Starting phenix.real_space_refine on Fri Mar 6 11:21:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wmr_21851/03_2026/6wmr_21851.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wmr_21851/03_2026/6wmr_21851.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6wmr_21851/03_2026/6wmr_21851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wmr_21851/03_2026/6wmr_21851.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wmr_21851/03_2026/6wmr_21851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wmr_21851/03_2026/6wmr_21851.map" } resolution = 3.46 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= 0.006 sd= 1.641 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 81 5.49 5 Mg 1 5.21 5 S 119 5.16 5 C 18995 2.51 5 N 5281 2.21 5 O 5961 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 151 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30440 Number of models: 1 Model: "" Number of chains: 13 Chain: "G" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 720 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain: "H" Number of atoms: 487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 487 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "X" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "J" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "S" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1583 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 193} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "M" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1598 Classifications: {'peptide': 201} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 189} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "Z" Number of atoms: 3772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3772 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 456} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASN:plan1': 3, 'TYR:plan': 3, 'ARG:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 94 Chain: "A" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1688 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 215} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1769 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 225} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 8922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 8922 Classifications: {'peptide': 1186} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'PTRANS': 42, 'TRANS': 1143} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 458 Unresolved non-hydrogen dihedrals: 305 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 23, 'TYR:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 10, 'HIS:plan': 1, 'ARG:plan': 3, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 214 Chain: "D" Number of atoms: 8880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1159, 8880 Classifications: {'peptide': 1159} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 1117} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 207 Unresolved non-hydrogen angles: 253 Unresolved non-hydrogen dihedrals: 169 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 12, 'ASP:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 110 Chain: "E" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 567 Classifications: {'peptide': 72} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 71} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 21447 SG CYS D 68 54.808 112.593 78.930 1.00101.55 S ATOM 21461 SG CYS D 70 54.068 114.400 81.620 1.00105.52 S ATOM 21568 SG CYS D 83 53.837 116.395 78.229 1.00101.89 S ATOM 21594 SG CYS D 86 57.024 115.077 79.776 1.00105.62 S ATOM 27252 SG CYS D 811 91.678 91.212 24.655 1.00112.74 S ATOM 27789 SG CYS D 884 91.914 91.954 28.120 1.00102.18 S ATOM 27845 SG CYS D 891 90.163 88.539 26.607 1.00106.21 S ATOM 27865 SG CYS D 894 93.572 89.157 26.499 1.00 98.73 S Time building chain proxies: 5.92, per 1000 atoms: 0.19 Number of scatterers: 30440 At special positions: 0 Unit cell: (161.12, 185.5, 146.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 119 16.00 P 81 15.00 Mg 1 11.99 O 5961 8.00 N 5281 7.00 C 18995 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: 2.55 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 83 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 86 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 68 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 884 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 891 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 811 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 894 " Number of angles added : 12 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7034 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 35 sheets defined 43.6% alpha, 9.7% beta 25 base pairs and 58 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 38 through 46 removed outlier: 3.916A pdb=" N THR S 46 " --> pdb=" O ILE S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 66 through 75 removed outlier: 3.539A pdb=" N PHE S 75 " --> pdb=" O ILE S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 84 through 101 removed outlier: 3.686A pdb=" N ARG S 92 " --> pdb=" O ARG S 88 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU S 101 " --> pdb=" O LYS S 97 " (cutoff:3.500A) Processing helix chain 'S' and resid 102 through 112 removed outlier: 3.774A pdb=" N LEU S 106 " --> pdb=" O TRP S 102 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN S 108 " --> pdb=" O PRO S 104 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE S 109 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 115 through 135 removed outlier: 3.720A pdb=" N ASP S 125 " --> pdb=" O SER S 121 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS S 135 " --> pdb=" O LEU S 131 " (cutoff:3.500A) Processing helix chain 'S' and resid 149 through 164 removed outlier: 3.691A pdb=" N CYS S 153 " --> pdb=" O THR S 149 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA S 156 " --> pdb=" O ASP S 152 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA S 157 " --> pdb=" O CYS S 153 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU S 158 " --> pdb=" O TYR S 154 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU S 162 " --> pdb=" O LEU S 158 " (cutoff:3.500A) Processing helix chain 'S' and resid 182 through 186 removed outlier: 3.541A pdb=" N ALA S 185 " --> pdb=" O ARG S 182 " (cutoff:3.500A) Processing helix chain 'S' and resid 203 through 209 Processing helix chain 'M' and resid 9 through 23 removed outlier: 3.594A pdb=" N LYS M 22 " --> pdb=" O ILE M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 35 No H-bonds generated for 'chain 'M' and resid 33 through 35' Processing helix chain 'M' and resid 36 through 47 Processing helix chain 'M' and resid 64 through 76 removed outlier: 3.517A pdb=" N ILE M 68 " --> pdb=" O ARG M 64 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 111 removed outlier: 4.256A pdb=" N GLN M 105 " --> pdb=" O LYS M 101 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASN M 106 " --> pdb=" O THR M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 116 through 148 removed outlier: 3.673A pdb=" N ALA M 120 " --> pdb=" O ASP M 116 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE M 132 " --> pdb=" O GLN M 128 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N SER M 133 " --> pdb=" O ARG M 129 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER M 148 " --> pdb=" O VAL M 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 156 through 171 removed outlier: 3.829A pdb=" N LEU M 160 " --> pdb=" O ASN M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 192 Processing helix chain 'M' and resid 193 through 201 removed