0055 (mtm) REVERT: H 467 LYS cc_start: 0.8464 (mmmt) cc_final: 0.7686 (mmmt) REVERT: H 475 TRP cc_start: 0.8250 (t60) cc_final: 0.7838 (t60) REVERT: H 486 THR cc_start: 0.7710 (m) cc_final: 0.7312 (t) REVERT: H 488 PHE cc_start: 0.7592 (p90) cc_final: 0.7292 (p90) REVERT: H 548 TYR cc_start: 0.7774 (t80) cc_final: 0.7370 (t80) REVERT: H 561 GLU cc_start: 0.5836 (mp0) cc_final: 0.5536 (mp0) REVERT: I 353 ILE cc_start: 0.8646 (tp) cc_final: 0.8292 (pt) REVERT: I 368 ASP cc_start: 0.7336 (t0) cc_final: 0.7119 (t0) REVERT: I 373 SER cc_start: 0.6645 (OUTLIER) cc_final: 0.6290 (p) REVERT: I 467 LYS cc_start: 0.8006 (mmmt) cc_final: 0.7167 (mmmt) REVERT: I 472 ARG cc_start: 0.8340 (mmt180) cc_final: 0.8033 (mmt180) REVERT: I 542 ASP cc_start: 0.7610 (m-30) cc_final: 0.6844 (t70) REVERT: I 575 GLU cc_start: 0.8614 (tt0) cc_final: 0.7920 (mt-10) REVERT: I 576 GLU cc_start: 0.8465 (pt0) cc_final: 0.8089 (pm20) REVERT: I 628 ARG cc_start: 0.8609 (ptm160) cc_final: 0.8391 (ptm160) REVERT: I 636 ILE cc_start: 0.7542 (mm) cc_final: 0.7325 (mt) REVERT: I 654 ASP cc_start: 0.3324 (OUTLIER) cc_final: 0.2706 (p0) REVERT: J 331 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8552 (tp) REVERT: J 335 LEU cc_start: 0.7206 (OUTLIER) cc_final: 0.6733 (tp) REVERT: J 415 ARG cc_start: 0.8425 (mtp180) cc_final: 0.7726 (mtp180) REVERT: J 429 PHE cc_start: 0.7909 (t80) cc_final: 0.7554 (t80) REVERT: J 475 TRP cc_start: 0.7930 (t60) cc_final: 0.7626 (t60) REVERT: J 486 THR cc_start: 0.7419 (m) cc_final: 0.6726 (p) REVERT: J 492 ASN cc_start: 0.7654 (t0) cc_final: 0.7074 (t0) REVERT: J 510 ARG cc_start: 0.7931 (tpp-160) cc_final: 0.7308 (mmm160) REVERT: J 562 ILE cc_start: 0.7726 (OUTLIER) cc_final: 0.7064 (tt) REVERT: J 576 GLU cc_start: 0.8230 (pt0) cc_final: 0.7716 (pm20) REVERT: J 640 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7835 (pt0) REVERT: K 438 MET cc_start: -0.1167 (mtm) cc_final: -0.1372 (mtm) REVERT: K 466 SER cc_start: 0.8638 (m) cc_final: 0.8322 (p) REVERT: K 467 LYS cc_start: 0.8098 (mmmt) cc_final: 0.7291 (mmmt) REVERT: K 472 ARG cc_start: 0.8667 (mtt180) cc_final: 0.8278 (mmm160) REVERT: K 488 PHE cc_start: 0.7875 (p90) cc_final: 0.7361 (p90) REVERT: K 492 ASN cc_start: 0.7208 (t0) cc_final: 0.6861 (t0) REVERT: K 493 TRP cc_start: 0.7744 (m-10) cc_final: 0.7230 (m100) REVERT: K 512 ILE cc_start: 0.8488 (tp) cc_final: 0.7843 (pt) REVERT: K 514 GLN cc_start: 0.8171 (tm130) cc_final: 0.7523 (tm130) REVERT: K 549 ARG cc_start: 0.7668 (ptm160) cc_final: 0.7258 (mtm180) REVERT: K 576 GLU cc_start: 0.7399 (pm20) cc_final: 0.6968 (pm20) REVERT: K 590 LEU cc_start: 0.8716 (tt) cc_final: 0.8175 (mp) REVERT: K 638 MET cc_start: 0.8146 (pmm) cc_final: 0.7823 (pmm) REVERT: L 321 LEU cc_start: 0.8713 (tt) cc_final: 0.8450 (pp) REVERT: L 357 LEU cc_start: 0.8558 (mt) cc_final: 0.8273 (pp) REVERT: L 368 ASP cc_start: 0.7148 (t0) cc_final: 0.6904 (t0) REVERT: L 372 HIS cc_start: 0.6944 (m90) cc_final: 0.6455 (m90) REVERT: L 389 LEU cc_start: 0.7884 (tp) cc_final: 0.7471 (tt) REVERT: L 406 PHE cc_start: 0.7980 (t80) cc_final: 0.7232 (t80) REVERT: L 418 ARG cc_start: 0.7895 (tmm160) cc_final: 0.7695 (ttp80) REVERT: L 426 ARG cc_start: 0.4029 (OUTLIER) cc_final: 0.3365 (mtp85) REVERT: L 467 LYS cc_start: 0.8428 (mmmt) cc_final: 0.7610 (mmmt) REVERT: L 468 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7673 (tm-30) REVERT: L 472 ARG cc_start: 0.8512 (mmt180) cc_final: 0.7650 (mmt180) REVERT: L 488 PHE cc_start: 0.7958 (p90) cc_final: 0.7651 (p90) REVERT: L 491 PHE cc_start: 0.7117 (m-10) cc_final: 0.6858 (m-80) REVERT: L 512 ILE cc_start: 0.8175 (tp) cc_final: 0.7714 (mm) REVERT: L 515 LEU cc_start: 0.8698 (mt) cc_final: 0.8449 (mt) REVERT: L 548 TYR cc_start: 0.7548 (t80) cc_final: 0.7315 (t80) REVERT: L 633 GLU cc_start: 0.8647 (pm20) cc_final: 0.8301 (pm20) outliers start: 195 outliers final: 130 residues processed: 1168 average time/residue: 0.2064 time to fit residues: 374.1289 Evaluate side-chains 1185 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1031 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 171 GLN Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 211 HIS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 209 GLU Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 377 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 469 LEU Chi-restraints excluded: chain G residue 489 ARG Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 533 GLN Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 644 GLU Chi-restraints excluded: chain G residue 654 ASP Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 346 LEU Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 410 PHE Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 456 VAL Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 648 PHE Chi-restraints excluded: chain H residue 649 PHE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 377 GLU Chi-restraints excluded: chain I residue 410 PHE Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 463 TYR Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 633 GLU Chi-restraints excluded: chain I residue 641 THR Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 335 LEU Chi-restraints excluded: chain J residue 376 ILE Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 480 LYS Chi-restraints excluded: chain J residue 494 MET Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 562 ILE Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 648 PHE Chi-restraints excluded: chain J residue 649 PHE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 573 SER Chi-restraints excluded: chain K residue 648 PHE Chi-restraints excluded: chain L residue 373 SER Chi-restraints excluded: chain L residue 380 VAL Chi-restraints excluded: chain L residue 426 ARG Chi-restraints excluded: chain L residue 427 ILE Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 463 TYR Chi-restraints excluded: chain L residue 469 LEU Chi-restraints excluded: chain L residue 480 LYS Chi-restraints excluded: chain L residue 487 LEU Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 585 PHE Chi-restraints excluded: chain L residue 638 MET Chi-restraints excluded: chain L residue 644 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 167 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 105 optimal weight: 0.6980 chunk 204 optimal weight: 0.0980 chunk 310 optimal weight: 0.9990 chunk 293 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 chunk 302 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS C 280 GLN E 291 GLN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.155762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.124467 restraints weight = 73712.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.127897 restraints weight = 53582.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.130357 restraints weight = 41944.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.132380 restraints weight = 34755.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.133763 restraints weight = 29733.213| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6802 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30234 Z= 0.137 Angle : 0.742 15.137 41070 Z= 0.369 Chirality : 0.047 0.225 4548 Planarity : 0.004 0.054 5322 Dihedral : 5.692 56.482 4084 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.34 % Favored : 95.64 % Rotamer: Outliers : 6.59 % Allowed : 28.95 % Favored : 64.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.14), residues: 3666 helix: -0.22 (0.14), residues: 1395 sheet: -0.12 (0.24), residues: 512 loop : -0.96 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 170 TYR 0.031 0.001 TYR L 344 PHE 0.021 0.001 PHE H 429 TRP 0.050 0.002 TRP I 493 HIS 0.022 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00295 (30234) covalent geometry : angle 0.74242 (41070) hydrogen bonds : bond 0.04084 ( 1130) hydrogen bonds : angle 5.60156 ( 3240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 1075 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 9 HIS cc_start: 0.7921 (m90) cc_final: 0.7678 (m90) REVERT: A 70 ARG cc_start: 0.8310 (mtm110) cc_final: 0.7795 (mtm110) REVERT: A 74 LEU cc_start: 0.5348 (OUTLIER) cc_final: 0.4537 (tp) REVERT: A 159 ILE cc_start: 0.8505 (mt) cc_final: 0.7751 (mm) REVERT: A 163 HIS cc_start: 0.8613 (m-70) cc_final: 0.8043 (m-70) REVERT: A 171 GLN cc_start: 0.8662 (pp30) cc_final: 0.8217 (pp30) REVERT: A 175 GLN cc_start: 0.8474 (pm20) cc_final: 0.7765 (pm20) REVERT: A 211 HIS cc_start: 0.6896 (p90) cc_final: 0.6506 (p90) REVERT: A 212 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7774 (mmtt) REVERT: A 215 SER cc_start: 0.8482 (p) cc_final: 0.8208 (t) REVERT: A 240 PHE cc_start: 0.7411 (p90) cc_final: 0.7095 (p90) REVERT: A 288 GLN cc_start: 0.5953 (tp40) cc_final: 0.5131 (mp10) REVERT: B 13 CYS cc_start: 0.8005 (m) cc_final: 0.7658 (m) REVERT: B 51 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7996 (mt-10) REVERT: B 70 ARG cc_start: 0.8781 (mpp80) cc_final: 0.8509 (mpp80) REVERT: B 91 GLU cc_start: 0.7985 (tp30) cc_final: 0.7253 (tp30) REVERT: B 134 ARG cc_start: 0.6162 (tpt-90) cc_final: 0.5784 (tpt-90) REVERT: B 163 HIS cc_start: 0.8779 (m-70) cc_final: 0.8405 (m-70) REVERT: B 175 GLN cc_start: 0.8300 (pm20) cc_final: 0.7716 (pm20) REVERT: B 212 LYS cc_start: 0.8467 (mmtp) cc_final: 0.8202 (mmtp) REVERT: B 291 GLN cc_start: 0.8493 (pt0) cc_final: 0.8209 (pt0) REVERT: B 298 LEU cc_start: 0.6522 (tp) cc_final: 0.6057 (mt) REVERT: C 13 CYS cc_start: 0.8328 (m) cc_final: 0.7751 (m) REVERT: C 70 ARG cc_start: 0.8166 (mtm-85) cc_final: 0.7626 (mtm-85) REVERT: C 119 TRP cc_start: 0.7055 (m100) cc_final: 0.6764 (m-10) REVERT: C 164 LYS cc_start: 0.8580 (mtmm) cc_final: 0.8299 (mtmm) REVERT: C 175 GLN cc_start: 0.8562 (pm20) cc_final: 0.8133 (pm20) REVERT: C 235 VAL cc_start: 0.8604 (p) cc_final: 0.8340 (m) REVERT: D 2 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7362 (tttt) REVERT: D 9 HIS cc_start: 0.7664 (t-90) cc_final: 0.7334 (t-170) REVERT: D 13 CYS cc_start: 0.8522 (m) cc_final: 0.7914 (m) REVERT: D 17 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8276 (mm-30) REVERT: D 83 TYR cc_start: 0.6723 (m-80) cc_final: 0.6088 (m-80) REVERT: D 84 TYR cc_start: 0.6656 (t80) cc_final: 0.6251 (t80) REVERT: D 103 LEU cc_start: 0.7656 (tp) cc_final: 0.7180 (tp) REVERT: D 164 LYS cc_start: 0.8789 (mmmm) cc_final: 0.8412 (mmmm) REVERT: D 167 HIS cc_start: 0.8381 (m90) cc_final: 0.8153 (m90) REVERT: D 175 GLN cc_start: 0.8501 (pm20) cc_final: 0.7987 (pm20) REVERT: D 216 VAL cc_start: 0.8649 (t) cc_final: 0.8428 (p) REVERT: D 226 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6076 (t70) REVERT: E 1 MET cc_start: 0.6761 (mtt) cc_final: 0.6163 (ptt) REVERT: E 5 VAL cc_start: 0.5548 (OUTLIER) cc_final: 0.5265 (m) REVERT: E 17 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8151 (pt0) REVERT: E 67 TRP cc_start: 0.7422 (m100) cc_final: 0.7164 (m100) REVERT: E 70 ARG cc_start: 0.8531 (ttm-80) cc_final: 0.8217 (ttm110) REVERT: E 104 HIS cc_start: 0.6714 (t-90) cc_final: 0.6245 (t70) REVERT: E 159 ILE cc_start: 0.8365 (tp) cc_final: 0.7661 (mm) REVERT: E 163 HIS cc_start: 0.8547 (m-70) cc_final: 0.7942 (m-70) REVERT: E 170 ARG cc_start: 0.7989 (tpp-160) cc_final: 0.7100 (tpp80) REVERT: E 175 GLN cc_start: 0.8226 (pm20) cc_final: 0.7449 (pm20) REVERT: E 187 GLU cc_start: 0.5435 (mp0) cc_final: 0.4575 (mp0) REVERT: E 220 MET cc_start: 0.7641 (mmt) cc_final: 0.7090 (mmt) REVERT: E 239 LYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5656 (tptp) REVERT: F 84 TYR cc_start: 0.5769 (t80) cc_final: 0.5364 (t80) REVERT: F 161 LEU cc_start: 0.8693 (pp) cc_final: 0.8470 (mt) REVERT: F 175 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7468 (mm-40) REVERT: F 213 PRO cc_start: 0.8315 (Cg_exo) cc_final: 0.8089 (Cg_endo) REVERT: F 220 MET cc_start: 0.7622 (mmp) cc_final: 0.7203 (mmp) REVERT: F 280 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.4770 (pp30) REVERT: G 316 MET cc_start: 0.2281 (OUTLIER) cc_final: 0.1907 (tpt) REVERT: G 327 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.7335 (mp) REVERT: G 338 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.4765 (mm-30) REVERT: G 339 ASP cc_start: 0.7851 (p0) cc_final: 0.7464 (p0) REVERT: G 412 GLU cc_start: 0.8090 (mp0) cc_final: 0.7885 (mp0) REVERT: G 415 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8016 (mtt180) REVERT: G 466 SER cc_start: 0.8529 (m) cc_final: 0.8265 (p) REVERT: G 467 LYS cc_start: 0.8393 (mmmt) cc_final: 0.7626 (mmmt) REVERT: G 475 TRP cc_start: 0.8036 (t-100) cc_final: 0.7721 (t60) REVERT: G 486 THR cc_start: 0.7619 (p) cc_final: 0.7238 (p) REVERT: G 514 GLN cc_start: 0.8632 (mt0) cc_final: 0.8191 (mt0) REVERT: G 542 ASP cc_start: 0.8308 (p0) cc_final: 0.7855 (m-30) REVERT: G 564 ASN cc_start: 0.8290 (m110) cc_final: 0.6776 (t0) REVERT: G 654 ASP cc_start: 0.2930 (OUTLIER) cc_final: 0.2282 (p0) REVERT: H 320 ILE cc_start: 0.8608 (OUTLIER) cc_final: 0.8335 (pt) REVERT: H 327 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7827 (pt) REVERT: H 404 ARG cc_start: 0.8084 (tpt170) cc_final: 0.7770 (tpm170) REVERT: H 428 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7537 (mm) REVERT: H 438 MET cc_start: 0.0291 (mtm) cc_final: 0.0020 (mtm) REVERT: H 467 LYS cc_start: 0.8471 (mmmt) cc_final: 0.7685 (mmmt) REVERT: H 475 TRP cc_start: 0.8183 (t60) cc_final: 0.7809 (t60) REVERT: H 486 THR cc_start: 0.7725 (m) cc_final: 0.7405 (t) REVERT: H 488 PHE cc_start: 0.7545 (p90) cc_final: 0.7264 (p90) REVERT: H 491 PHE cc_start: 0.7664 (m-10) cc_final: 0.6051 (m-10) REVERT: H 548 TYR cc_start: 0.7685 (t80) cc_final: 0.7363 (t80) REVERT: H 564 ASN cc_start: 0.7925 (m110) cc_final: 0.6007 (t0) REVERT: H 591 ARG cc_start: 0.8510 (ttp-110) cc_final: 0.8286 (ttp-110) REVERT: I 368 ASP cc_start: 0.7273 (t0) cc_final: 0.7018 (t0) REVERT: I 373 SER cc_start: 0.6468 (OUTLIER) cc_final: 0.6121 (p) REVERT: I 467 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7202 (mmmt) REVERT: I 469 LEU cc_start: 0.9099 (tp) cc_final: 0.8825 (mm) REVERT: I 479 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6552 (pm20) REVERT: I 542 ASP cc_start: 0.7519 (m-30) cc_final: 0.6792 (t70) REVERT: I 562 ILE cc_start: 0.7949 (mt) cc_final: 0.7316 (tt) REVERT: I 570 ASN cc_start: 0.8214 (m-40) cc_final: 0.7474 (p0) REVERT: I 576 GLU cc_start: 0.8479 (pt0) cc_final: 0.8029 (pm20) REVERT: I 636 ILE cc_start: 0.7616 (mm) cc_final: 0.7352 (mt) REVERT: I 654 ASP cc_start: 0.3369 (OUTLIER) cc_final: 0.2753 (p0) REVERT: J 327 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7511 (mt) REVERT: J 331 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8527 (tp) REVERT: J 335 LEU cc_start: 0.7220 (OUTLIER) cc_final: 0.6745 (tp) REVERT: J 355 ARG cc_start: 0.7305 (ttp80) cc_final: 0.6965 (ttp80) REVERT: J 407 GLU cc_start: 0.8446 (mm-30) cc_final: 0.8208 (mm-30) REVERT: J 412 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: J 415 ARG cc_start: 0.8407 (mtp180) cc_final: 0.7990 (mtp180) REVERT: J 428 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7379 (mm) REVERT: J 429 PHE cc_start: 0.7883 (t80) cc_final: 0.7598 (t80) REVERT: J 475 TRP cc_start: 0.7787 (t60) cc_final: 0.7552 (t60) REVERT: J 477 TYR cc_start: 0.7958 (OUTLIER) cc_final: 0.7514 (t80) REVERT: J 486 THR cc_start: 0.7506 (m) cc_final: 0.6825 (p) REVERT: J 492 ASN cc_start: 0.7701 (t0) cc_final: 0.7099 (t0) REVERT: J 510 ARG cc_start: 0.7835 (tpp-160) cc_final: 0.7217 (mmm160) REVERT: J 639 GLN cc_start: 0.8381 (pm20) cc_final: 0.8159 (pm20) REVERT: J 640 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7732 (pt0) REVERT: K 327 ILE cc_start: 0.8246 (pt) cc_final: 0.7906 (mp) REVERT: K 466 SER cc_start: 0.8613 (m) cc_final: 0.8303 (p) REVERT: K 467 LYS cc_start: 0.8097 (mmmt) cc_final: 0.7303 (mmmt) REVERT: K 472 ARG cc_start: 0.8629 (mtt180) cc_final: 0.8175 (mmm160) REVERT: K 480 LYS cc_start: 0.8359 (OUTLIER) cc_final: 0.7954 (pttm) REVERT: K 488 PHE cc_start: 0.7976 (p90) cc_final: 0.7534 (p90) REVERT: K 492 ASN cc_start: 0.7137 (t0) cc_final: 0.6791 (t0) REVERT: K 514 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7474 (tm130) REVERT: K 549 ARG cc_start: 0.7531 (ptm160) cc_final: 0.7180 (mtm180) REVERT: K 576 GLU cc_start: 0.7363 (pm20) cc_final: 0.6965 (pm20) REVERT: K 590 LEU cc_start: 0.8632 (tt) cc_final: 0.8055 (mp) REVERT: L 319 LEU cc_start: 0.7140 (tt) cc_final: 0.6701 (pp) REVERT: L 321 LEU cc_start: 0.8697 (tt) cc_final: 0.8381 (pp) REVERT: L 344 TYR cc_start: 0.5590 (m-10) cc_final: 0.5293 (m-10) REVERT: L 347 ASP cc_start: 0.7300 (t70) cc_final: 0.6683 (p0) REVERT: L 348 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7822 (tp) REVERT: L 357 LEU cc_start: 0.8467 (mt) cc_final: 0.8189 (pp) REVERT: L 368 ASP cc_start: 0.7153 (t0) cc_final: 0.6845 (t0) REVERT: L 372 HIS cc_start: 0.7066 (m90) cc_final: 0.6647 (m90) REVERT: L 389 LEU cc_start: 0.7921 (tp) cc_final: 0.7470 (tt) REVERT: L 404 ARG cc_start: 0.8318 (tpt170) cc_final: 0.7717 (tpt170) REVERT: L 412 GLU cc_start: 0.7912 (mp0) cc_final: 0.7644 (mp0) REVERT: L 414 LEU cc_start: 0.8700 (pp) cc_final: 0.8161 (pp) REVERT: L 423 TYR cc_start: 0.6847 (t80) cc_final: 0.6619 (t80) REVERT: L 426 ARG cc_start: 0.4172 (OUTLIER) cc_final: 0.1563 (mtp85) REVERT: L 467 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7583 (mmmt) REVERT: L 468 GLN cc_start: 0.7864 (tm-30) cc_final: 0.7597 (tm-30) REVERT: L 472 ARG cc_start: 0.8520 (mmt180) cc_final: 0.7659 (mmt180) REVERT: L 488 PHE cc_start: 0.7952 (p90) cc_final: 0.7644 (p90) REVERT: L 491 PHE cc_start: 0.7113 (m-10) cc_final: 0.6834 (m-80) REVERT: L 512 ILE cc_start: 0.8104 (tp) cc_final: 0.7634 (mm) REVERT: L 515 LEU cc_start: 0.8688 (mt) cc_final: 0.8444 (mt) REVERT: L 548 TYR cc_start: 0.7460 (t80) cc_final: 0.7236 (t80) outliers start: 206 outliers final: 131 residues processed: 1170 average time/residue: 0.2095 time to fit residues: 380.4117 Evaluate side-chains 1192 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1034 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 149 ARG Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 239 LYS Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 489 ARG Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 533 GLN Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 644 GLU Chi-restraints excluded: chain G residue 654 ASP Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 410 PHE Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 469 LEU Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 638 MET Chi-restraints excluded: chain H residue 648 PHE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 377 GLU Chi-restraints excluded: chain I residue 410 PHE Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 463 TYR Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain I residue 480 LYS Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 633 GLU Chi-restraints excluded: chain I residue 641 THR Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 335 LEU Chi-restraints excluded: chain J residue 376 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 412 GLU Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 480 LYS Chi-restraints excluded: chain J residue 494 MET Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 574 ILE Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 649 PHE Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 410 PHE Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 465 VAL Chi-restraints excluded: chain K residue 480 LYS Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 514 GLN Chi-restraints excluded: chain K residue 648 PHE Chi-restraints excluded: chain L residue 348 ILE Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 373 SER Chi-restraints excluded: chain L residue 380 VAL Chi-restraints excluded: chain L residue 408 LEU Chi-restraints excluded: chain L residue 422 LYS Chi-restraints excluded: chain L residue 426 ARG Chi-restraints excluded: chain L residue 427 ILE Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 480 LYS Chi-restraints excluded: chain L residue 487 LEU Chi-restraints excluded: chain L residue 526 LYS Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 585 PHE Chi-restraints excluded: chain L residue 638 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 269 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 176 optimal weight: 0.8980 chunk 335 optimal weight: 0.7980 chunk 221 optimal weight: 0.9990 chunk 157 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 332 optimal weight: 1.9990 chunk 167 optimal weight: 10.0000 chunk 86 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 171 GLN ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN H 361 HIS ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 564 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.153965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.122332 restraints weight = 74553.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.125690 restraints weight = 54868.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.128217 restraints weight = 43321.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.130109 restraints weight = 35952.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.131619 restraints weight = 30989.267| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30234 Z= 0.161 Angle : 0.758 15.662 41070 Z= 0.381 Chirality : 0.047 0.331 4548 Planarity : 0.005 0.122 5322 Dihedral : 5.715 56.892 4081 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 6.56 % Allowed : 29.88 % Favored : 63.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.14), residues: 3666 helix: -0.24 (0.14), residues: 1397 sheet: -0.29 (0.24), residues: 517 loop : -0.96 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG D 170 TYR 0.029 0.001 TYR J 378 PHE 0.027 0.002 PHE J 491 TRP 0.046 0.002 TRP K 493 HIS 0.021 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00327 (30234) covalent geometry : angle 0.75825 (41070) hydrogen bonds : bond 0.04178 ( 1130) hydrogen bonds : angle 5.67557 ( 3240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 1051 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 HIS cc_start: 0.7976 (m90) cc_final: 0.7738 (m90) REVERT: A 11 MET cc_start: 0.6883 (mmt) cc_final: 0.6607 (mmt) REVERT: A 70 ARG cc_start: 0.8309 (mtm110) cc_final: 0.8063 (mtm-85) REVERT: A 74 LEU cc_start: 0.5408 (OUTLIER) cc_final: 0.4765 (tp) REVERT: A 159 ILE cc_start: 0.8570 (mt) cc_final: 0.7834 (mm) REVERT: A 163 HIS cc_start: 0.8606 (m-70) cc_final: 0.8063 (m-70) REVERT: A 171 GLN cc_start: 0.8701 (pp30) cc_final: 0.8331 (pp30) REVERT: A 175 GLN cc_start: 0.8504 (pm20) cc_final: 0.8059 (pm20) REVERT: A 212 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7506 (mmtp) REVERT: A 215 SER cc_start: 0.8540 (p) cc_final: 0.8284 (t) REVERT: A 288 GLN cc_start: 0.5701 (tp40) cc_final: 0.4964 (mp10) REVERT: B 8 TYR cc_start: 0.6820 (t80) cc_final: 0.6192 (t80) REVERT: B 13 CYS cc_start: 0.7957 (m) cc_final: 0.7522 (m) REVERT: B 20 LEU cc_start: 0.8609 (tp) cc_final: 0.8286 (pp) REVERT: B 74 LEU cc_start: 0.5047 (OUTLIER) cc_final: 0.4736 (mt) REVERT: B 163 HIS cc_start: 0.8791 (m-70) cc_final: 0.8433 (m-70) REVERT: B 175 GLN cc_start: 0.8315 (pm20) cc_final: 0.7931 (pm20) REVERT: B 298 LEU cc_start: 0.6633 (tp) cc_final: 0.6188 (mt) REVERT: C 13 CYS cc_start: 0.8335 (m) cc_final: 0.7759 (m) REVERT: C 70 ARG cc_start: 0.8245 (mtm-85) cc_final: 0.7710 (mtm-85) REVERT: C 104 HIS cc_start: 0.5573 (t70) cc_final: 0.5024 (t70) REVERT: C 119 TRP cc_start: 0.7046 (m100) cc_final: 0.6624 (m-10) REVERT: C 164 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8203 (mtmm) REVERT: C 175 GLN cc_start: 0.8580 (pm20) cc_final: 0.8126 (pm20) REVERT: C 197 CYS cc_start: 0.5641 (t) cc_final: 0.4462 (m) REVERT: C 235 VAL cc_start: 0.8592 (p) cc_final: 0.8298 (m) REVERT: D 9 HIS cc_start: 0.7654 (t-90) cc_final: 0.7372 (t-170) REVERT: D 13 CYS cc_start: 0.8443 (m) cc_final: 0.7942 (m) REVERT: D 17 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8262 (mm-30) REVERT: D 32 HIS cc_start: 0.6964 (t70) cc_final: 0.6755 (t70) REVERT: D 83 TYR cc_start: 0.6661 (m-80) cc_final: 0.6110 (m-80) REVERT: D 103 LEU cc_start: 0.7608 (tp) cc_final: 0.7073 (tp) REVERT: D 157 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7485 (mm) REVERT: D 164 LYS cc_start: 0.8687 (mmmm) cc_final: 0.8398 (mmmm) REVERT: D 175 GLN cc_start: 0.8514 (pm20) cc_final: 0.7924 (pm20) REVERT: D 177 LEU cc_start: 0.8171 (mt) cc_final: 0.7967 (pp) REVERT: D 226 ASP cc_start: 0.6907 (OUTLIER) cc_final: 0.6426 (m-30) REVERT: E 1 MET cc_start: 0.6758 (mtt) cc_final: 0.6275 (ptt) REVERT: E 5 VAL cc_start: 0.5435 (OUTLIER) cc_final: 0.5187 (m) REVERT: E 17 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8085 (pt0) REVERT: E 51 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8261 (mt-10) REVERT: E 67 TRP cc_start: 0.7490 (m100) cc_final: 0.6541 (m100) REVERT: E 69 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7818 (pp20) REVERT: E 70 ARG cc_start: 0.8557 (ttm-80) cc_final: 0.8251 (mtm-85) REVERT: E 159 ILE cc_start: 0.8411 (tp) cc_final: 0.7670 (mm) REVERT: E 163 HIS cc_start: 0.8602 (m-70) cc_final: 0.7986 (m-70) REVERT: E 175 GLN cc_start: 0.8144 (pm20) cc_final: 0.7313 (pm20) REVERT: E 220 MET cc_start: 0.7605 (mmt) cc_final: 0.7109 (mmt) REVERT: F 84 TYR cc_start: 0.5682 (OUTLIER) cc_final: 0.5325 (t80) REVERT: F 94 GLN cc_start: 0.8174 (tt0) cc_final: 0.7954 (tp40) REVERT: F 161 LEU cc_start: 0.8665 (pp) cc_final: 0.8429 (mt) REVERT: F 175 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7429 (mm-40) REVERT: F 213 PRO cc_start: 0.8450 (Cg_exo) cc_final: 0.8249 (Cg_endo) REVERT: F 220 MET cc_start: 0.7694 (mmp) cc_final: 0.7264 (mmp) REVERT: F 280 GLN cc_start: 0.6339 (OUTLIER) cc_final: 0.4709 (pp30) REVERT: G 316 MET cc_start: 0.2530 (OUTLIER) cc_final: 0.2137 (tpt) REVERT: G 327 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7313 (mp) REVERT: G 338 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.4834 (mm-30) REVERT: G 339 ASP cc_start: 0.7948 (p0) cc_final: 0.7504 (p0) REVERT: G 382 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.6865 (pttp) REVERT: G 383 CYS cc_start: 0.6515 (m) cc_final: 0.6005 (t) REVERT: G 412 GLU cc_start: 0.8115 (mp0) cc_final: 0.7886 (mp0) REVERT: G 415 ARG cc_start: 0.8420 (mtt180) cc_final: 0.8008 (mtt180) REVERT: G 467 LYS cc_start: 0.8443 (mmmt) cc_final: 0.7635 (mmmt) REVERT: G 475 TRP cc_start: 0.7998 (t-100) cc_final: 0.7650 (t60) REVERT: G 514 GLN cc_start: 0.8674 (mt0) cc_final: 0.8233 (mt0) REVERT: G 564 ASN cc_start: 0.8264 (m110) cc_final: 0.6707 (t0) REVERT: G 654 ASP cc_start: 0.3044 (OUTLIER) cc_final: 0.2431 (p0) REVERT: H 320 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8386 (pt) REVERT: H 327 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7918 (pt) REVERT: H 404 ARG cc_start: 0.8057 (tpt170) cc_final: 0.7762 (tpm170) REVERT: H 428 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7652 (mm) REVERT: H 438 MET cc_start: 0.0261 (mtm) cc_final: -0.0004 (mtm) REVERT: H 467 LYS cc_start: 0.8440 (mmmt) cc_final: 0.7684 (mmmt) REVERT: H 475 TRP cc_start: 0.8180 (t-100) cc_final: 0.7802 (t60) REVERT: H 486 THR cc_start: 0.7717 (m) cc_final: 0.7492 (t) REVERT: H 488 PHE cc_start: 0.7627 (p90) cc_final: 0.7362 (p90) REVERT: H 493 TRP cc_start: 0.8496 (m-10) cc_final: 0.8067 (m-10) REVERT: H 514 GLN cc_start: 0.8673 (mt0) cc_final: 0.8100 (mt0) REVERT: H 548 TYR cc_start: 0.7742 (t80) cc_final: 0.7416 (t80) REVERT: H 561 GLU cc_start: 0.6163 (mp0) cc_final: 0.5762 (mp0) REVERT: H 654 ASP cc_start: 0.3927 (OUTLIER) cc_final: 0.3642 (t0) REVERT: I 368 ASP cc_start: 0.7435 (t0) cc_final: 0.7167 (t0) REVERT: I 373 SER cc_start: 0.6427 (OUTLIER) cc_final: 0.6088 (p) REVERT: I 467 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7250 (mmmt) REVERT: I 479 GLU cc_start: 0.7074 (OUTLIER) cc_final: 0.6685 (pm20) REVERT: I 488 PHE cc_start: 0.7997 (p90) cc_final: 0.7645 (p90) REVERT: I 528 ILE cc_start: 0.6369 (mm) cc_final: 0.6094 (mm) REVERT: I 542 ASP cc_start: 0.7472 (m-30) cc_final: 0.6678 (t70) REVERT: I 570 ASN cc_start: 0.8084 (m-40) cc_final: 0.7395 (p0) REVERT: I 575 GLU cc_start: 0.8569 (tp30) cc_final: 0.7842 (mt-10) REVERT: I 576 GLU cc_start: 0.8526 (pt0) cc_final: 0.7785 (pm20) REVERT: I 654 ASP cc_start: 0.3385 (OUTLIER) cc_final: 0.2735 (p0) REVERT: J 327 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7476 (mt) REVERT: J 331 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8474 (tp) REVERT: J 335 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6760 (tp) REVERT: J 407 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8235 (pp20) REVERT: J 412 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: J 415 ARG cc_start: 0.8376 (mtp180) cc_final: 0.8017 (mtp180) REVERT: J 426 ARG cc_start: 0.6147 (tpt90) cc_final: 0.5754 (tpt90) REVERT: J 428 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7412 (mm) REVERT: J 429 PHE cc_start: 0.7915 (t80) cc_final: 0.7652 (t80) REVERT: J 477 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7484 (t80) REVERT: J 486 THR cc_start: 0.7623 (m) cc_final: 0.7096 (t) REVERT: J 488 PHE cc_start: 0.7739 (p90) cc_final: 0.7233 (p90) REVERT: J 492 ASN cc_start: 0.7775 (t0) cc_final: 0.7180 (t0) REVERT: J 510 ARG cc_start: 0.7910 (tpp-160) cc_final: 0.7542 (mmm160) REVERT: J 576 GLU cc_start: 0.8291 (pt0) cc_final: 0.7915 (pm20) REVERT: J 627 HIS cc_start: 0.7394 (t-90) cc_final: 0.7184 (t-90) REVERT: J 637 ASP cc_start: 0.5479 (t0) cc_final: 0.4545 (t0) REVERT: J 639 GLN cc_start: 0.8429 (pm20) cc_final: 0.8154 (pm20) REVERT: J 640 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: K 327 ILE cc_start: 0.8276 (pt) cc_final: 0.7944 (mp) REVERT: K 335 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6554 (tp) REVERT: K 427 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.6528 (mp) REVERT: K 466 SER cc_start: 0.8627 (m) cc_final: 0.8319 (p) REVERT: K 467 LYS cc_start: 0.8095 (mmmt) cc_final: 0.7304 (mmmt) REVERT: K 472 ARG cc_start: 0.8623 (mtt180) cc_final: 0.8150 (mmm160) REVERT: K 480 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7925 (pttm) REVERT: K 488 PHE cc_start: 0.7977 (p90) cc_final: 0.7487 (p90) REVERT: K 492 ASN cc_start: 0.7278 (t0) cc_final: 0.7077 (t0) REVERT: K 549 ARG cc_start: 0.7579 (ptm160) cc_final: 0.7246 (mtm180) REVERT: K 576 GLU cc_start: 0.7338 (pm20) cc_final: 0.6900 (pm20) REVERT: L 321 LEU cc_start: 0.8713 (tt) cc_final: 0.8464 (pp) REVERT: L 344 TYR cc_start: 0.5588 (m-10) cc_final: 0.5281 (m-10) REVERT: L 357 LEU cc_start: 0.8492 (mt) cc_final: 0.8236 (pp) REVERT: L 368 ASP cc_start: 0.7193 (t0) cc_final: 0.6926 (t0) REVERT: L 372 HIS cc_start: 0.7067 (m90) cc_final: 0.6666 (m90) REVERT: L 389 LEU cc_start: 0.7866 (tp) cc_final: 0.7381 (tt) REVERT: L 404 ARG cc_start: 0.8357 (tpt170) cc_final: 0.7717 (tpt170) REVERT: L 414 LEU cc_start: 0.8737 (pp) cc_final: 0.7850 (pp) REVERT: L 415 ARG cc_start: 0.8166 (mmm160) cc_final: 0.7918 (mmm160) REVERT: L 423 TYR cc_start: 0.7149 (t80) cc_final: 0.6737 (t80) REVERT: L 426 ARG cc_start: 0.4579 (OUTLIER) cc_final: 0.3961 (mmm160) REVERT: L 467 LYS cc_start: 0.8429 (mmmt) cc_final: 0.7639 (mmmt) REVERT: L 468 GLN cc_start: 0.7927 (tm-30) cc_final: 0.7666 (tm-30) REVERT: L 472 ARG cc_start: 0.8590 (mmt180) cc_final: 0.7790 (mmt180) REVERT: L 488 PHE cc_start: 0.7924 (p90) cc_final: 0.7611 (p90) REVERT: L 491 PHE cc_start: 0.7091 (m-10) cc_final: 0.6795 (m-80) REVERT: L 512 ILE cc_start: 0.8170 (tp) cc_final: 0.7714 (mm) REVERT: L 515 LEU cc_start: 0.8691 (mt) cc_final: 0.8444 (mt) REVERT: L 548 TYR cc_start: 0.7514 (t80) cc_final: 0.7297 (t80) REVERT: L 565 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6435 (mt) outliers start: 205 outliers final: 145 residues processed: 1142 average time/residue: 0.1981 time to fit residues: 350.8654 Evaluate side-chains 1197 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 1020 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 11 MET Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 260 ILE Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 382 LYS Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 489 ARG Chi-restraints excluded: chain G residue 494 MET Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 533 GLN Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 654 ASP Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 372 HIS Chi-restraints excluded: chain H residue 376 ILE Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 410 PHE Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 456 VAL Chi-restraints excluded: chain H residue 469 LEU Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain H residue 638 MET Chi-restraints excluded: chain H residue 641 THR Chi-restraints excluded: chain H residue 648 PHE Chi-restraints excluded: chain H residue 649 PHE Chi-restraints excluded: chain H residue 654 ASP Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 377 GLU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 410 PHE Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 429 PHE Chi-restraints excluded: chain I residue 463 TYR Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain I residue 480 LYS Chi-restraints excluded: chain I residue 489 ARG Chi-restraints excluded: chain I residue 564 ASN Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 633 GLU Chi-restraints excluded: chain I residue 641 THR Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 335 LEU Chi-restraints excluded: chain J residue 376 ILE Chi-restraints excluded: chain J residue 412 GLU Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 444 PHE Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 469 LEU Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 480 LYS Chi-restraints excluded: chain J residue 489 ARG Chi-restraints excluded: chain J residue 494 MET Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 648 PHE Chi-restraints excluded: chain J residue 649 PHE Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 410 PHE Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 465 VAL Chi-restraints excluded: chain K residue 480 LYS Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain K residue 573 SER Chi-restraints excluded: chain K residue 648 PHE Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 373 SER Chi-restraints excluded: chain L residue 407 GLU Chi-restraints excluded: chain L residue 426 ARG Chi-restraints excluded: chain L residue 427 ILE Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 469 LEU Chi-restraints excluded: chain L residue 480 LYS Chi-restraints excluded: chain L residue 487 LEU Chi-restraints excluded: chain L residue 526 LYS Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 565 ILE Chi-restraints excluded: chain L residue 585 PHE Chi-restraints excluded: chain L residue 638 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 348 optimal weight: 0.7980 chunk 366 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 46 optimal weight: 0.0470 chunk 190 optimal weight: 0.0980 chunk 108 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 313 optimal weight: 0.0970 chunk 301 optimal weight: 0.9980 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 73 GLN B 147 GLN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 GLN ** D 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS E 291 GLN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 448 HIS ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 468 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** K 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 593 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.156159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.123585 restraints weight = 73670.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.127009 restraints weight = 54323.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.129590 restraints weight = 42926.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.131565 restraints weight = 35629.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.133081 restraints weight = 30706.604| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30234 Z= 0.133 Angle : 0.774 16.287 41070 Z= 0.383 Chirality : 0.047 0.302 4548 Planarity : 0.004 0.052 5322 Dihedral : 5.653 59.439 4081 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.56 % Favored : 95.42 % Rotamer: Outliers : 5.63 % Allowed : 31.64 % Favored : 62.