outlier: 3.729A pdb=" N LYS M 198 " --> pdb=" O PRO M 194 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N THR M 199 " --> pdb=" O ASN M 195 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE M 200 " --> pdb=" O PHE M 196 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS M 201 " --> pdb=" O ILE M 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 86 through 96 removed outlier: 3.930A pdb=" N MET Z 90 " --> pdb=" O ASP Z 86 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N GLU Z 94 " --> pdb=" O MET Z 90 " (cutoff:3.500A) Processing helix chain 'Z' and resid 102 through 125 Processing helix chain 'Z' and resid 128 through 150 removed outlier: 3.975A pdb=" N LYS Z 132 " --> pdb=" O PRO Z 128 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR Z 148 " --> pdb=" O LYS Z 144 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N MET Z 149 " --> pdb=" O ALA Z 145 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN Z 150 " --> pdb=" O ILE Z 146 " (cutoff:3.500A) Processing helix chain 'Z' and resid 194 through 213 Processing helix chain 'Z' and resid 216 through 229 removed outlier: 3.629A pdb=" N LEU Z 229 " --> pdb=" O GLU Z 225 " (cutoff:3.500A) Processing helix chain 'Z' and resid 233 through 262 Proline residue: Z 246 - end of helix Processing helix chain 'Z' and resid 271 through 276 removed outlier: 3.518A pdb=" N VAL Z 275 " --> pdb=" O GLU Z 271 " (cutoff:3.500A) Processing helix chain 'Z' and resid 285 through 290 Processing helix chain 'Z' and resid 294 through 316 Processing helix chain 'Z' and resid 318 through 321 Processing helix chain 'Z' and resid 322 through 345 Processing helix chain 'Z' and resid 347 through 355 removed outlier: 3.909A pdb=" N VAL Z 351 " --> pdb=" O ASN Z 347 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL Z 352 " --> pdb=" O LEU Z 348 " (cutoff:3.500A) Processing helix chain 'Z' and resid 364 through 381 removed outlier: 3.683A pdb=" N ILE Z 368 " --> pdb=" O HIS Z 364 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA Z 379 " --> pdb=" O GLY Z 375 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ASP Z 381 " --> pdb=" O MET Z 377 " (cutoff:3.500A) Processing helix chain 'Z' and resid 390 through 411 removed outlier: 3.554A pdb=" N TYR Z 394 " --> pdb=" O LYS Z 390 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR Z 396 " --> pdb=" O SER Z 392 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TRP Z 397 " --> pdb=" O THR Z 393 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP Z 398 " --> pdb=" O TYR Z 394 " (cutoff:3.500A) Processing helix chain 'Z' and resid 417 through 439 Processing helix chain 'Z' and resid 443 through 450 removed outlier: 3.598A pdb=" N HIS Z 450 " --> pdb=" O GLU Z 446 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 463 removed outlier: 3.704A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 483 through 487 Processing helix chain 'Z' and resid 502 through 507 Processing helix chain 'Z' and resid 508 through 513 Processing helix chain 'Z' and resid 514 through 516 No H-bonds generated for 'chain 'Z' and resid 514 through 516' Processing helix chain 'Z' and resid 519 through 530 Processing helix chain 'Z' and resid 538 through 546 removed outlier: 3.722A pdb=" N LYS Z 544 " --> pdb=" O GLU Z 540 " (cutoff:3.500A) Processing helix chain 'Z' and resid 551 through 565 removed outlier: 3.851A pdb=" N GLN Z 555 " --> pdb=" O GLU Z 551 " (cutoff:3.500A) Processing helix chain 'Z' and resid 572 through 577 removed outlier: 3.723A pdb=" N THR Z 575 " --> pdb=" O PHE Z 572 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU Z 577 " --> pdb=" O LYS Z 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 49 removed outlier: 3.825A pdb=" N ASN A 42 " --> pdb=" O HIS A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 88 removed outlier: 3.989A pdb=" N LYS A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 205 through 222 Processing helix chain 'B' and resid 32 through 48 removed outlier: 3.730A pdb=" N THR B 36 " --> pdb=" O GLY B 32 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 204 through 219 removed outlier: 3.597A pdb=" N ILE B 216 " --> pdb=" O ALA B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.904A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 58 removed outlier: 3.613A pdb=" N GLN C 58 " --> pdb=" O ILE C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 91 removed outlier: 3.500A pdb=" N GLN C 89 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 3.894A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 354 removed outlier: 4.052A pdb=" N LYS C 354 " --> pdb=" O SER C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 373 removed outlier: 3.569A pdb=" N ALA C 364 " --> pdb=" O ASN C 360 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 365 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS C 370 " --> pdb=" O VAL C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 391 removed outlier: 3.853A pdb=" N GLU C 388 " --> pdb=" O LYS C 384 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE C 391 " --> pdb=" O PHE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 412 removed outlier: 3.538A pdb=" N ARG C 410 " --> pdb=" O LYS C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 441 Processing helix chain 'C' and resid 450 through 452 No H-bonds generated for 'chain 'C' and resid 450 through 452' Processing helix chain 'C' and resid 458 through 479 removed outlier: 4.080A pdb=" N GLU C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 512 removed outlier: 3.849A pdb=" N THR C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ALA C 504 " --> pdb=" O PRO C 500 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N GLU C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.566A pdb=" N GLU C 526 " --> pdb=" O ASN C 522 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 527 " --> pdb=" O PRO C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 558 removed outlier: 3.995A pdb=" N TYR C 558 " --> pdb=" O ALA C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 616 Processing helix chain 'C' and resid 651 through 653 No H-bonds generated for 'chain 'C' and resid 651 through 653' Processing helix chain 'C' and resid 673 through 677 Processing helix chain 'C' and resid 679 through 689 removed outlier: 3.738A pdb=" N MET C 684 " --> pdb=" O ASN C 680 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN C 689 " --> pdb=" O GLY C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 712 removed outlier: 3.877A pdb=" N ALA C 712 " --> pdb=" O GLU C 708 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 715 No H-bonds generated for 'chain 'C' and resid 713 through 715' Processing helix chain 'C' and resid 741 through 744 Processing helix chain 'C' and resid 822 through 827 removed outlier: 3.599A pdb=" N LYS C 826 " --> pdb=" O GLU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 908 removed outlier: 3.562A pdb=" N PHE C 908 " --> pdb=" O LEU C 904 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 980 removed outlier: 4.230A pdb=" N ILE C 950 " --> pdb=" O ARG C 946 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASP C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 1030 through 1046 Processing helix chain 'C' and resid 1095 through 1099 removed outlier: 3.706A pdb=" N MET C1099 " --> pdb=" O VAL C1096 " (cutoff:3.500A) Processing helix chain 'C' and resid 1115 through 1120 removed outlier: 4.374A pdb=" N SER C1119 " --> pdb=" O LEU C1115 " (cutoff:3.500A) Processing helix chain 'C' and resid 1123 through 1147 removed outlier: 3.725A pdb=" N LEU C1127 " --> pdb=" O ILE C1123 " (cutoff:3.500A) Processing helix chain 'C' and resid 1152 through 1165 removed