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.14), residues: 3666 helix: -0.16 (0.14), residues: 1393 sheet: -0.27 (0.23), residues: 535 loop : -0.92 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 52 TYR 0.027 0.001 TYR G 423 PHE 0.031 0.001 PHE J 491 TRP 0.036 0.002 TRP H 375 HIS 0.020 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00293 (30234) covalent geometry : angle 0.77436 (41070) hydrogen bonds : bond 0.03952 ( 1130) hydrogen bonds : angle 5.53093 ( 3240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1239 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 1063 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 9 HIS cc_start: 0.7951 (m90) cc_final: 0.7718 (m90) REVERT: A 64 HIS cc_start: 0.5959 (m-70) cc_final: 0.5701 (m90) REVERT: A 77 ASP cc_start: 0.6186 (m-30) cc_final: 0.5534 (p0) REVERT: A 119 TRP cc_start: 0.7221 (m-10) cc_final: 0.6929 (m-10) REVERT: A 159 ILE cc_start: 0.8561 (mt) cc_final: 0.7816 (mm) REVERT: A 163 HIS cc_start: 0.8613 (m-70) cc_final: 0.8047 (m-70) REVERT: A 171 GLN cc_start: 0.8718 (pp30) cc_final: 0.8260 (pp30) REVERT: A 175 GLN cc_start: 0.8494 (pm20) cc_final: 0.7713 (pm20) REVERT: A 212 LYS cc_start: 0.8047 (mmmt) cc_final: 0.7636 (mmtp) REVERT: A 215 SER cc_start: 0.8534 (p) cc_final: 0.8193 (t) REVERT: A 240 PHE cc_start: 0.7464 (p90) cc_final: 0.7058 (p90) REVERT: B 8 TYR cc_start: 0.6773 (t80) cc_final: 0.6135 (t80) REVERT: B 13 CYS cc_start: 0.7911 (m) cc_final: 0.7543 (m) REVERT: B 20 LEU cc_start: 0.8620 (tp) cc_final: 0.8328 (pp) REVERT: B 134 ARG cc_start: 0.6128 (tpt-90) cc_final: 0.5776 (tpt-90) REVERT: B 147 GLN cc_start: 0.5985 (tm130) cc_final: 0.5753 (tm-30) REVERT: B 163 HIS cc_start: 0.8852 (m-70) cc_final: 0.8529 (m-70) REVERT: B 175 GLN cc_start: 0.8282 (pm20) cc_final: 0.7760 (pm20) REVERT: B 298 LEU cc_start: 0.6639 (tp) cc_final: 0.6157 (mt) REVERT: C 13 CYS cc_start: 0.8349 (m) cc_final: 0.7789 (m) REVERT: C 70 ARG cc_start: 0.8403 (mtm-85) cc_final: 0.7880 (mtm-85) REVERT: C 104 HIS cc_start: 0.5584 (t70) cc_final: 0.4950 (t70) REVERT: C 119 TRP cc_start: 0.7023 (m100) cc_final: 0.6581 (m-10) REVERT: C 144 ILE cc_start: 0.5130 (OUTLIER) cc_final: 0.4908 (pp) REVERT: C 150 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7490 (tp) REVERT: C 164 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8243 (mtmm) REVERT: C 175 GLN cc_start: 0.8593 (pm20) cc_final: 0.8187 (pm20) REVERT: C 197 CYS cc_start: 0.5663 (t) cc_final: 0.4417 (m) REVERT: C 235 VAL cc_start: 0.8580 (p) cc_final: 0.8311 (m) REVERT: D 9 HIS cc_start: 0.7674 (t-90) cc_final: 0.7369 (t-170) REVERT: D 13 CYS cc_start: 0.8431 (m) cc_final: 0.7936 (m) REVERT: D 17 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8301 (mm-30) REVERT: D 83 TYR cc_start: 0.6723 (m-80) cc_final: 0.6178 (m-80) REVERT: D 84 TYR cc_start: 0.6752 (t80) cc_final: 0.6362 (t80) REVERT: D 157 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7731 (mm) REVERT: D 164 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8403 (mmmm) REVERT: D 175 GLN cc_start: 0.8519 (pm20) cc_final: 0.7883 (pm20) REVERT: D 177 LEU cc_start: 0.8177 (mt) cc_final: 0.7977 (pp) REVERT: D 226 ASP cc_start: 0.6793 (OUTLIER) cc_final: 0.6072 (t70) REVERT: E 1 MET cc_start: 0.6767 (mtt) cc_final: 0.6320 (ptt) REVERT: E 5 VAL cc_start: 0.5545 (OUTLIER) cc_final: 0.5288 (m) REVERT: E 51 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8271 (mt-10) REVERT: E 67 TRP cc_start: 0.7496 (m100) cc_final: 0.7200 (m100) REVERT: E 69 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7776 (pp20) REVERT: E 70 ARG cc_start: 0.8544 (ttm-80) cc_final: 0.8139 (ttm110) REVERT: E 159 ILE cc_start: 0.8376 (tp) cc_final: 0.7531 (mt) REVERT: E 163 HIS cc_start: 0.8636 (m-70) cc_final: 0.7996 (m-70) REVERT: E 170 ARG cc_start: 0.8081 (tpp-160) cc_final: 0.7665 (tpp-160) REVERT: E 175 GLN cc_start: 0.8208 (pm20) cc_final: 0.7689 (pm20) REVERT: E 220 MET cc_start: 0.7598 (mmt) cc_final: 0.7146 (mmt) REVERT: F 84 TYR cc_start: 0.5915 (OUTLIER) cc_final: 0.5577 (t80) REVERT: F 94 GLN cc_start: 0.8208 (tt0) cc_final: 0.7990 (tp40) REVERT: F 149 ARG cc_start: 0.7015 (OUTLIER) cc_final: 0.6625 (ttp80) REVERT: F 161 LEU cc_start: 0.8697 (pp) cc_final: 0.8412 (mt) REVERT: F 170 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7809 (ptt-90) REVERT: F 175 GLN cc_start: 0.7951 (tm-30) cc_final: 0.7703 (mp10) REVERT: F 213 PRO cc_start: 0.8371 (Cg_exo) cc_final: 0.8161 (Cg_endo) REVERT: F 220 MET cc_start: 0.7675 (mmp) cc_final: 0.7247 (mmp) REVERT: F 280 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.4733 (pp30) REVERT: G 316 MET cc_start: 0.2353 (OUTLIER) cc_final: 0.1904 (tpt) REVERT: G 320 ILE cc_start: 0.8231 (pt) cc_final: 0.7603 (mp) REVERT: G 327 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7320 (mp) REVERT: G 338 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.5001 (mm-30) REVERT: G 339 ASP cc_start: 0.7928 (p0) cc_final: 0.7549 (p0) REVERT: G 382 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.6897 (pttm) REVERT: G 383 CYS cc_start: 0.6402 (m) cc_final: 0.5843 (t) REVERT: G 403 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7724 (mp) REVERT: G 412 GLU cc_start: 0.8154 (mp0) cc_final: 0.7861 (mp0) REVERT: G 415 ARG cc_start: 0.8460 (mtt180) cc_final: 0.8053 (mtt180) REVERT: G 467 LYS cc_start: 0.8374 (mmmt) cc_final: 0.7545 (mmmt) REVERT: G 475 TRP cc_start: 0.8039 (t-100) cc_final: 0.7758 (t60) REVERT: G 497 ARG cc_start: 0.7686 (mtt-85) cc_final: 0.7466 (mpt-90) REVERT: G 514 GLN cc_start: 0.8701 (mt0) cc_final: 0.8188 (mt0) REVERT: G 534 LYS cc_start: 0.6129 (mmmt) cc_final: 0.5771 (mmmt) REVERT: G 542 ASP cc_start: 0.8288 (p0) cc_final: 0.7858 (m-30) REVERT: G 564 ASN cc_start: 0.8244 (m110) cc_final: 0.6749 (t0) REVERT: G 654 ASP cc_start: 0.3047 (OUTLIER) cc_final: 0.2436 (p0) REVERT: H 320 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8380 (pt) REVERT: H 327 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7864 (pt) REVERT: H 404 ARG cc_start: 0.8071 (tpt170) cc_final: 0.7677 (tpm170) REVERT: H 428 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7562 (mm) REVERT: H 438 MET cc_start: 0.0245 (mtm) cc_final: -0.0042 (mtm) REVERT: H 467 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7588 (mmmt) REVERT: H 475 TRP cc_start: 0.8183 (t-100) cc_final: 0.7857 (t60) REVERT: H 486 THR cc_start: 0.7718 (m) cc_final: 0.7490 (t) REVERT: H 488 PHE cc_start: 0.7651 (p90) cc_final: 0.7414 (p90) REVERT: H 548 TYR cc_start: 0.7814 (t80) cc_final: 0.7460 (t80) REVERT: H 588 HIS cc_start: 0.7748 (t70) cc_final: 0.7399 (t70) REVERT: H 591 ARG cc_start: 0.8642 (ttp-110) cc_final: 0.8407 (ttp-110) REVERT: H 654 ASP cc_start: 0.3912 (OUTLIER) cc_final: 0.3624 (t0) REVERT: I 347 ASP cc_start: 0.7956 (t70) cc_final: 0.7275 (p0) REVERT: I 353 ILE cc_start: 0.8616 (tp) cc_final: 0.8275 (pt) REVERT: I 368 ASP cc_start: 0.7555 (t0) cc_final: 0.7249 (t0) REVERT: I 373 SER cc_start: 0.6485 (OUTLIER) cc_final: 0.6173 (p) REVERT: I 467 LYS cc_start: 0.8012 (mmmt) cc_final: 0.7200 (mmmt) REVERT: I 479 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6705 (pm20) REVERT: I 494 MET cc_start: 0.6666 (mmt) cc_final: 0.6438 (mmt) REVERT: I 545 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7247 (mm-30) REVERT: I 549 ARG cc_start: 0.8278 (mmt180) cc_final: 0.7647 (tpt90) REVERT: I 575 GLU cc_start: 0.8499 (tp30) cc_final: 0.8239 (tp30) REVERT: I 576 GLU cc_start: 0.8481 (pt0) cc_final: 0.7720 (pm20) REVERT: I 636 ILE cc_start: 0.7895 (mm) cc_final: 0.7480 (mt) REVERT: I 654 ASP cc_start: 0.3431 (OUTLIER) cc_final: 0.2775 (p0) REVERT: J 327 ILE cc_start: 0.8221 (OUTLIER) cc_final: 0.7583 (mt) REVERT: J 331 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8462 (tp) REVERT: J 335 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6665 (tt) REVERT: J 412 GLU cc_start: 0.7840 (mm-30) cc_final: 0.6741 (mp0) REVERT: J 415 ARG cc_start: 0.8426 (mtp180) cc_final: 0.8014 (mtp180) REVERT: J 428 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7426 (mm) REVERT: J 429 PHE cc_start: 0.7859 (t80) cc_final: 0.7618 (t80) REVERT: J 461 TRP cc_start: 0.6795 (m-90) cc_final: 0.6006 (m-90) REVERT: J 486 THR cc_start: 0.7589 (m) cc_final: 0.6983 (t) REVERT: J 488 PHE cc_start: 0.7744 (p90) cc_final: 0.7287 (p90) REVERT: J 492 ASN cc_start: 0.7705 (t0) cc_final: 0.7104 (t0) REVERT: J 510 ARG cc_start: 0.7884 (tpp-160) cc_final: 0.7493 (mmm160) REVERT: J 628 ARG cc_start: 0.8342 (ptm-80) cc_final: 0.8072 (ptm-80) REVERT: J 637 ASP cc_start: 0.5681 (t0) cc_final: 0.5074 (t0) REVERT: J 639 GLN cc_start: 0.8503 (pm20) cc_final: 0.8295 (pm20) REVERT: J 640 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8072 (mp0) REVERT: K 327 ILE cc_start: 0.8331 (pt) cc_final: 0.8008 (mp) REVERT: K 344 TYR cc_start: 0.6032 (m-80) cc_final: 0.5819 (m-80) REVERT: K 427 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.6554 (mp) REVERT: K 466 SER cc_start: 0.8610 (m) cc_final: 0.8292 (p) REVERT: K 467 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7269 (mmmt) REVERT: K 469 LEU cc_start: 0.8985 (tt) cc_final: 0.8740 (mm) REVERT: K 472 ARG cc_start: 0.8653 (mtt180) cc_final: 0.8181 (mmm160) REVERT: K 475 TRP cc_start: 0.8111 (t60) cc_final: 0.7831 (t60) REVERT: K 480 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7853 (pttm) REVERT: K 488 PHE cc_start: 0.7959 (p90) cc_final: 0.7436 (p90) REVERT: K 492 ASN cc_start: 0.7092 (t0) cc_final: 0.6729 (t0) REVERT: K 514 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7524 (tm130) REVERT: K 549 ARG cc_start: 0.7582 (ptm160) cc_final: 0.7327 (mtm180) REVERT: K 576 GLU cc_start: 0.7416 (pm20) cc_final: 0.7000 (pm20) REVERT: K 590 LEU cc_start: 0.8691 (tp) cc_final: 0.8296 (mp) REVERT: L 319 LEU cc_start: 0.7138 (tt) cc_final: 0.6785 (pp) REVERT: L 321 LEU cc_start: 0.8683 (tt) cc_final: 0.8382 (pp) REVERT: L 344 TYR cc_start: 0.5626 (m-10) cc_final: 0.5386 (m-10) REVERT: L 357 LEU cc_start: 0.8474 (mt) cc_final: 0.8209 (pp) REVERT: L 368 ASP cc_start: 0.7242 (t0) cc_final: 0.6992 (t0) REVERT: L 372 HIS cc_start: 0.7024 (m90) cc_final: 0.6706 (m90) REVERT: L 387 LEU cc_start: 0.7101 (OUTLIER) cc_final: 0.6800 (mt) REVERT: L 389 LEU cc_start: 0.7863 (tp) cc_final: 0.7321 (tt) REVERT: L 404 ARG cc_start: 0.8367 (tpt170) cc_final: 0.7679 (tpt170) REVERT: L 411 GLU cc_start: 0.7973 (mp0) cc_final: 0.7717 (pm20) REVERT: L 414 LEU cc_start: 0.8721 (pp) cc_final: 0.7894 (pp) REVERT: L 423 TYR cc_start: 0.6985 (t80) cc_final: 0.6596 (t80) REVERT: L 426 ARG cc_start: 0.4433 (OUTLIER) cc_final: 0.3931 (mmm160) REVERT: L 467 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7628 (mmmt) REVERT: L 468 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7657 (tm-30) REVERT: L 472 ARG cc_start: 0.8585 (mmt180) cc_final: 0.7799 (mmt180) REVERT: L 488 PHE cc_start: 0.7960 (p90) cc_final: 0.7636 (p90) REVERT: L 491 PHE cc_start: 0.7084 (m-10) cc_final: 0.6823 (m-80) REVERT: L 512 ILE cc_start: 0.8137 (tp) cc_final: 0.7683 (mm) REVERT: L 515 LEU cc_start: 0.8669 (mt) cc_final: 0.8417 (mt) REVERT: L 565 ILE cc_start: 0.6806 (OUTLIER) cc_final: 0.6452 (mt) REVERT: L 579 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7758 (mp0) outliers start: 176 outliers final: 119 residues processed: 1142 average time/residue: 0.2110 time to fit residues: 372.6695 Evaluate side-chains 1183 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 1032 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 375 TRP Chi-restraints excluded: chain G residue 382 LYS Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 403 LEU Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 489 ARG Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 654 ASP Chi-restraints excluded: chain H residue 320 ILE Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 410 PHE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 469 LEU Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain H residue 638 MET Chi-restraints excluded: chain H residue 648 PHE Chi-restraints excluded: chain H residue 649 PHE Chi-restraints excluded: chain H residue 654 ASP Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 377 GLU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain I residue 480 LYS Chi-restraints excluded: chain I residue 489 ARG Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 633 GLU Chi-restraints excluded: chain I residue 641 THR Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 335 LEU Chi-restraints excluded: chain J residue 376 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 480 LYS Chi-restraints excluded: chain J residue 489 ARG Chi-restraints excluded: chain J residue 494 MET Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 648 PHE Chi-restraints excluded: chain J residue 649 PHE Chi-restraints excluded: chain K residue 335 LEU Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 407 GLU Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 480 LYS Chi-restraints excluded: chain K residue 514 GLN Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain K residue 573 SER Chi-restraints excluded: chain K residue 639 GLN Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 373 SER Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 407 GLU Chi-restraints excluded: chain L residue 408 LEU Chi-restraints excluded: chain L residue 426 ARG Chi-restraints excluded: chain L residue 427 ILE Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 469 LEU Chi-restraints excluded: chain L residue 480 LYS Chi-restraints excluded: chain L residue 526 LYS Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 565 ILE Chi-restraints excluded: chain L residue 585 PHE Chi-restraints excluded: chain L residue 593 HIS Chi-restraints excluded: chain L residue 638 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 266 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 361 optimal weight: 3.9990 chunk 334 optimal weight: 0.6980 chunk 259 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 220 optimal weight: 30.0000 chunk 6 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 184 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 9 HIS ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 GLN ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 HIS E 104 HIS ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 592 HIS ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** J 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.153819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.121319 restraints weight = 75267.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.124723 restraints weight = 55590.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.127248 restraints weight = 44006.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.129211 restraints weight = 36588.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.130683 restraints weight = 31637.679| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30234 Z= 0.162 Angle : 0.791 16.543 41070 Z= 0.398 Chirality : 0.048 0.306 4548 Planarity : 0.005 0.179 5322 Dihedral : 5.682 59.342 4079 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.86 % Favored : 95.12 % Rotamer: Outliers : 5.79 % Allowed : 31.83 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -0.98 (0.14), residues: 3666 helix: -0.26 (0.14), residues: 1406 sheet: -0.36 (0.24), residues: 532 loop : -0.98 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 170 TYR 0.039 0.001 TYR L 548 PHE 0.052 0.002 PHE A 6 TRP 0.050 0.002 TRP G 493 HIS 0.018 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00336 (30234) covalent geometry : angle 0.79131 (41070) hydrogen bonds : bond 0.04152 ( 1130) hydrogen bonds : angle 5.69854 ( 3240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1241 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 1060 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 9 HIS cc_start: 0.7921 (m90) cc_final: 0.7679 (m90) REVERT: A 64 HIS cc_start: 0.6100 (m-70) cc_final: 0.5771 (m90) REVERT: A 119 TRP cc_start: 0.7282 (m-10) cc_final: 0.7000 (m-10) REVERT: A 159 ILE cc_start: 0.8607 (mt) cc_final: 0.7861 (mm) REVERT: A 163 HIS cc_start: 0.8598 (m-70) cc_final: 0.8058 (m-70) REVERT: A 171 GLN cc_start: 0.8703 (pp30) cc_final: 0.8283 (pp30) REVERT: A 175 GLN cc_start: 0.8500 (pm20) cc_final: 0.7722 (pm20) REVERT: A 212 LYS cc_start: 0.8031 (mmmt) cc_final: 0.7406 (mmtp) REVERT: A 215 SER cc_start: 0.8585 (p) cc_final: 0.8233 (t) REVERT: B 8 TYR cc_start: 0.6971 (t80) cc_final: 0.6367 (t80) REVERT: B 13 CYS cc_start: 0.7895 (m) cc_final: 0.7522 (m) REVERT: B 20 LEU cc_start: 0.8604 (tp) cc_final: 0.8316 (pp) REVERT: B 70 ARG cc_start: 0.8758 (mpp80) cc_final: 0.8485 (mpp80) REVERT: B 85 ARG cc_start: 0.4809 (OUTLIER) cc_final: 0.3557 (ptp90) REVERT: B 134 ARG cc_start: 0.6183 (tpt-90) cc_final: 0.5833 (tpt-90) REVERT: B 163 HIS cc_start: 0.8820 (m-70) cc_final: 0.8472 (m-70) REVERT: B 175 GLN cc_start: 0.8313 (pm20) cc_final: 0.7711 (pm20) REVERT: B 246 ARG cc_start: 0.7840 (mtm110) cc_final: 0.7593 (mtm110) REVERT: B 291 GLN cc_start: 0.8498 (pt0) cc_final: 0.8096 (pm20) REVERT: B 298 LEU cc_start: 0.6672 (tp) cc_final: 0.6189 (mt) REVERT: C 9 HIS cc_start: 0.7760 (t-90) cc_final: 0.7459 (t70) REVERT: C 13 CYS cc_start: 0.8294 (m) cc_final: 0.7743 (m) REVERT: C 70 ARG cc_start: 0.8428 (mtm-85) cc_final: 0.7877 (mtm-85) REVERT: C 119 TRP cc_start: 0.7016 (m100) cc_final: 0.6588 (m-10) REVERT: C 150 ILE cc_start: 0.7802 (OUTLIER) cc_final: 0.7428 (tp) REVERT: C 164 LYS cc_start: 0.8568 (mtmm) cc_final: 0.8284 (mtmm) REVERT: C 172 LEU cc_start: 0.8575 (pp) cc_final: 0.8326 (tp) REVERT: C 175 GLN cc_start: 0.8608 (pm20) cc_final: 0.8173 (pm20) REVERT: C 235 VAL cc_start: 0.8595 (p) cc_final: 0.8344 (m) REVERT: D 9 HIS cc_start: 0.7628 (t-90) cc_final: 0.7344 (t-170) REVERT: D 13 CYS cc_start: 0.8440 (m) cc_final: 0.7974 (m) REVERT: D 17 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8261 (mm-30) REVERT: D 101 PHE cc_start: 0.7686 (m-80) cc_final: 0.7483 (m-80) REVERT: D 163 HIS cc_start: 0.8618 (m-70) cc_final: 0.8318 (m-70) REVERT: D 164 LYS cc_start: 0.8716 (mmmm) cc_final: 0.8412 (mmmm) REVERT: D 222 ARG cc_start: 0.7587 (ttt180) cc_final: 0.5906 (mmm160) REVERT: D 226 ASP cc_start: 0.6909 (OUTLIER) cc_final: 0.6433 (m-30) REVERT: E 1 MET cc_start: 0.6766 (mtt) cc_final: 0.6277 (ptt) REVERT: E 5 VAL cc_start: 0.5623 (OUTLIER) cc_final: 0.5363 (m) REVERT: E 64 HIS cc_start: 0.6193 (m-70) cc_final: 0.5683 (m170) REVERT: E 67 TRP cc_start: 0.7570 (m100) cc_final: 0.7303 (m100) REVERT: E 70 ARG cc_start: 0.8554 (ttm-80) cc_final: 0.8207 (ttm110) REVERT: E 159 ILE cc_start: 0.8425 (tp) cc_final: 0.7702 (mm) REVERT: E 163 HIS cc_start: 0.8634 (m-70) cc_final: 0.8027 (m-70) REVERT: E 170 ARG cc_start: 0.8046 (tpp-160) cc_final: 0.7585 (tpp-160) REVERT: E 175 GLN cc_start: 0.8170 (pm20) cc_final: 0.7382 (pm20) REVERT: E 220 MET cc_start: 0.7577 (mmt) cc_final: 0.7334 (mmt) REVERT: F 84 TYR cc_start: 0.5747 (OUTLIER) cc_final: 0.5420 (t80) REVERT: F 94 GLN cc_start: 0.8193 (tt0) cc_final: 0.7976 (tp40) REVERT: F 149 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6451 (ttp80) REVERT: F 161 LEU cc_start: 0.8713 (pp) cc_final: 0.8401 (mt) REVERT: F 170 ARG cc_start: 0.8321 (mtt180) cc_final: 0.8075 (ptp-170) REVERT: F 175 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7710 (mp10) REVERT: F 213 PRO cc_start: 0.8461 (Cg_exo) cc_final: 0.8258 (Cg_endo) REVERT: F 220 MET cc_start: 0.7697 (mmp) cc_final: 0.7266 (mmp) REVERT: F 280 GLN cc_start: 0.6373 (OUTLIER) cc_final: 0.4652 (pp30) REVERT: G 316 MET cc_start: 0.2634 (OUTLIER) cc_final: 0.2201 (tpt) REVERT: G 321 LEU cc_start: 0.8349 (mp) cc_final: 0.7830 (pp) REVERT: G 327 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7267 (mp) REVERT: G 338 GLU cc_start: 0.7164 (OUTLIER) cc_final: 0.5167 (mm-30) REVERT: G 339 ASP cc_start: 0.7979 (p0) cc_final: 0.7590 (p0) REVERT: G 383 CYS cc_start: 0.6590 (m) cc_final: 0.6084 (t) REVERT: G 389 LEU cc_start: 0.8012 (tp) cc_final: 0.7578 (tt) REVERT: G 412 GLU cc_start: 0.8138 (mp0) cc_final: 0.7858 (mp0) REVERT: G 415 ARG cc_start: 0.8370 (mtt180) cc_final: 0.7970 (mtt180) REVERT: G 467 LYS cc_start: 0.8426 (mmmt) cc_final: 0.7634 (mmmt) REVERT: G 475 TRP cc_start: 0.7994 (t-100) cc_final: 0.7699 (t60) REVERT: G 514 GLN cc_start: 0.8671 (mt0) cc_final: 0.8190 (mt0) REVERT: G 542 ASP cc_start: 0.8296 (p0) cc_final: 0.7876 (m-30) REVERT: H 327 ILE cc_start: 0.8341 (OUTLIER) cc_final: 0.7988 (pt) REVERT: H 438 MET cc_start: 0.0241 (mtm) cc_final: -0.0031 (mtm) REVERT: H 467 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7569 (mmmt) REVERT: H 475 TRP cc_start: 0.8159 (t-100) cc_final: 0.7836 (t60) REVERT: H 488 PHE cc_start: 0.7691 (p90) cc_final: 0.7462 (p90) REVERT: H 493 TRP cc_start: 0.8516 (m-10) cc_final: 0.8243 (m-10) REVERT: H 514 GLN cc_start: 0.8663 (mt0) cc_final: 0.8088 (mt0) REVERT: H 548 TYR cc_start: 0.7767 (t80) cc_final: 0.7430 (t80) REVERT: H 588 HIS cc_start: 0.7742 (t70) cc_final: 0.7326 (t70) REVERT: I 353 ILE cc_start: 0.8606 (tp) cc_final: 0.8302 (pt) REVERT: I 368 ASP cc_start: 0.7510 (t0) cc_final: 0.7211 (t0) REVERT: I 373 SER cc_start: 0.6408 (OUTLIER) cc_final: 0.6105 (p) REVERT: I 467 LYS cc_start: 0.8026 (mmmt) cc_final: 0.7231 (mmmt) REVERT: I 479 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6821 (pm20) REVERT: I 488 PHE cc_start: 0.8016 (p90) cc_final: 0.7702 (p90) REVERT: I 494 MET cc_start: 0.6570 (mmt) cc_final: 0.6257 (mmt) REVERT: I 654 ASP cc_start: 0.3561 (OUTLIER) cc_final: 0.2929 (p0) REVERT: J 327 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7460 (mt) REVERT: J 331 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8424 (tp) REVERT: J 412 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: J 415 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8020 (mtp180) REVERT: J 428 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7404 (mm) REVERT: J 461 TRP cc_start: 0.6885 (m-90) cc_final: 0.6025 (m-90) REVERT: J 475 TRP cc_start: 0.7787 (t60) cc_final: 0.7571 (t60) REVERT: J 486 THR cc_start: 0.7630 (m) cc_final: 0.6841 (p) REVERT: J 488 PHE cc_start: 0.7825 (p90) cc_final: 0.7296 (p90) REVERT: J 492 ASN cc_start: 0.7676 (t0) cc_final: 0.7066 (t0) REVERT: J 510 ARG cc_start: 0.7853 (tpp-160) cc_final: 0.7511 (mmm160) REVERT: J 528 ILE cc_start: 0.7518 (OUTLIER) cc_final: 0.6983 (tt) REVERT: J 576 GLU cc_start: 0.8307 (pt0) cc_final: 0.7880 (pm20) REVERT: J 628 ARG cc_start: 0.8323 (ptm-80) cc_final: 0.8033 (ptm-80) REVERT: J 637 ASP cc_start: 0.5624 (t0) cc_final: 0.4949 (t0) REVERT: J 639 GLN cc_start: 0.8462 (pm20) cc_final: 0.8092 (pm20) REVERT: J 640 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: K 427 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.6385 (mp) REVERT: K 466 SER cc_start: 0.8624 (m) cc_final: 0.8292 (p) REVERT: K 467 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7295 (mmmt) REVERT: K 472 ARG cc_start: 0.8612 (mtt180) cc_final: 0.8211 (mmm160) REVERT: K 475 TRP cc_start: 0.8082 (t60) cc_final: 0.7827 (t60) REVERT: K 480 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8024 (ttpp) REVERT: K 488 PHE cc_start: 0.7896 (p90) cc_final: 0.7405 (p90) REVERT: K 492 ASN cc_start: 0.7091 (t0) cc_final: 0.6716 (t0) REVERT: K 548 TYR cc_start: 0.7697 (t80) cc_final: 0.7472 (t80) REVERT: K 576 GLU cc_start: 0.7358 (pm20) cc_final: 0.6915 (pm20) REVERT: K 601 ARG cc_start: 0.7112 (mmp80) cc_final: 0.6877 (mmp80) REVERT: L 319 LEU cc_start: 0.7152 (tt) cc_final: 0.6784 (pp) REVERT: L 321 LEU cc_start: 0.8720 (tt) cc_final: 0.8450 (pp) REVERT: L 344 TYR cc_start: 0.5695 (m-10) cc_final: 0.5463 (m-10) REVERT: L 357 LEU cc_start: 0.8432 (mt) cc_final: 0.8213 (pp) REVERT: L 368 ASP cc_start: 0.7321 (t0) cc_final: 0.7068 (t0) REVERT: L 372 HIS cc_start: 0.6988 (m90) cc_final: 0.6715 (m90) REVERT: L 387 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6861 (mt) REVERT: L 389 LEU cc_start: 0.7814 (tp) cc_final: 0.7297 (tt) REVERT: L 404 ARG cc_start: 0.8347 (tpt170) cc_final: 0.7686 (tpt170) REVERT: L 414 LEU cc_start: 0.8683 (pp) cc_final: 0.7792 (pp) REVERT: L 415 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7731 (mmm160) REVERT: L 423 TYR cc_start: 0.7098 (t80) cc_final: 0.6636 (t80) REVERT: L 426 ARG cc_start: 0.4740 (OUTLIER) cc_final: 0.3681 (mmm160) REVERT: L 428 