outlier: 3.693A pdb=" N SER C1165 " --> pdb=" O GLU C1161 " (cutoff:3.500A) Processing helix chain 'C' and resid 1172 through 1176 removed outlier: 3.506A pdb=" N ALA C1175 " --> pdb=" O ASN C1172 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU C1176 " --> pdb=" O LEU C1173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1172 through 1176' Processing helix chain 'C' and resid 1179 through 1188 removed outlier: 3.622A pdb=" N ASP C1186 " --> pdb=" O LEU C1182 " (cutoff:3.500A) Processing helix chain 'C' and resid 1203 through 1215 Processing helix chain 'C' and resid 1284 through 1293 removed outlier: 3.707A pdb=" N TRP C1288 " --> pdb=" O GLU C1284 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA C1289 " --> pdb=" O MET C1285 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C1290 " --> pdb=" O GLU C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1295 through 1301 Processing helix chain 'C' and resid 1309 through 1323 removed outlier: 3.820A pdb=" N SER C1314 " --> pdb=" O ILE C1310 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL C1321 " --> pdb=" O TYR C1317 " (cutoff:3.500A) Processing helix chain 'C' and resid 1333 through 1344 Processing helix chain 'D' and resid 24 through 32 removed outlier: 3.519A pdb=" N SER D 32 " --> pdb=" O ILE D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 96 Processing helix chain 'D' and resid 120 through 127 Processing helix chain 'D' and resid 129 through 138 removed outlier: 3.515A pdb=" N VAL D 136 " --> pdb=" O ASN D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 Processing helix chain 'D' and resid 179 through 189 removed outlier: 3.540A pdb=" N ILE D 183 " --> pdb=" O GLY D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.567A pdb=" N GLU D 202 " --> pdb=" O LEU D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 229 removed outlier: 3.929A pdb=" N LEU D 219 " --> pdb=" O ALA D 215 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG D 220 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY D 229 " --> pdb=" O PHE D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 234 Processing helix chain 'D' and resid 244 through 248 Processing helix chain 'D' and resid 261 through 284 removed outlier: 3.856A pdb=" N ASP D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU D 266 " --> pdb=" O ASP D 262 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASN D 272 " --> pdb=" O ARG D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 307 removed outlier: 3.709A pdb=" N GLN D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 329 Processing helix chain 'D' and resid 335 through 340 removed outlier: 3.659A pdb=" N ASN D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 375 Processing helix chain 'D' and resid 375 through 387 Processing helix chain 'D' and resid 391 through 400 removed outlier: 3.917A pdb=" N ALA D 395 " --> pdb=" O THR D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 414 removed outlier: 4.021A pdb=" N TRP D 407 " --> pdb=" O GLU D 403 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP D 408 " --> pdb=" O ALA D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 430 No H-bonds generated for 'chain 'D' and resid 428 through 430' Processing helix chain 'D' and resid 448 through 452 Processing helix chain 'D' and resid 473 through 482 removed outlier: 4.183A pdb=" N ARG D 479 " --> pdb=" O GLN D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 487 Processing helix chain 'D' and resid 503 through 512 removed outlier: 3.722A pdb=" N LEU D 508 " --> pdb=" O ILE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 537 Processing helix chain 'D' and resid 572 through 577 removed outlier: 3.591A pdb=" N LEU D 576 " --> pdb=" O VAL D 572 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 572 through 577' Processing helix chain 'D' and resid 586 through 590 Processing helix chain 'D' and resid 595 through 611 removed outlier: 3.635A pdb=" N LYS D 601 " --> pdb=" O LYS D 597 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 611 " --> pdb=" O PHE D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 630 removed outlier: 3.696A pdb=" N LYS D 628 " --> pdb=" O TYR D 624 " (cutoff:3.500A) Processing helix chain 'D' and resid 647 through 668 removed outlier: 3.822A pdb=" N ALA D 655 " --> pdb=" O LYS D 651 " (cutoff:3.500A) Processing helix chain 'D' and resid 673 through 700 removed outlier: 3.737A pdb=" N MET D 695 " --> pdb=" O VAL D 691 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET D 696 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASP D 697 " --> pdb=" O ALA D 693 " (cutoff:3.500A) Processing helix chain 'D' and resid 717 through 725 removed outlier: 3.847A pdb=" N ALA D 723 " --> pdb=" O VAL D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 739 removed outlier: 3.513A pdb=" N MET D 734 " --> pdb=" O SER D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 785 removed outlier: 3.568A pdb=" N SER D 772 " --> pdb=" O GLN D 768 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS D 774 " --> pdb=" O PHE D 770 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLY D 775 " --> pdb=" O THR D 771 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N THR D 783 " --> pdb=" O GLY D 779 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA D 784 " --> pdb=" O LEU D 780 " (cutoff:3.500A) Processing helix chain 'D' and resid 788 through 802 Processing helix chain 'D' and resid 831 through 836 Processing helix chain 'D' and resid 865 through 870 removed outlier: 4.464A pdb=" N ASP D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 880 through 884 Processing helix chain 'D' and resid 910 through 918 removed outlier: 3.647A pdb=" N ILE D 914 " --> pdb=" O SER D 910 " (cutoff:3.500A) Processing helix chain 'D' and resid 921 through 925 Processing helix chain 'D' and resid 1125 through 1133 Processing helix chain 'D' and resid 1207 through 1212 Processing helix chain 'D' and resid 1212 through 1231 removed outlier: 4.435A pdb=" N GLU D1216 " --> pdb=" O LYS D1212 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N PHE D1217 " --> pdb=" O GLY D1213 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER D1227 " --> pdb=" O ILE D1223 " (cutoff:3.500A) Processing helix chain 'D' and resid 1237 through 1246 removed outlier: 3.970A pdb=" N ILE D1241 " --> pdb=" O ASN D1237 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D1243 " --> pdb=" O LYS D1239 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE D1244 " --> pdb=" O HIS D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1247 through 1249 No H-bonds generated for 'chain 'D' and resid 1247 through 1249' Processing helix chain 'D' and resid 1268 through 1282 removed outlier: 3.943A pdb=" N GLU D1276 " --> pdb=" O ARG D1272 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU D1280 " --> pdb=" O GLU D1276 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG D1281 " --> pdb=" O ASN D1277 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D1282 " --> pdb=" O ASP D1278 " (cutoff:3.500A) Processing helix chain 'D' and resid 1296 through 1303 Processing helix chain 'D' and resid 1306 through 1314 removed outlier: 3.659A pdb=" N GLN D1314 " --> pdb=" O ALA D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1315 through 1326 removed outlier: 4.053A pdb=" N ILE D1325 " --> pdb=" O THR D1321 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN D1326 " --> pdb=" O GLU D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1357 removed outlier: 3.637A pdb=" N ALA D1352 " --> pdb=" O GLY D1348 " (cutoff:3.500A) Processing helix chain 'D' and resid 1357 through 1365 removed outlier: 3.627A pdb=" N GLU D1361 " --> pdb=" O SER D1357 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS D1362 " --> pdb=" O ALA D1358 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET D1363 " --> pdb=" O LYS D1359 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 10 Processing helix chain 'E' and resid 17 through 33 Processing helix chain 'E' and resid 46 through 57 removed outlier: 4.196A pdb=" N LEU E 52 " --> pdb=" O THR E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 67 removed outlier: 4.180A pdb=" N ARG E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 5 through 8 Processing sheet with id=AA2, first strand: chain 'M' and resid 27 through 29 removed outlier: 6.249A pdb=" N LEU M 3 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR M 54 " --> pdb=" O TYR M 4 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Z' and resid 470 through 471 removed outlier: 6.955A pdb=" N ILE Z 470 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 14 through 15 Processing sheet with id=AA5, first strand: chain 'A' and resid 99 through 106 removed outlier: 7.302A pdb=" N SER A 142 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE A 62 " --> pdb=" O SER A 142 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR A 144 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 60 " --> pdb=" O THR A 144 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR A 146 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 111 through 113 Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 18 removed outlier: 3.589A pdb=" N TYR B 17 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ALA B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP B 191 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU B 190 " --> pdb=" O ALA B 182 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA B 182 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 98 through 101 removed outlier: 6.784A pdb=" N GLU B 142 " --> pdb=" O ILE B 57 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE B 57 " --> pdb=" O GLU B 142 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LYS B 144 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 112 removed outlier: 7.062A pdb=" N ILE B 111 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 7.202A pdb=" N LYS C 13 " --> pdb=" O ALA C1195 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 78 removed outlier: 6.117A pdb=" N TYR C 73 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG C 104 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP C 75 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY C 130 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL C 101 " --> pdb=" O TYR C 128 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N TYR C 128 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU C 103 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR C 126 " --> pdb=" O LEU C 103 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AB4, first strand: chain 'C' and resid 454 through 457 Processing sheet with id=AB5, first strand: chain 'C' and resid 175 through 176 removed outlier: 3.826A pdb=" N ILE C 176 " --> pdb=" O LEU C 184 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 185 " --> pdb=" O ARG C 197 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG C 197 " --> pdb=" O ASP C 185 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 601 through 609 removed outlier: 5.502A pdb=" N LYS C 596 " --> pdb=" O THR C 603 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLU C 605 " --> pdb=" O TYR C 594 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N TYR C 594 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLU C 607 " --> pdb=" O ALA C 592 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA C 592 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 636 through 640 Processing sheet with id=AB8, first strand: chain 'C' and resid 751 through 754 removed outlier: 7.084A pdb=" N ARG C 734 " --> pdb=" O VAL C 730 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N VAL C 730 " --> pdb=" O ARG C 734 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C 736 " --> pdb=" O ALA C 728 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY C 725 " --> pdb=" O VAL C 779 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 791 through 792 Processing sheet with id=AC1, first strand: chain 'C' and resid 1110 through 1112 removed outlier: 3.660A pdb=" N LEU C1112 " --> pdb=" O ALA C 805 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 806 " --> pdb=" O THR C1238 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR C1238 " --> pdb=" O PHE C 806 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 818 through 820 removed outlier: 7.208A pdb=" N ILE C 818 " --> pdb=" O SER C1091 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL C1093 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU C 820 " --> pdb=" O VAL C1093 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 848 through 849 removed outlier: 3.697A pdb=" N LYS C1062 " --> pdb=" O ALA C 842 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ASP C 844 " --> pdb=" O VAL C1060 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL C1060 " --> pdb=" O ASP C 844 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN C 932 " --> pdb=" O PHE C1067 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C1069 " --> pdb=" O VAL C 930 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N VAL C 930 " --> pdb=" O ALA C1069 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 884 through 886 removed outlier: 6.633A pdb=" N LEU C 920 " --> pdb=" O LEU C 885 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 890 through 891 Processing sheet with id=AC6, first strand: chain 'C' and resid 1101 through 1102 Processing sheet with id=AC7, first strand: chain 'C' and resid 1257 through 1258 removed outlier: 6.110A pdb=" N CYS D 364 " --> pdb=" O ARG D 438 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE D 440 " --> pdb=" O CYS D 364 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU D 366 " --> pdb=" O ILE D 440 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 1257 through 1258 Processing sheet with id=AC9, first strand: chain 'C' and resid 1350 through 1352 removed outlier: 3.534A pdb=" N LYS D 19 " --> pdb=" O ASP C1350 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 17 " --> pdb=" O ASP C1352 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE D 18 " --> pdb=" O ASP D1330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 103 through 110 removed outlier: 11.013A pdb=" N CYS D 107 " --> pdb=" O VAL D 239 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N VAL D 239 " --> pdb=" O CYS D 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 142 through 143 Processing sheet with id=AD3, first strand: chain 'D' and resid 524 through 525 Processing sheet with id=AD4, first strand: chain 'D' and resid 701 through 706 Processing sheet with id=AD5, first strand: chain 'D' and resid 806 through 808 Processing sheet with id=AD6, first strand: chain 'D' and resid 817 through 819 removed outlier: 3.506A pdb=" N ILE D 876 " --> pdb=" O PHE D 819 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 845 through 846 removed outlier: 6.722A pdb=" N VAL D 845 " --> pdb=" O LEU D 853 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 1265 through 1267 removed outlier: 4.799A pdb=" N LYS D1251 " --> pdb=" O VAL D1293 " (cutoff:3.500A) 1134 hydrogen bonds defined for protein. 