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7410 (mm) REVERT: L 467 LYS cc_start: 0.8441 (mmmt) cc_final: 0.7661 (mmmt) REVERT: L 468 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7674 (tm-30) REVERT: L 472 ARG cc_start: 0.8585 (mmt180) cc_final: 0.7963 (mmt180) REVERT: L 488 PHE cc_start: 0.7926 (p90) cc_final: 0.7571 (p90) REVERT: L 491 PHE cc_start: 0.7061 (m-10) cc_final: 0.6759 (m-80) REVERT: L 512 ILE cc_start: 0.8145 (tp) cc_final: 0.7688 (mm) REVERT: L 515 LEU cc_start: 0.8657 (mt) cc_final: 0.8399 (mt) REVERT: L 565 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6481 (mt) outliers start: 181 outliers final: 131 residues processed: 1141 average time/residue: 0.2170 time to fit residues: 382.7654 Evaluate side-chains 1188 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 157 poor density : 1031 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 211 HIS Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 320 ILE Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 375 TRP Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 489 ARG Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 630 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 331 LEU Chi-restraints excluded: chain H residue 372 HIS Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 410 PHE Chi-restraints excluded: chain H residue 428 ILE Chi-restraints excluded: chain H residue 469 LEU Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain H residue 638 MET Chi-restraints excluded: chain H residue 648 PHE Chi-restraints excluded: chain H residue 649 PHE Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 377 GLU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 410 PHE Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain I residue 480 LYS Chi-restraints excluded: chain I residue 489 ARG Chi-restraints excluded: chain I residue 564 ASN Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 376 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 412 GLU Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 480 LYS Chi-restraints excluded: chain J residue 489 ARG Chi-restraints excluded: chain J residue 494 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 577 LEU Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 648 PHE Chi-restraints excluded: chain J residue 649 PHE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 387 LEU Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 480 LYS Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 514 GLN Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain K residue 573 SER Chi-restraints excluded: chain K residue 639 GLN Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 373 SER Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 407 GLU Chi-restraints excluded: chain L residue 408 LEU Chi-restraints excluded: chain L residue 426 ARG Chi-restraints excluded: chain L residue 427 ILE Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 469 LEU Chi-restraints excluded: chain L residue 480 LYS Chi-restraints excluded: chain L residue 526 LYS Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 565 ILE Chi-restraints excluded: chain L residue 585 PHE Chi-restraints excluded: chain L residue 638 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 320 optimal weight: 0.9990 chunk 368 optimal weight: 9.9990 chunk 361 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 283 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 261 optimal weight: 3.9990 chunk 337 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 HIS ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 64 HIS ** E 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 518 ASN ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 533 GLN ** L 330 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 = 0.4353 r_free = 0.4353 target = 0.153842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.122188 restraints weight = 74050.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.125484 restraints weight = 54304.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.128090 restraints weight = 42927.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.129919 restraints weight = 35528.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.131513 restraints weight = 30672.602| |-----------------------------------------------------------------------------| r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30234 Z= 0.151 Angle : 0.813 16.333 41070 Z= 0.406 Chirality : 0.048 0.319 4548 Planarity : 0.005 0.149 5322 Dihedral : 5.607 57.642 4073 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.77 % Favored : 95.20 % Rotamer: Outliers : 5.53 % Allowed : 32.63 % Favored : 61.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % 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: -1.00 (0.14), residues: 3666 helix: -0.28 (0.14), residues: 1411 sheet: -0.44 (0.23), residues: 538 loop : -0.97 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 170 TYR 0.037 0.001 TYR L 548 PHE 0.051 0.002 PHE A 6 TRP 0.047 0.003 TRP H 375 HIS 0.021 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00327 (30234) covalent geometry : angle 0.81262 (41070) hydrogen bonds : bond 0.04154 ( 1130) hydrogen bonds : angle 5.64759 ( 3240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1221 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 1048 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 9 HIS cc_start: 0.7916 (m90) cc_final: 0.7680 (m90) REVERT: A 159 ILE cc_start: 0.8641 (mt) cc_final: 0.7870 (mm) REVERT: A 163 HIS cc_start: 0.8600 (m-70) cc_final: 0.8072 (m-70) REVERT: A 212 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7356 (mmtp) REVERT: A 215 SER cc_start: 0.8585 (p) cc_final: 0.8231 (t) REVERT: B 8 TYR cc_start: 0.6978 (t80) cc_final: 0.6363 (t80) REVERT: B 13 CYS cc_start: 0.7746 (m) cc_final: 0.7403 (m) REVERT: B 20 LEU cc_start: 0.8597 (tp) cc_final: 0.8298 (pp) REVERT: B 85 ARG cc_start: 0.4898 (OUTLIER) cc_final: 0.3699 (ptp90) REVERT: B 134 ARG cc_start: 0.6130 (tpt-90) cc_final: 0.5768 (tpt-90) REVERT: B 163 HIS cc_start: 0.8809 (m-70) cc_final: 0.8448 (m-70) REVERT: B 170 ARG cc_start: 0.7687 (tpp-160) cc_final: 0.7458 (tpp-160) REVERT: B 246 ARG cc_start: 0.7876 (mtm110) cc_final: 0.7629 (mtm110) REVERT: B 291 GLN cc_start: 0.8538 (pt0) cc_final: 0.8187 (pm20) REVERT: B 298 LEU cc_start: 0.6584 (tp) cc_final: 0.6072 (mt) REVERT: C 13 CYS cc_start: 0.8283 (m) cc_final: 0.7740 (m) REVERT: C 70 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.7788 (mtm-85) REVERT: C 119 TRP cc_start: 0.6973 (m100) cc_final: 0.6581 (m-10) REVERT: C 150 ILE cc_start: 0.7781 (OUTLIER) cc_final: 0.7381 (tp) REVERT: C 161 LEU cc_start: 0.8813 (pp) cc_final: 0.8471 (pp) REVERT: C 164 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8257 (mtmm) REVERT: C 172 LEU cc_start: 0.8593 (pp) cc_final: 0.8341 (tp) REVERT: C 175 GLN cc_start: 0.8616 (pm20) cc_final: 0.8208 (pm20) REVERT: C 235 VAL cc_start: 0.8636 (p) cc_final: 0.8409 (m) REVERT: D 9 HIS cc_start: 0.7604 (t-90) cc_final: 0.7356 (t-170) REVERT: D 13 CYS cc_start: 0.8397 (m) cc_final: 0.7968 (m) REVERT: D 17 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8263 (mm-30) REVERT: D 101 PHE cc_start: 0.7693 (m-80) cc_final: 0.7467 (m-80) REVERT: D 163 HIS cc_start: 0.8655 (m-70) cc_final: 0.8335 (m-70) REVERT: D 164 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8386 (mmmm) REVERT: D 175 GLN cc_start: 0.8561 (pm20) cc_final: 0.8180 (pm20) REVERT: D 226 ASP cc_start: 0.6889 (OUTLIER) cc_final: 0.6430 (m-30) REVERT: E 1 MET cc_start: 0.6747 (mtt) cc_final: 0.6301 (ptt) REVERT: E 5 VAL cc_start: 0.5653 (OUTLIER) cc_final: 0.5404 (m) REVERT: E 64 HIS cc_start: 0.6139 (m-70) cc_final: 0.5717 (m170) REVERT: E 69 GLU cc_start: 0.8133 (tm-30) cc_final: 0.7538 (pp20) REVERT: E 101 PHE cc_start: 0.7480 (m-80) cc_final: 0.7131 (m-80) REVERT: E 132 LEU cc_start: 0.7300 (OUTLIER) cc_final: 0.7066 (mm) REVERT: E 159 ILE cc_start: 0.8434 (tp) cc_final: 0.7696 (mm) REVERT: E 163 HIS cc_start: 0.8614 (m-70) cc_final: 0.7969 (m-70) REVERT: E 175 GLN cc_start: 0.8175 (pm20) cc_final: 0.7377 (pm20) REVERT: E 220 MET cc_start: 0.7542 (mmt) cc_final: 0.7303 (mmt) REVERT: F 84 TYR cc_start: 0.5710 (OUTLIER) cc_final: 0.5399 (t80) REVERT: F 94 GLN cc_start: 0.8178 (tt0) cc_final: 0.7956 (tp40) REVERT: F 117 LEU cc_start: 0.5937 (OUTLIER) cc_final: 0.5437 (mt) REVERT: F 149 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6445 (ttp80) REVERT: F 161 LEU cc_start: 0.8738 (pp) cc_final: 0.8436 (mt) REVERT: F 170 ARG cc_start: 0.8265 (mtt180) cc_final: 0.8025 (ptp-170) REVERT: F 175 GLN cc_start: 0.7909 (tm-30) cc_final: 0.7697 (mp10) REVERT: F 213 PRO cc_start: 0.8382 (Cg_exo) cc_final: 0.8173 (Cg_endo) REVERT: F 220 MET cc_start: 0.7667 (mmp) cc_final: 0.7277 (mmp) REVERT: F 246 ARG cc_start: 0.7616 (mpp80) cc_final: 0.7327 (ptp90) REVERT: F 280 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.4671 (pp30) REVERT: G 316 MET cc_start: 0.2499 (tpt) cc_final: 0.2084 (tpt) REVERT: G 320 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7589 (mp) REVERT: G 327 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7304 (mp) REVERT: G 403 LEU cc_start: 0.8601 (mp) cc_final: 0.8017 (mt) REVERT: G 412 GLU cc_start: 0.8108 (mp0) cc_final: 0.7831 (mp0) REVERT: G 415 ARG cc_start: 0.8368 (mtt180) cc_final: 0.8083 (mtt180) REVERT: G 467 LYS cc_start: 0.8414 (mmmt) cc_final: 0.7619 (mmmt) REVERT: G 475 TRP cc_start: 0.8009 (t-100) cc_final: 0.7699 (t60) REVERT: G 491 PHE cc_start: 0.6354 (m-10) cc_final: 0.5190 (m-10) REVERT: G 514 GLN cc_start: 0.8675 (mt0) cc_final: 0.8168 (mt0) REVERT: G 527 LEU cc_start: 0.8679 (mp) cc_final: 0.8290 (pp) REVERT: G 542 ASP cc_start: 0.8233 (p0) cc_final: 0.7863 (m-30) REVERT: G 564 ASN cc_start: 0.8241 (m110) cc_final: 0.6555 (t0) REVERT: H 327 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8065 (pt) REVERT: H 438 MET cc_start: 0.0267 (mtm) cc_final: -0.0010 (mtm) REVERT: H 467 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7516 (mmmt) REVERT: H 475 TRP cc_start: 0.8046 (t-100) cc_final: 0.7751 (t60) REVERT: H 493 TRP cc_start: 0.8515 (m-10) cc_final: 0.8239 (m-10) REVERT: H 514 GLN cc_start: 0.8653 (mt0) cc_final: 0.8001 (mt0) REVERT: H 548 TYR cc_start: 0.7804 (t80) cc_final: 0.7470 (t80) REVERT: H 588 HIS cc_start: 0.7634 (t70) cc_final: 0.7314 (t70) REVERT: H 654 ASP cc_start: 0.3983 (OUTLIER) cc_final: 0.3690 (t0) REVERT: I 347 ASP cc_start: 0.8020 (t70) cc_final: 0.7315 (p0) REVERT: I 353 ILE cc_start: 0.8603 (tp) cc_final: 0.8272 (pt) REVERT: I 368 ASP cc_start: 0.7511 (t0) cc_final: 0.7242 (t0) REVERT: I 373 SER cc_start: 0.6347 (OUTLIER) cc_final: 0.6039 (p) REVERT: I 411 GLU cc_start: 0.7825 (tp30) cc_final: 0.7454 (tp30) REVERT: I 467 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7211 (mmmt) REVERT: I 479 GLU cc_start: 0.7158 (OUTLIER) cc_final: 0.6807 (pm20) REVERT: I 488 PHE cc_start: 0.8017 (p90) cc_final: 0.7677 (p90) REVERT: I 494 MET cc_start: 0.6539 (mmt) cc_final: 0.6280 (mmt) REVERT: I 549 ARG cc_start: 0.8375 (mmt180) cc_final: 0.8065 (mpp80) REVERT: I 576 GLU cc_start: 0.8447 (pt0) cc_final: 0.7764 (pm20) REVERT: I 654 ASP cc_start: 0.3552 (OUTLIER) cc_final: 0.2890 (p0) REVERT: J 327 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7383 (mt) REVERT: J 331 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8302 (tp) REVERT: J 412 GLU cc_start: 0.7792 (mm-30) cc_final: 0.6732 (mp0) REVERT: J 415 ARG cc_start: 0.8425 (mtp180) cc_final: 0.8013 (mtp180) REVERT: J 428 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7503 (mm) REVERT: J 461 TRP cc_start: 0.6812 (m-90) cc_final: 0.6093 (m-90) REVERT: J 477 TYR cc_start: 0.7961 (OUTLIER) cc_final: 0.7512 (t80) REVERT: J 486 THR cc_start: 0.7644 (m) cc_final: 0.7141 (t) REVERT: J 488 PHE cc_start: 0.7825 (p90) cc_final: 0.7262 (p90) REVERT: J 492 ASN cc_start: 0.7663 (t0) cc_final: 0.7061 (t0) REVERT: J 510 ARG cc_start: 0.7844 (tpp-160) cc_final: 0.7519 (mmm160) REVERT: J 528 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.6991 (tt) REVERT: J 576 GLU cc_start: 0.8337 (pt0) cc_final: 0.7921 (pm20) REVERT: J 628 ARG cc_start: 0.8343 (ptm-80) cc_final: 0.8003 (ptm-80) REVERT: J 640 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7735 (pt0) REVERT: K 427 ILE cc_start: 0.7349 (OUTLIER) cc_final: 0.6407 (mm) REVERT: K 466 SER cc_start: 0.8614 (m) cc_final: 0.8307 (p) REVERT: K 467 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7295 (mmmt) REVERT: K 469 LEU cc_start: 0.8944 (tt) cc_final: 0.8712 (mm) REVERT: K 473 VAL cc_start: 0.8309 (t) cc_final: 0.7974 (p) REVERT: K 475 TRP cc_start: 0.8098 (t60) cc_final: 0.7850 (t60) REVERT: K 480 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7860 (pttm) REVERT: K 488 PHE cc_start: 0.7871 (p90) cc_final: 0.7363 (p90) REVERT: K 514 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7647 (tm130) REVERT: K 548 TYR cc_start: 0.7726 (t80) cc_final: 0.7455 (t80) REVERT: L 319 LEU cc_start: 0.7215 (tt) cc_final: 0.6816 (pp) REVERT: L 321 LEU cc_start: 0.8700 (tt) cc_final: 0.8434 (pp) REVERT: L 344 TYR cc_start: 0.5679 (m-10) cc_final: 0.5468 (m-10) REVERT: L 357 LEU cc_start: 0.8486 (mt) cc_final: 0.8263 (pp) REVERT: L 368 ASP cc_start: 0.7345 (t0) cc_final: 0.7080 (t0) REVERT: L 372 HIS cc_start: 0.6940 (m90) cc_final: 0.6653 (m90) REVERT: L 387 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6837 (mt) REVERT: L 389 LEU cc_start: 0.7767 (tp) cc_final: 0.7268 (tt) REVERT: L 404 ARG cc_start: 0.8364 (tpt170) cc_final: 0.7679 (tpt170) REVERT: L 423 TYR cc_start: 0.7082 (t80) cc_final: 0.6764 (t80) REVERT: L 426 ARG cc_start: 0.4902 (OUTLIER) cc_final: 0.3788 (mmm160) REVERT: L 428 ILE cc_start: 0.8034 (OUTLIER) cc_final: 0.7407 (mm) REVERT: L 467 LYS cc_start: 0.8433 (mmmt) cc_final: 0.7656 (mmmt) REVERT: L 468 GLN cc_start: 0.7877 (tm-30) cc_final: 0.7641 (tm-30) REVERT: L 472 ARG cc_start: 0.8572 (mmt180) cc_final: 0.7948 (mmt180) REVERT: L 488 PHE cc_start: 0.7997 (p90) cc_final: 0.7665 (p90) REVERT: L 491 PHE cc_start: 0.7114 (m-10) cc_final: 0.6832 (m-80) REVERT: L 512 ILE cc_start: 0.8039 (tp) cc_final: 0.7574 (mm) REVERT: L 515 LEU cc_start: 0.8651 (mt) cc_final: 0.8401 (mt) REVERT: L 549 ARG cc_start: 0.8270 (ptm160) cc_final: 0.7190 (ptp90) REVERT: L 565 ILE cc_start: 0.6915 (OUTLIER) cc_final: 0.6566 (mt) outliers start: 173 outliers final: 125 residues processed: 1124 average time/residue: 0.2115 time to fit residues: 367.7886 Evaluate side-chains 1187 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 1033 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 54 ILE Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 121 LEU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 191 ARG Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 134 ARG Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 85 ARG Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 320 ILE Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 375 TRP Chi-restraints excluded: chain G residue 376 ILE Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 489 ARG Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 581 LEU Chi-restraints excluded: chain G residue 630 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 329 ASN Chi-restraints excluded: chain H residue 372 HIS Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 410 PHE Chi-restraints excluded: chain H residue 469 LEU Chi-restraints excluded: chain H residue 487 LEU Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain H residue 638 MET Chi-restraints excluded: chain H residue 648 PHE Chi-restraints excluded: chain H residue 649 PHE Chi-restraints excluded: chain H residue 654 ASP Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 377 GLU Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 410 PHE Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain I residue 480 LYS Chi-restraints excluded: chain I residue 489 ARG Chi-restraints excluded: chain I residue 564 ASN Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 376 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 477 TYR Chi-restraints excluded: chain J residue 480 LYS Chi-restraints excluded: chain J residue 494 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 648 PHE Chi-restraints excluded: chain J residue 649 PHE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 480 LYS Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 514 GLN Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain K residue 573 SER Chi-restraints excluded: chain K residue 639 GLN Chi-restraints excluded: chain K residue 648 PHE Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 373 SER Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 407 GLU Chi-restraints excluded: chain L residue 408 LEU Chi-restraints excluded: chain L residue 426 ARG Chi-restraints excluded: chain L residue 427 ILE Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 469 LEU Chi-restraints excluded: chain L residue 480 LYS Chi-restraints excluded: chain L residue 526 LYS Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 565 ILE Chi-restraints excluded: chain L residue 585 PHE Chi-restraints excluded: chain L residue 638 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 47 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 202 optimal weight: 0.0060 chunk 169 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 4 optimal weight: 0.0270 chunk 273 optimal weight: 5.9990 chunk 234 optimal weight: 0.9980 chunk 313 optimal weight: 0.5980 chunk 124 optimal weight: 6.9990 overall best weight: 0.4854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 GLN ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 9 HIS E 104 HIS ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 329 ASN ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 627 HIS J 533 GLN K 593 HIS ** L 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.155231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.122806 restraints weight = 73955.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.126198 restraints weight = 54616.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.128753 restraints weight = 43247.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.130581 restraints weight = 36031.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.132240 restraints weight = 31257.079| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30234 Z= 0.145 Angle : 0.845 16.894 41070 Z= 0.418 Chirality : 0.049 0.337 4548 Planarity : 0.005 0.101 5322 Dihedral : 5.569 57.598 4073 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 4.99 % Allowed : 33.30 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.14), residues: 3666 helix: -0.29 (0.14), residues: 1407 sheet: -0.41 (0.23), residues: 531 loop : -0.92 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 52 TYR 0.040 0.001 TYR K 423 PHE 0.025 0.001 PHE G 410 TRP 0.055 0.003 TRP H 375 HIS 0.023 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00322 (30234) covalent geometry : angle 0.84519 (41070) hydrogen bonds : bond 0.04120 ( 1130) hydrogen bonds : angle 5.59421 ( 3240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 1056 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 9 HIS cc_start: 0.7914 (m90) cc_final: 0.7712 (m90) REVERT: A 11 MET cc_start: 0.6761 (mmt) cc_final: 0.6480 (mmt) REVERT: A 70 ARG cc_start: 0.8444 (mtm-85) cc_final: 0.7847 (mtm-85) REVERT: A 159 ILE cc_start: 0.8679 (mt) cc_final: 0.7903 (mm) REVERT: A 163 HIS cc_start: 0.8656 (m-70) cc_final: 0.8114 (m-70) REVERT: A 175 GLN cc_start: 0.8469 (pm20) cc_final: 0.8007 (pm20) REVERT: A 212 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7342 (mmtp) REVERT: B 8 TYR cc_start: 0.6985 (t80) cc_final: 0.6398 (t80) REVERT: B 13 CYS cc_start: 0.7719 (m) cc_final: 0.7374 (m) REVERT: B 20 LEU cc_start: 0.8595 (tp) cc_final: 0.8300 (pp) REVERT: B 85 ARG cc_start: 0.4977 (OUTLIER) cc_final: 0.3914 (ptp90) REVERT: B 134 ARG cc_start: 0.6212 (tpt-90) cc_final: 0.5906 (tpt-90) REVERT: B 147 GLN cc_start: 0.5920 (tm-30) cc_final: 0.5717 (tm-30) REVERT: B 163 HIS cc_start: 0.8844 (m-70) cc_final: 0.8484 (m-70) REVERT: B 170 ARG cc_start: 0.7752 (tpp-160) cc_final: 0.7517 (tpp-160) REVERT: B 172 LEU cc_start: 0.8197 (tp) cc_final: 0.7974 (tp) REVERT: B 175 GLN cc_start: 0.8275 (pm20) cc_final: 0.7685 (pm20) REVERT: B 246 ARG cc_start: 0.7823 (mtm110) cc_final: 0.7539 (mtm110) REVERT: B 291 GLN cc_start: 0.8559 (pt0) cc_final: 0.8162 (pm20) REVERT: C 13 CYS cc_start: 0.8278 (m) cc_final: 0.7720 (m) REVERT: C 17 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8444 (mm-30) REVERT: C 70 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.7809 (mtm-85) REVERT: C 119 TRP cc_start: 0.7034 (m100) cc_final: 0.6663 (m-10) REVERT: C 150 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7442 (tp) REVERT: C 161 LEU cc_start: 0.8797 (pp) cc_final: 0.8562 (pp) REVERT: C 164 LYS cc_start: 0.8574 (mtmm) cc_final: 0.8366 (mtmm) REVERT: C 172 LEU cc_start: 0.8603 (pp) cc_final: 0.8351 (tp) REVERT: C 175 GLN cc_start: 0.8619 (pm20) cc_final: 0.8223 (pm20) REVERT: C 235 VAL cc_start: 0.8625 (p) cc_final: 0.8405 (m) REVERT: D 9 HIS cc_start: 0.7648 (t-90) cc_final: 0.7378 (t-170) REVERT: D 13 CYS cc_start: 0.8396 (m) cc_final: 0.7997 (m) REVERT: D 17 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8287 (mm-30) REVERT: D 101 PHE cc_start: 0.7660 (m-80) cc_final: 0.7174 (m-80) REVERT: D 104 HIS cc_start: 0.7532 (t-90) cc_final: 0.7215 (t-90) REVERT: D 134 ARG cc_start: 0.5733 (mmp-170) cc_final: 0.4703 (mmm160) REVERT: D 164 LYS cc_start: 0.8634 (mmmm) cc_final: 0.8331 (mmmm) REVERT: D 175 GLN cc_start: 0.8500 (pm20) cc_final: 0.8207 (pm20) REVERT: D 226 ASP cc_start: 0.6872 (OUTLIER) cc_final: 0.6132 (t70) REVERT: E 1 MET cc_start: 0.6752 (mtt) cc_final: 0.6265 (ptt) REVERT: E 5 VAL cc_start: 0.5538 (OUTLIER) cc_final: 0.5303 (m) REVERT: E 101 PHE cc_start: 0.7491 (m-80) cc_final: 0.6996 (m-80) REVERT: E 132 LEU cc_start: 0.7237 (OUTLIER) cc_final: 0.6992 (mm) REVERT: E 159 ILE cc_start: 0.8476 (tp) cc_final: 0.7780 (mm) REVERT: E 163 HIS cc_start: 0.8658 (m-70) cc_final: 0.8097 (m-70) REVERT: E 175 GLN cc_start: 0.8184 (pm20) cc_final: 0.7717 (pm20) REVERT: E 220 MET cc_start: 0.7586 (mmt) cc_final: 0.7345 (mmt) REVERT: F 84 TYR cc_start: 0.5807 (OUTLIER) cc_final: 0.5511 (t80) REVERT: F 94 GLN cc_start: 0.8212 (tt0) cc_final: 0.8003 (tp40) REVERT: F 149 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6444 (ttp80) REVERT: F 161 LEU cc_start: 0.8742 (pp) cc_final: 0.8422 (mt) REVERT: F 170 ARG cc_start: 0.8256 (mtt180) cc_final: 0.8020 (ptp-170) REVERT: F 213 PRO cc_start: 0.8207 (Cg_exo) cc_final: 0.7993 (Cg_endo) REVERT: F 220 MET cc_start: 0.7867 (mmp) cc_final: 0.7383 (mmp) REVERT: F 246 ARG cc_start: 0.7596 (mpp80) cc_final: 0.7312 (ptp90) REVERT: F 280 GLN cc_start: 0.6326 (OUTLIER) cc_final: 0.4571 (pp30) REVERT: G 316 MET cc_start: 0.2470 (OUTLIER) cc_final: 0.2023 (tpt) REVERT: G 320 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.7574 (mp) REVERT: G 327 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7309 (mp) REVERT: G 338 GLU cc_start: 0.7111 (OUTLIER) cc_final: 0.5127 (mm-30) REVERT: G 339 ASP cc_start: 0.8096 (p0) cc_final: 0.7679 (p0) REVERT: G 412 GLU cc_start: 0.8243 (mp0) cc_final: 0.7760 (mp0) REVERT: G 415 ARG cc_start: 0.8482 (mtt180) cc_final: 0.8027 (mtt180) REVERT: G 418 ARG cc_start: 0.8137 (mtm110) cc_final: 0.7743 (mtm110) REVERT: G 467 LYS cc_start: 0.8372 (mmmt) cc_final: 0.7567 (mmmt) REVERT: G 475 TRP cc_start: 0.8041 (t-100) cc_final: 0.7706 (t60) REVERT: G 514 GLN cc_start: 0.8687 (mt0) cc_final: 0.8192 (mt0) REVERT: G 527 LEU cc_start: 0.8695 (mp) cc_final: 0.8324 (pp) REVERT: G 542 ASP cc_start: 0.8255 (p0) cc_final: 0.7872 (m-30) REVERT: G 654 ASP cc_start: 0.2900 (OUTLIER) cc_final: 0.2334 (p0) REVERT: H 327 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8027 (pt) REVERT: H 356 PHE cc_start: 0.8163 (m-10) cc_final: 0.7924 (m-80) REVERT: H 438 MET cc_start: 0.0259 (mtm) cc_final: -0.0012 (mtm) REVERT: H 467 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7464 (mmmt) REVERT: H 475 TRP cc_start: 0.8109 (t-100) cc_final: 0.7815 (t60) REVERT: H 488 PHE cc_start: 0.7817 (p90) cc_final: 0.7420 (p90) REVERT: H 493 TRP cc_start: 0.8517 (m-10) cc_final: 0.8253 (m-10) REVERT: H 514 GLN cc_start: 