3210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 25 basepair parallelities 58 stacking parallelities Total time for adding SS restraints: 6.64 Time building geometry restraints manager: 3.30 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: 8531 1.33 - 1.45: 5074 1.45 - 1.57: 17077 1.57 - 1.69: 158 1.69 - 1.81: 206 Bond restraints: 31046 Sorted by residual: bond pdb=" CA GLN D 736 " pdb=" C GLN D 736 " ideal model delta sigma weight residual 1.522 1.468 0.055 1.38e-02 5.25e+03 1.56e+01 bond pdb=" C VAL M 84 " pdb=" N PHE M 85 " ideal model delta sigma weight residual 1.332 1.285 0.047 1.44e-02 4.82e+03 1.08e+01 bond pdb=" CA ALA C1344 " pdb=" C ALA C1344 " ideal model delta sigma weight residual 1.523 1.469 0.054 1.80e-02 3.09e+03 9.14e+00 bond pdb=" CA ASN D1326 " pdb=" C ASN D1326 " ideal model delta sigma weight residual 1.523 1.472 0.051 1.80e-02 3.09e+03 8.10e+00 bond pdb=" C ARG C1073 " pdb=" N ILE C1074 " ideal model delta sigma weight residual 1.334 1.303 0.031 1.29e-02 6.01e+03 5.69e+00 ... (remaining 31041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 41011 2.00 - 3.99: 1125 3.99 - 5.99: 117 5.99 - 7.98: 21 7.98 - 9.98: 3 Bond angle restraints: 42277 Sorted by residual: angle pdb=" N VAL E 49 " pdb=" CA VAL E 49 " pdb=" C VAL E 49 " ideal model delta sigma weight residual 112.96 108.35 4.61 1.00e+00 1.00e+00 2.12e+01 angle pdb=" N GLU Z 271 " pdb=" CA GLU Z 271 " pdb=" C GLU Z 271 " ideal model delta sigma weight residual 112.57 107.61 4.96 1.13e+00 7.83e-01 1.92e+01 angle pdb=" C PRO S 52 " pdb=" N VAL S 53 " pdb=" CA VAL S 53 " ideal model delta sigma weight residual 121.97 115.32 6.65 1.80e+00 3.09e-01 1.37e+01 angle pdb=" C VAL M 84 " pdb=" N PHE M 85 " pdb=" CA PHE M 85 " ideal model delta sigma weight residual 122.28 116.16 6.12 1.77e+00 3.19e-01 1.19e+01 angle pdb=" C ILE C 198 " pdb=" N ASP C 199 " pdb=" CA ASP C 199 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 ... (remaining 42272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.20: 15868 18.20 - 36.40: 2164 36.40 - 54.60: 645 54.60 - 72.79: 148 72.79 - 90.99: 43 Dihedral angle restraints: 18868 sinusoidal: 7999 harmonic: 10869 Sorted by residual: dihedral pdb=" CA LYS Z 213 " pdb=" C LYS Z 213 " pdb=" N PRO Z 214 " pdb=" CA PRO Z 214 " ideal model delta harmonic sigma weight residual -180.00 -148.56 -31.44 0 5.00e+00 4.00e-02 3.95e+01 dihedral pdb=" CA GLN D1283 " pdb=" C GLN D1283 " pdb=" N GLY D1284 " pdb=" CA GLY D1284 " ideal model delta harmonic sigma weight residual 180.00 152.13 27.87 0 5.00e+00 4.00e-02 3.11e+01 dihedral pdb=" CA THR D 354 " pdb=" C THR D 354 " pdb=" N VAL D 355 " pdb=" CA VAL D 355 " ideal model delta harmonic sigma weight residual -180.00 -152.66 -27.34 0 5.00e+00 4.00e-02 2.99e+01 ... (remaining 18865 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 3210 0.042 - 0.084: 1351 0.084 - 0.126: 333 0.126 - 0.168: 29 0.168 - 0.210: 4 Chirality restraints: 4927 Sorted by residual: chirality pdb=" CA TYR C 812 " pdb=" N TYR C 812 " pdb=" C TYR C 812 " pdb=" CB TYR C 812 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA PRO C 523 " pdb=" N PRO C 523 " pdb=" C PRO C 523 " pdb=" CB PRO C 523 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA PHE C 60 " pdb=" N PHE C 60 " pdb=" C PHE C 60 " pdb=" CB PHE C 60 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.49e-01 ... (remaining 4924 not shown) Planarity restraints: 5167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR Z 267 " 0.043 5.00e-02 4.00e+02 6.52e-02 6.80e+00 pdb=" N PRO Z 268 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO Z 268 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO Z 268 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 159 " 0.039 5.00e-02 4.00e+02 5.88e-02 5.54e+00 pdb=" N PRO A 160 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 160 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 160 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS Z 566 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.16e+00 pdb=" N PRO Z 567 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO Z 567 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO Z 567 " 0.031 5.00e-02 4.00e+02 ... (remaining 5164 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 662 2.61 - 3.18: 29279 3.18 - 3.76: 45709 3.76 - 4.33: 62370 4.33 - 4.90: 98810 Nonbonded interactions: 236830 Sorted by model distance: nonbonded pdb=" O ILE Z 447 " pdb=" OG1 THR Z 451 " model vdw 2.040 3.040 nonbonded pdb=" O GLU C1161 " pdb=" OG SER C1165 " model vdw 2.058 3.040 nonbonded pdb=" O ASP C 519 " pdb=" OG SER C 525 " model vdw 2.080 3.040 nonbonded pdb=" OD2 ASP M 13 " pdb=" OH TYR M 168 " model vdw 2.110 3.040 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1501 " model vdw 2.112 2.170 ... (remaining 236825 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 32.460 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 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 : 0.008 0.123 31054 Z= 0.372 Angle : 0.817 28.366 42289 Z= 0.444 Chirality : 0.046 0.210 4927 Planarity : 0.004 0.065 5167 Dihedral : 18.640 90.994 11834 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 14.67 % Favored : 85.20 % Rotamer: Outliers : 9.74 % Allowed : 22.41 % Favored : 67.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.79 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.89 (0.11), residues: 3715 helix: -2.62 (0.11), residues: 1442 sheet: -3.36 (0.22), residues: 367 loop : -3.83 (0.12), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 457 TYR 0.019 0.002 TYR C 35 PHE 0.020 0.002 PHE A 183 TRP 0.022 0.002 TRP C 183 HIS 0.008 0.001 HIS Z 566 Details of bonding type rmsd covalent geometry : bond 0.00821 (31046) covalent geometry : angle 0.78716 (42277) hydrogen bonds : bond 0.17827 ( 1194) hydrogen bonds : angle 7.53225 ( 3334) metal coordination : bond 0.08108 ( 8) metal coordination : angle 13.08250 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 907 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 296 poor density : 611 time to evaluate : 1.085 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: S 44 LYS cc_start: 0.7048 (OUTLIER) cc_final: 0.6741 (mmtt) REVERT: S 54 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6251 (tp) REVERT: S 90 LYS cc_start: 0.8212 (mttp) cc_final: 0.7852 (ptpt) REVERT: S 110 ARG cc_start: 0.7591 (ttm110) cc_final: 0.7003 (tpm170) REVERT: S 133 MET cc_start: 0.8912 (mmm) cc_final: 0.8651 (mmt) REVERT: S 154 TYR cc_start: 0.8027 (OUTLIER) cc_final: 0.7296 (m-10) REVERT: M 76 TYR cc_start: 0.8695 (m-80) cc_final: 0.8487 (m-80) REVERT: M 153 GLN cc_start: 0.7809 (pp30) cc_final: 0.7355 (pp30) REVERT: Z 124 ILE cc_start: 0.9030 (mm) cc_final: 0.8821 (mm) REVERT: Z 127 TYR cc_start: 0.7214 (m-80) cc_final: 0.6793 (m-80) REVERT: Z 149 MET cc_start: 0.3731 (ttt) cc_final: 0.3302 (tpp) REVERT: Z 230 ARG cc_start: 0.7394 (tmt-80) cc_final: 0.5571 (mtt90) REVERT: Z 315 MET cc_start: 0.9081 (tpp) cc_final: 0.8578 (tpp) REVERT: Z 343 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8511 (ttt) REVERT: Z 366 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8097 (mp) REVERT: Z 458 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (ttmm) REVERT: Z 467 HIS cc_start: 0.6387 (t-170) cc_final: 0.5402 (t-90) REVERT: Z 472 MET cc_start: 0.8098 (ptp) cc_final: 0.7883 (ptt) REVERT: Z 521 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7181 (mt-10) REVERT: Z 523 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8245 (mttt) REVERT: Z 541 GLU cc_start: 0.8397 (tp30) cc_final: 0.7907 (tp30) REVERT: Z 569 ARG cc_start: 0.8272 (mpp80) cc_final: 0.7875 (mpt-90) REVERT: A 121 GLN cc_start: 0.5629 (OUTLIER) cc_final: 0.5237 (pp30) REVERT: A 128 LYS cc_start: 0.8615 (mmtt) cc_final: 0.8374 (mtmm) REVERT: B 31 ARG cc_start: 0.8432 (ttp-170) cc_final: 0.8173 (ttp80) REVERT: B 75 GLU cc_start: 0.8333 (mp0) cc_final: 0.8129 (mp0) REVERT: B 133 TYR cc_start: 0.7489 (t80) cc_final: 0.6462 (t80) REVERT: B 206 