0.8678 (mt0) cc_final: 0.8006 (mt0) REVERT: H 548 TYR cc_start: 0.7823 (t80) cc_final: 0.7495 (t80) REVERT: H 584 SER cc_start: 0.8614 (p) cc_final: 0.8239 (m) REVERT: H 588 HIS cc_start: 0.7639 (t70) cc_final: 0.7325 (t70) REVERT: H 654 ASP cc_start: 0.3973 (OUTLIER) cc_final: 0.3690 (t0) REVERT: I 347 ASP cc_start: 0.7860 (t70) cc_final: 0.7093 (p0) REVERT: I 353 ILE cc_start: 0.8606 (tp) cc_final: 0.8268 (pt) REVERT: I 368 ASP cc_start: 0.7574 (t0) cc_final: 0.7283 (t0) REVERT: I 373 SER cc_start: 0.6219 (OUTLIER) cc_final: 0.5919 (p) REVERT: I 411 GLU cc_start: 0.7811 (tp30) cc_final: 0.7422 (tp30) REVERT: I 423 TYR cc_start: 0.5918 (m-10) cc_final: 0.5699 (m-10) REVERT: I 467 LYS cc_start: 0.7981 (mmmt) cc_final: 0.7178 (mmmt) REVERT: I 479 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: I 488 PHE cc_start: 0.7977 (p90) cc_final: 0.7628 (p90) REVERT: I 494 MET cc_start: 0.6526 (mmt) cc_final: 0.6202 (mmt) REVERT: I 549 ARG cc_start: 0.8375 (mmt180) cc_final: 0.8043 (mpp80) REVERT: I 576 GLU cc_start: 0.8444 (pt0) cc_final: 0.7796 (pm20) REVERT: I 654 ASP cc_start: 0.3546 (OUTLIER) cc_final: 0.2894 (p0) REVERT: J 327 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7503 (mt) REVERT: J 347 ASP cc_start: 0.7726 (t70) cc_final: 0.7251 (p0) REVERT: J 412 GLU cc_start: 0.7850 (mm-30) cc_final: 0.6677 (mp0) REVERT: J 415 ARG cc_start: 0.8446 (mtp180) cc_final: 0.7982 (mtp180) REVERT: J 428 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7412 (mm) REVERT: J 461 TRP cc_start: 0.6839 (m-90) cc_final: 0.6083 (m-90) REVERT: J 480 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7638 (mmtt) REVERT: J 486 THR cc_start: 0.7615 (m) cc_final: 0.6848 (p) REVERT: J 488 PHE cc_start: 0.7830 (p90) cc_final: 0.7300 (p90) REVERT: J 492 ASN cc_start: 0.7603 (t0) cc_final: 0.6937 (t0) REVERT: J 510 ARG cc_start: 0.7883 (tpp-160) cc_final: 0.7533 (mmm160) REVERT: J 528 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.6974 (tt) REVERT: J 576 GLU cc_start: 0.8360 (pt0) cc_final: 0.7847 (pm20) REVERT: J 590 LEU cc_start: 0.8565 (tp) cc_final: 0.8122 (tp) REVERT: J 628 ARG cc_start: 0.8355 (ptm-80) cc_final: 0.8048 (ptm-80) REVERT: J 640 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7967 (pt0) REVERT: K 414 LEU cc_start: 0.8974 (tt) cc_final: 0.8385 (tp) REVERT: K 425 LYS cc_start: 0.6019 (tptt) cc_final: 0.5446 (tptm) REVERT: K 427 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6321 (mm) REVERT: K 466 SER cc_start: 0.8598 (m) cc_final: 0.8254 (p) REVERT: K 467 LYS cc_start: 0.8063 (mmmt) cc_final: 0.7323 (mmmt) REVERT: K 469 LEU cc_start: 0.8956 (tt) cc_final: 0.8726 (mm) REVERT: K 472 ARG cc_start: 0.8600 (mtt180) cc_final: 0.8151 (mmm160) REVERT: K 475 TRP cc_start: 0.8105 (t60) cc_final: 0.7853 (t60) REVERT: K 488 PHE cc_start: 0.7858 (p90) cc_final: 0.7400 (p90) REVERT: K 514 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7597 (tm130) REVERT: K 548 TYR cc_start: 0.7747 (t80) cc_final: 0.7506 (t80) REVERT: K 549 ARG cc_start: 0.7605 (mtm180) cc_final: 0.6506 (ptt-90) REVERT: K 601 ARG cc_start: 0.7088 (mmp80) cc_final: 0.6855 (mmp80) REVERT: L 319 LEU cc_start: 0.7250 (tt) cc_final: 0.6829 (pp) REVERT: L 321 LEU cc_start: 0.8697 (tt) cc_final: 0.8403 (pp) REVERT: L 357 LEU cc_start: 0.8509 (mt) cc_final: 0.8293 (pp) REVERT: L 368 ASP cc_start: 0.7396 (t0) cc_final: 0.7136 (t0) REVERT: L 372 HIS cc_start: 0.6836 (m90) cc_final: 0.6590 (m90) REVERT: L 387 LEU cc_start: 0.7080 (OUTLIER) cc_final: 0.6836 (mt) REVERT: L 389 LEU cc_start: 0.7747 (tp) cc_final: 0.7193 (tt) REVERT: L 404 ARG cc_start: 0.8409 (tpt170) cc_final: 0.7680 (tpt170) REVERT: L 411 GLU cc_start: 0.7830 (pm20) cc_final: 0.7523 (pm20) REVERT: L 415 ARG cc_start: 0.8380 (mmm160) cc_final: 0.7572 (mmp80) REVERT: L 423 TYR cc_start: 0.7122 (t80) cc_final: 0.6730 (t80) REVERT: L 426 ARG cc_start: 0.4911 (OUTLIER) cc_final: 0.3960 (mmm160) REVERT: L 428 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7395 (mm) REVERT: L 467 LYS cc_start: 0.8427 (mmmt) cc_final: 0.7624 (mmmt) REVERT: L 468 GLN cc_start: 0.7908 (tm-30) cc_final: 0.7643 (tm-30) REVERT: L 472 ARG cc_start: 0.8598 (mmt180) cc_final: 0.7885 (mmt180) REVERT: L 488 PHE cc_start: 0.8012 (p90) cc_final: 0.7643 (p90) REVERT: L 491 PHE cc_start: 0.7117 (m-10) cc_final: 0.6799 (m-80) REVERT: L 512 ILE cc_start: 0.8091 (tp) cc_final: 0.7630 (mm) REVERT: L 515 LEU cc_start: 0.8641 (mt) cc_final: 0.8397 (mt) REVERT: L 549 ARG cc_start: 0.8293 (ptm160) cc_final: 0.7343 (mtm180) REVERT: L 565 ILE cc_start: 0.6862 (OUTLIER) cc_final: 0.6528 (mt) REVERT: L 631 ASP cc_start: 0.7315 (m-30) cc_final: 0.6495 (m-30) outliers start: 156 outliers final: 111 residues processed: 1124 average time/residue: 0.2084 time to fit residues: 362.8273 Evaluate side-chains 1163 residues out of total 3168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 1023 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 145 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 85 ARG Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 188 ILE Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 94 GLN Chi-restraints excluded: chain C residue 121 LEU Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 159 ILE Chi-restraints excluded: chain C residue 171 GLN Chi-restraints excluded: chain C residue 241 THR Chi-restraints excluded: chain C residue 259 VAL Chi-restraints excluded: chain C residue 276 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 118 ASN Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain D residue 160 THR Chi-restraints excluded: chain D residue 209 GLU Chi-restraints excluded: chain D residue 226 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 17 GLU Chi-restraints excluded: chain E residue 27 SER Chi-restraints excluded: chain E residue 44 SER Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 132 LEU Chi-restraints excluded: chain E residue 172 LEU Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain F residue 3 THR Chi-restraints excluded: chain F residue 74 LEU Chi-restraints excluded: chain F residue 84 TYR Chi-restraints excluded: chain F residue 92 ILE Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 149 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 188 ILE Chi-restraints excluded: chain F residue 218 HIS Chi-restraints excluded: chain F residue 276 ILE Chi-restraints excluded: chain F residue 280 GLN Chi-restraints excluded: chain G residue 316 MET Chi-restraints excluded: chain G residue 320 ILE Chi-restraints excluded: chain G residue 327 ILE Chi-restraints excluded: chain G residue 331 LEU Chi-restraints excluded: chain G residue 338 GLU Chi-restraints excluded: chain G residue 390 VAL Chi-restraints excluded: chain G residue 405 VAL Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 464 SER Chi-restraints excluded: chain G residue 489 ARG Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 540 ILE Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 562 ILE Chi-restraints excluded: chain G residue 630 LEU Chi-restraints excluded: chain G residue 654 ASP Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 372 HIS Chi-restraints excluded: chain H residue 405 VAL Chi-restraints excluded: chain H residue 410 PHE Chi-restraints excluded: chain H residue 469 LEU Chi-restraints excluded: chain H residue 534 LYS Chi-restraints excluded: chain H residue 540 ILE Chi-restraints excluded: chain H residue 577 LEU Chi-restraints excluded: chain H residue 627 HIS Chi-restraints excluded: chain H residue 638 MET Chi-restraints excluded: chain H residue 648 PHE Chi-restraints excluded: chain H residue 649 PHE Chi-restraints excluded: chain H residue 654 ASP Chi-restraints excluded: chain I residue 327 ILE Chi-restraints excluded: chain I residue 373 SER Chi-restraints excluded: chain I residue 387 LEU Chi-restraints excluded: chain I residue 410 PHE Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 421 VAL Chi-restraints excluded: chain I residue 479 GLU Chi-restraints excluded: chain I residue 480 LYS Chi-restraints excluded: chain I residue 489 ARG Chi-restraints excluded: chain I residue 586 GLU Chi-restraints excluded: chain I residue 631 ASP Chi-restraints excluded: chain I residue 647 ASP Chi-restraints excluded: chain I residue 654 ASP Chi-restraints excluded: chain J residue 327 ILE Chi-restraints excluded: chain J residue 331 LEU Chi-restraints excluded: chain J residue 376 ILE Chi-restraints excluded: chain J residue 405 VAL Chi-restraints excluded: chain J residue 421 VAL Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain J residue 428 ILE Chi-restraints excluded: chain J residue 464 SER Chi-restraints excluded: chain J residue 480 LYS Chi-restraints excluded: chain J residue 494 MET Chi-restraints excluded: chain J residue 528 ILE Chi-restraints excluded: chain J residue 533 GLN Chi-restraints excluded: chain J residue 640 GLU Chi-restraints excluded: chain J residue 648 PHE Chi-restraints excluded: chain J residue 649 PHE Chi-restraints excluded: chain K residue 357 LEU Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain K residue 427 ILE Chi-restraints excluded: chain K residue 480 LYS Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 514 GLN Chi-restraints excluded: chain K residue 528 ILE Chi-restraints excluded: chain K residue 573 SER Chi-restraints excluded: chain K residue 639 GLN Chi-restraints excluded: chain L residue 353 ILE Chi-restraints excluded: chain L residue 373 SER Chi-restraints excluded: chain L residue 387 LEU Chi-restraints excluded: chain L residue 407 GLU Chi-restraints excluded: chain L residue 408 LEU Chi-restraints excluded: chain L residue 426 ARG Chi-restraints excluded: chain L residue 427 ILE Chi-restraints excluded: chain L residue 428 ILE Chi-restraints excluded: chain L residue 469 LEU Chi-restraints excluded: chain L residue 480 LYS Chi-restraints excluded: chain L residue 562 ILE Chi-restraints excluded: chain L residue 565 ILE Chi-restraints excluded: chain L residue 585 PHE Chi-restraints excluded: chain L residue 638 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 123 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 58 optimal weight: 7.9990 chunk 232 optimal weight: 0.0170 chunk 301 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 313 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 HIS E 291 GLN ** F 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 533 GLN ** H 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 448 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 593 HIS ** I 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 593 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 330 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 = 0.4362 r_free = 0.4362 target = 0.154718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.122168 restraints weight = 74395.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.125524 restraints weight = 54966.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.128105 restraints weight = 43578.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.129983 restraints weight = 36294.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.131499 restraints weight = 31453.591| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30234 Z= 0.147 Angle : 0.852 16.193 41070 Z= 0.422 Chirality : 0.049 0.348 4548 Planarity : 0.005 0.058 5322 Dihedral : 5.570 59.765 4073 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.17 % Rotamer: Outliers : 4.83 % Allowed : 33.81 % Favored : 61.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.97 (0.14), residues: 3666 helix: -0.31 (0.14), residues: 1407 sheet: -0.36 (0.23), residues: 522 loop : -0.90 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG L 418 TYR 0.041 0.001 TYR L 548 PHE 0.025 0.002 PHE H 429 TRP 0.073 0.003 TRP J 375 HIS 0.022 0.001 HIS B 167 Details of bonding type rmsd covalent geometry : bond 0.00331 (30234) covalent geometry : angle 0.85152 (41070) hydrogen bonds : bond 0.04112 ( 1130) hydrogen bonds : angle 5.58606 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7802.89 seconds wall clock time: 134 minutes 24.83 seconds (8064.83 seconds total)