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8811 (tm-30) REVERT: B 221 ARG cc_start: 0.8838 (ttm170) cc_final: 0.8343 (ptt180) REVERT: C 185 ASP cc_start: 0.6280 (p0) cc_final: 0.6066 (p0) REVERT: C 405 MET cc_start: 0.7937 (ttp) cc_final: 0.7698 (ptp) REVERT: C 634 GLU cc_start: 0.8031 (tp30) cc_final: 0.7544 (tp30) REVERT: C 697 LYS cc_start: 0.9105 (tttm) cc_final: 0.8817 (ptpt) REVERT: C 738 LYS cc_start: 0.8560 (pttp) cc_final: 0.8308 (ptmm) REVERT: C 815 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7681 (tp30) REVERT: C 852 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8728 (mt) REVERT: C 1256 HIS cc_start: 0.7853 (t70) cc_final: 0.7630 (t70) REVERT: C 1271 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7245 (mt) REVERT: C 1286 GLU cc_start: 0.8298 (mp0) cc_final: 0.7914 (mp0) REVERT: C 1351 PHE cc_start: 0.8081 (m-80) cc_final: 0.7668 (m-80) REVERT: D 48 LYS cc_start: 0.8805 (mtpt) cc_final: 0.8309 (mptt) REVERT: D 76 LEU cc_start: 0.8779 (mp) cc_final: 0.8567 (mp) REVERT: D 135 LYS cc_start: 0.8720 (mttt) cc_final: 0.8474 (mtpt) REVERT: D 279 LYS cc_start: 0.8197 (tttt) cc_final: 0.7865 (mmtt) REVERT: D 328 MET cc_start: 0.8774 (mtm) cc_final: 0.8491 (mtp) REVERT: D 556 ASP cc_start: 0.7203 (m-30) cc_final: 0.6368 (m-30) REVERT: D 562 TYR cc_start: 0.7396 (p90) cc_final: 0.6597 (p90) REVERT: D 571 THR cc_start: 0.9419 (m) cc_final: 0.9178 (p) REVERT: D 849 LYS cc_start: 0.7248 (mttt) cc_final: 0.6887 (tmtt) REVERT: D 899 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8036 (tt) REVERT: D 1230 ARG cc_start: 0.8435 (mmt90) cc_final: 0.8023 (mmm160) REVERT: D 1269 GLU cc_start: 0.7650 (tp30) cc_final: 0.7340 (tm-30) REVERT: D 1279 LYS cc_start: 0.8189 (tptm) cc_final: 0.7672 (tptp) REVERT: E 26 ARG cc_start: 0.8682 (tpt170) cc_final: 0.8199 (tpp80) outliers start: 296 outliers final: 200 residues processed: 853 average time/residue: 0.1837 time to fit residues: 250.1398 Evaluate side-chains 707 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 497 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 44 LYS Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 125 ASP Chi-restraints excluded: chain S residue 149 THR Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 155 ILE Chi-restraints excluded: chain S residue 191 LYS Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 74 ASP Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 84 VAL Chi-restraints excluded: chain M residue 106 ASN Chi-restraints excluded: chain M residue 108 ILE Chi-restraints excluded: chain M residue 112 SER Chi-restraints excluded: chain M residue 154 ASN Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 166 PHE Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 120 VAL Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 265 SER Chi-restraints excluded: chain Z residue 271 GLU Chi-restraints excluded: chain Z residue 275 VAL Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 297 THR Chi-restraints excluded: chain Z residue 305 THR Chi-restraints excluded: chain Z residue 343 MET Chi-restraints excluded: chain Z residue 344 ILE Chi-restraints excluded: chain Z residue 358 TYR Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 389 PHE Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 423 THR Chi-restraints excluded: chain Z residue 427 VAL Chi-restraints excluded: chain Z residue 453 ASN Chi-restraints excluded: chain Z residue 458 LYS Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 534 ASN Chi-restraints excluded: chain Z residue 542 VAL Chi-restraints excluded: chain Z residue 549 THR Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 70 SER Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 121 GLN Chi-restraints excluded: chain A residue 146 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 49 ILE Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 61 ASP Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 156 ASP Chi-restraints excluded: chain B residue 157 ASN Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 426 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 495 ILE Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 515 SER Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 556 THR Chi-restraints excluded: chain C residue 576 ASN Chi-restraints excluded: chain C residue 580 SER Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 613 ASP Chi-restraints excluded: chain C residue 626 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 652 ARG Chi-restraints excluded: chain C residue 698 SER Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 744 SER Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 754 SER Chi-restraints excluded: chain C residue 756 THR Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 839 THR Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 867 LEU Chi-restraints excluded: chain C residue 870 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 889 ILE Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1091 SER Chi-restraints excluded: chain C residue 1098 ASP Chi-restraints excluded: chain C residue 1119 SER Chi-restraints excluded: chain C residue 1123 ILE Chi-restraints excluded: chain C residue 1145 THR Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1168 ASP Chi-restraints excluded: chain C residue 1206 ASP Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1350 ASP Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 112 ILE Chi-restraints excluded: chain D residue 117 SER Chi-restraints excluded: chain D residue 130 LEU Chi-restraints excluded: chain D residue 136 VAL Chi-restraints excluded: chain D residue 159 THR Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 272 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 290 VAL Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 388 HIS Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 463 GLN Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 530 ASP Chi-restraints excluded: chain D residue 540 ILE Chi-restraints excluded: chain D residue 567 VAL Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 652 ILE Chi-restraints excluded: chain D residue 674 ASN Chi-restraints excluded: chain D residue 680 ILE Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 750 THR Chi-restraints excluded: chain D residue 773 THR Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 871 ASN Chi-restraints excluded: chain D residue 891 CYS Chi-restraints excluded: chain D residue 899 LEU Chi-restraints excluded: chain D residue 1128 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1228 VAL Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 35 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 100 ASN S 112 HIS M 88 GLN M 111 GLN M 128 GLN M 154 ASN Z 347 ASN ** Z 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 453 ASN Z 464 ASN B 204 ASN B 230 ASN C 31 GLN C 66 ASN C 144 ASN C 631 HIS C 717 ASN C1122 ASN C1130 HIS C1172 ASN C1268 GLN ** C1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1336 ASN D 102 HIS ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 362 HIS D 417 HIS D 428 HIS D 433 GLN D 475 GLN D 487 ASN D 774 HIS D1206 HIS D1277 ASN D1331 ASN E 68 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.148450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.111032 restraints weight = 55593.434| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.86 r_work: 0.3250 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31054 Z= 0.136 Angle : 0.655 9.650 42289 Z= 0.349 Chirality : 0.044 0.175 4927 Planarity : 0.005 0.080 5167 Dihedral : 15.969 88.737 5272 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.64 % Favored : 90.36 % Rotamer: Outliers : 4.87 % Allowed : 26.13 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.13), residues: 3715 helix: -0.94 (0.13), residues: 1449 sheet: -2.64 (0.23), residues: 391 loop : -3.11 (0.13), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 359 TYR 0.031 0.002 TYR M 168 PHE 0.028 0.001 PHE D 607 TRP 0.013 0.001 TRP C 183 HIS 0.006 0.001 HIS Z 235 Details of bonding type rmsd covalent geometry : bond 0.00294 (31046) covalent geometry : angle 0.65151 (42277) hydrogen bonds : bond 0.04599 ( 1194) hydrogen bonds : angle 5.21944 ( 3334) metal coordination : bond 0.00586 ( 8) metal coordination : angle 4.03945 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 607 time to evaluate : 0.939 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: S 88 ARG cc_start: 0.7804 (ttm170) cc_final: 0.7416 (mtm-85) REVERT: S 90 LYS cc_start: 0.8350 (mttp) cc_final: 0.8010 (ttmm) REVERT: S 133 MET cc_start: 0.8937 (mmm) cc_final: 0.8634 (mmt) REVERT: S 154 TYR cc_start: 0.7744 (OUTLIER) cc_final: 0.7388 (m-10) REVERT: S 207 ARG cc_start: 0.7219 (mpt-90) cc_final: 0.5737 (ptt-90) REVERT: M 13 ASP cc_start: 0.7956 (m-30) cc_final: 0.7637 (m-30) REVERT: M 81 MET cc_start: 0.8536 (mmt) cc_final: 0.8218 (mmt) REVERT: M 103 PHE cc_start: 0.8266 (m-80) cc_final: 0.8017 (m-80) REVERT: M 121 ASN cc_start: 0.6533 (m-40) cc_final: 0.5861 (m110) REVERT: M 153 GLN cc_start: 0.7940 (pp30) cc_final: 0.7507 (pp30) REVERT: M 168 TYR cc_start: 0.7437 (m-80) cc_final: 0.7140 (m-80) REVERT: M 169 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7901 (t80) REVERT: M 193 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7199 (tm-30) REVERT: Z 149 MET cc_start: 0.3889 (ttt) cc_final: 0.3556 (mmp) REVERT: Z 230 ARG cc_start: 0.7425 (tmt-80) cc_final: 0.5535 (mtt90) REVERT: Z 283 TRP cc_start: 0.5996 (OUTLIER) cc_final: 0.4278 (t60) REVERT: Z 295 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5802 (pp20) REVERT: Z 315 MET cc_start: 0.8757 (tpp) cc_final: 0.8311 (tpp) REVERT: Z 457 GLU cc_start: 0.9003 (tt0) cc_final: 0.8505 (tp30) REVERT: Z 472 MET cc_start: 0.8268 (ptp) cc_final: 0.7939 (ptt) REVERT: Z 476 ILE cc_start: 0.5844 (OUTLIER) cc_final: 0.5389 (pt) REVERT: Z 521 GLU cc_start: 0.7486 (mt-10) cc_final: 0.7122 (mt-10) REVERT: Z 541 GLU cc_start: 0.8446 (tp30) cc_final: 0.8040 (tp30) REVERT: Z 569 ARG cc_start: 0.8226 (mpp80) cc_final: 0.7791 (mtt90) REVERT: A 128 LYS cc_start: 0.8896 (mmtt) cc_final: 0.8618 (mtmm) REVERT: B 133 TYR cc_start: 0.7424 (t80) cc_final: 0.6587 (t80) REVERT: B 221 ARG cc_start: 0.8944 (ttm170) cc_final: 0.8708 (mtm110) REVERT: C 405 MET cc_start: 0.7933 (ttp) cc_final: 0.7722 (ptp) REVERT: C 434 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8885 (mm-30) REVERT: C 442 LYS cc_start: 0.7293 (mppt) cc_final: 0.5986 (tptp) REVERT: C 457 ARG cc_start: 0.8617 (ttp-170) cc_final: 0.7844 (ttm110) REVERT: C 475 GLU cc_start: 0.8843 (pp20) cc_final: 0.8415 (tp30) REVERT: C 556 THR cc_start: 0.9371 (p) cc_final: 0.9127 (p) REVERT: C 634 GLU cc_start: 0.8148 (tp30) cc_final: 0.7698 (tp30) REVERT: C 697 LYS cc_start: 0.9203 (tttm) cc_final: 0.8813 (ptpt) REVERT: C 720 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8200 (pt) REVERT: C 852 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8616 (mt) REVERT: C 1256 HIS cc_start: 0.7745 (t70) cc_final: 0.7363 (t70) REVERT: C 1286 GLU cc_start: 0.8635 (mp0) cc_final: 0.8357 (mp0) REVERT: C 1351 PHE cc_start: 0.8090 (m-80) cc_final: 0.7580 (m-80) REVERT: D 48 LYS cc_start: 0.8996 (mtpt) cc_final: 0.8562 (mptt) REVERT: D 76 LEU cc_start: 0.8786 (mp) cc_final: 0.8573 (mp) REVERT: D 100 MET cc_start: 0.7655 (mtt) cc_final: 0.7371 (mtt) REVERT: D 135 LYS cc_start: 0.8872 (mttt) cc_final: 0.8562 (mtpt) REVERT: D 163 TYR cc_start: 0.7711 (OUTLIER) cc_final: 0.7374 (t80) REVERT: D 165 GLU cc_start: 0.7957 (mm-30) cc_final: 0.7210 (mm-30) REVERT: D 195 GLU cc_start: 0.8338 (tp30) cc_final: 0.7935 (tp30) REVERT: D 257 ARG cc_start: 0.7434 (mmt180) cc_final: 0.6941 (mmm160) REVERT: D 279 LYS cc_start: 0.8501 (tttt) cc_final: 0.8037 (mmtt) REVERT: D 327 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8230 (t0) REVERT: D 403 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7109 (mt-10) REVERT: D 512 THR cc_start: 0.8927 (p) cc_final: 0.8653 (p) REVERT: D 734 MET cc_start: 0.8829 (mtp) cc_final: 0.8612 (mtm) REVERT: D 746 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7866 (pttt) REVERT: D 786 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8168 (tmmt) REVERT: D 796 ARG cc_start: 0.8860 (mtm-85) cc_final: 0.8303 (mtm-85) REVERT: D 849 LYS cc_start: 0.7243 (mttt) cc_final: 0.6824 (tmtt) REVERT: D 875 MET cc_start: 0.8098 (ttp) cc_final: 0.7819 (tmm) REVERT: D 1132 PHE cc_start: 0.8722 (m-80) cc_final: 0.8344 (m-80) REVERT: D 1230 ARG cc_start: 0.8468 (mmt90) cc_final: 0.7971 (mmm160) REVERT: D 1269 GLU cc_start: 0.7863 (tp30) cc_final: 0.7482 (tm-30) REVERT: D 1279 LYS cc_start: 0.8211 (tptm) cc_final: 0.7759 (tptp) REVERT: E 26 ARG cc_start: 0.8838 (tpt170) cc_final: 0.8418 (tpp-160) REVERT: E 35 TYR cc_start: 0.4262 (OUTLIER) cc_final: 0.2852 (p90) outliers start: 148 outliers final: 89 residues processed: 720 average time/residue: 0.1798 time to fit residues: 206.9423 Evaluate side-chains 616 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 516 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 100 ASN Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 99 VAL Chi-restraints excluded: chain M residue 147 GLU Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 170 ILE Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 283 TRP Chi-restraints excluded: chain Z residue 295 GLU Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 453 ASN Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 518 THR Chi-restraints excluded: chain Z residue 542 VAL Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 93 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 436 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 680 ASN Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1229 THR Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 451 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 35 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 59 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 234 optimal weight: 1.9990 chunk 296 optimal weight: 0.0970 chunk 157 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 166 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 63 ASN ** M 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 ASN ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1206 HIS E 68 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.149284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112185 restraints weight = 56173.277| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.13 r_work: 0.3245 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31054 Z= 0.127 Angle : 0.617 10.746 42289 Z= 0.328 Chirality : 0.043 0.234 4927 Planarity : 0.004 0.070 5167 Dihedral : 15.470 87.020 5031 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.96 % Favored : 91.01 % Rotamer: Outliers : 5.10 % Allowed : 27.11 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.63 (0.13), residues: 3715 helix: -0.35 (0.13), residues: 1463 sheet: -2.34 (0.24), residues: 397 loop : -2.85 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG S 110 TYR 0.018 0.001 TYR M 168 PHE 0.020 0.001 PHE C 172 TRP 0.011 0.001 TRP C 183 HIS 0.009 0.001 HIS Z 467 Details of bonding type rmsd covalent geometry : bond 0.00280 (31046) covalent geometry : angle 0.61323 (42277) hydrogen bonds : bond 0.04135 ( 1194) hydrogen bonds : angle 4.86737 ( 3334) metal coordination : bond 0.00709 ( 8) metal coordination : angle 3.84051 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 567 time to evaluate : 1.082 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: S 56 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7486 (mm-30) REVERT: S 88 ARG cc_start: 0.7873 (ttm170) cc_final: 0.7403 (ttm170) REVERT: S 90 LYS cc_start: 0.8369 (mttp) cc_final: 0.7978 (ttmm) REVERT: S 133 MET cc_start: 0.8899 (mmm) cc_final: 0.8587 (mmt) REVERT: S 150 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8768 (tt) REVERT: S 154 TYR cc_start: 0.7856 (OUTLIER) cc_final: 0.7387 (m-10) REVERT: S 207 ARG cc_start: 0.7304 (mpt-90) cc_final: 0.5784 (ptt-90) REVERT: M 9 ASP cc_start: 0.6596 (t70) cc_final: 0.6315 (t70) REVERT: M 13 ASP cc_start: 0.7998 (m-30) cc_final: 0.7599 (m-30) REVERT: M 52 ILE cc_start: 0.8455 (mm) cc_final: 0.7911 (mp) REVERT: M 62 VAL cc_start: 0.8535 (OUTLIER) cc_final: 0.8295 (m) REVERT: M 63 TYR cc_start: 0.8674 (p90) cc_final: 0.8345 (p90) REVERT: M 127 MET cc_start: 0.8656 (mpp) cc_final: 0.8223 (mpp) REVERT: M 153 GLN cc_start: 0.7998 (pp30) cc_final: 0.7652 (pp30) REVERT: M 168 TYR cc_start: 0.7525 (m-80) cc_final: 0.7043 (m-80) REVERT: M 169 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7986 (t80) REVERT: M 190 LEU cc_start: 0.7008 (tp) cc_final: 0.6761 (tp) REVERT: M 193 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7493 (tm-30) REVERT: Z 149 MET cc_start: 0.3833 (ttt) cc_final: 0.3455 (mmp) REVERT: Z 230 ARG cc_start: 0.7272 (tmt-80) cc_final: 0.5419 (mtt90) REVERT: Z 295 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5865 (pp20) REVERT: Z 401 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8217 (pp30) REVERT: Z 457 GLU cc_start: 0.8992 (tt0) cc_final: 0.8541 (tp30) REVERT: Z 472 MET cc_start: 0.8330 (ptp) cc_final: 0.8055 (ptt) REVERT: Z 476 ILE cc_start: 0.5755 (OUTLIER) cc_final: 0.5259 (pt) REVERT: Z 521 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7069 (mt-10) REVERT: Z 541 GLU cc_start: 0.8396 (tp30) cc_final: 0.8017 (tp30) REVERT: Z 569 ARG cc_start: 0.8196 (mpp80) cc_final: 0.7735 (mtt90) REVERT: Z 572 PHE cc_start: 0.7504 (t80) cc_final: 0.7224 (t80) REVERT: A 128 LYS cc_start: 0.8901 (mmtt) cc_final: 0.8633 (mtmm) REVERT: B 80 ILE cc_start: 0.9294 (OUTLIER) cc_final: 0.9078 (tp) REVERT: B 133 TYR cc_start: 0.7289 (t80) cc_final: 0.6563 (t80) REVERT: B 221 ARG cc_start: 0.8919 (ttm170) cc_final: 0.8700 (mtm110) REVERT: C 35 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8111 (t80) REVERT: C 185 ASP cc_start: 0.6841 (p0) cc_final: 0.6576 (p0) REVERT: C 394 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6358 (pp20) REVERT: C 405 MET cc_start: 0.7925 (ttp) cc_final: 0.7657 (ptp) REVERT: C 442 LYS cc_start: 0.7703 (mppt) cc_final: 0.6309 (tptp) REVERT: C 556 THR cc_start: 0.9379 (p) cc_final: 0.9144 (p) REVERT: C 634 GLU cc_start: 0.8139 (tp30) cc_final: 0.7691 (tp30) REVERT: C 697 LYS cc_start: 0.9229 (tttm) cc_final: 0.8779 (ptpt) REVERT: C 720 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8148 (pt) REVERT: C 852 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8686 (mt) REVERT: C 1182 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8686 (mm) REVERT: C 1256 HIS cc_start: 0.7654 (t70) cc_final: 0.7277 (t70) REVERT: C 1286 GLU cc_start: 0.8633 (mp0) cc_final: 0.8405 (mp0) REVERT: C 1351 PHE cc_start: 0.8040 (m-80) cc_final: 0.7276 (m-80) REVERT: D 48 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8572 (mptt) REVERT: D 100 MET cc_start: 0.7645 (mtt) cc_final: 0.7385 (mtt) REVERT: D 135 LYS cc_start: 0.8893 (mttt) cc_final: 0.8593 (mtpt) REVERT: D 163 TYR cc_start: 0.7761 (OUTLIER) cc_final: 0.7390 (t80) REVERT: D 165 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7175 (mm-30) REVERT: D 195 GLU cc_start: 0.8346 (tp30) cc_final: 0.7916 (tp30) REVERT: D 279 LYS cc_start: 0.8527 (tttt) cc_final: 0.8061 (mmtt) REVERT: D 403 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7014 (mm-30) REVERT: D 512 THR cc_start: 0.8949 (p) cc_final: 0.8689 (p) REVERT: D 651 LYS cc_start: 0.8925 (tptt) cc_final: 0.8444 (mmtt) REVERT: D 782 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8305 (m-30) REVERT: D 786 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8224 (tmmt) REVERT: D 796 ARG cc_start: 0.8924 (mtm-85) cc_final: 0.8563 (mtm-85) REVERT: D 829 LYS cc_start: 0.8032 (OUTLIER) cc_final: 0.7764 (pttp) REVERT: D 849 LYS cc_start: 0.7220 (mttt) cc_final: 0.6801 (tmtt) REVERT: D 1133 GLU cc_start: 0.7686 (tp30) cc_final: 0.7437 (mm-30) REVERT: D 1230 ARG cc_start: 0.8433 (mmt90) cc_final: 0.7803 (mmm160) REVERT: D 1269 GLU cc_start: 0.7847 (tp30) cc_final: 0.7505 (tm-30) REVERT: D 1279 LYS cc_start: 0.8307 (tptm) cc_final: 0.7707 (tptp) REVERT: E 26 ARG cc_start: 0.8859 (tpt170) cc_final: 0.8524 (tpp-160) REVERT: E 31 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8453 (mt) REVERT: E 35 TYR cc_start: 0.4324 (OUTLIER) cc_final: 0.2700 (p90) outliers start: 155 outliers final: 91 residues processed: 691 average time/residue: 0.1744 time to fit residues: 194.6389 Evaluate side-chains 622 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 512 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 150 LEU Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 62 VAL Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 199 THR Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 118 THR Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 241 ASP Chi-restraints excluded: chain Z residue 295 GLU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 450 HIS Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 518 THR Chi-restraints excluded: chain Z residue 542 VAL Chi-restraints excluded: chain Z residue 549 THR Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 775 VAL Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 163 TYR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 829 LYS Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain D residue 1357 SER Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 35 TYR Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 71 optimal weight: 5.9990 chunk 263 optimal weight: 0.0370 chunk 174 optimal weight: 6.9990 chunk 12 optimal weight: 8.9990 chunk 58 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 346 optimal weight: 9.9990 chunk 311 optimal weight: 6.9990 chunk 135 optimal weight: 9.9990 overall best weight: 4.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 309 ASN ** Z 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN C1236 HIS ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1319 ASN ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 543 HIS D 553 GLN D 563 ASN E 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.146580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108959 restraints weight = 55558.148| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.84 r_work: 0.3215 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 31054 Z= 0.206 Angle : 0.672 12.030 42289 Z= 0.354 Chirality : 0.045 0.180 4927 Planarity : 0.005 0.063 5167 Dihedral : 15.396 86.364 5008 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % Rotamer: Outliers : 6.09 % Allowed : 26.75 % Favored : 67.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.13), residues: 3715 helix: -0.28 (0.13), residues: 1475 sheet: -2.10 (0.25), residues: 378 loop : -2.83 (0.13), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 397 TYR 0.029 0.002 TYR Z 385 PHE 0.021 0.002 PHE C 172 TRP 0.010 0.001 TRP C 183 HIS 0.009 0.001 HIS Z 467 Details of bonding type rmsd covalent geometry : bond 0.00484 (31046) covalent geometry : angle 0.66807 (42277) hydrogen bonds : bond 0.04637 ( 1194) hydrogen bonds : angle 4.89324 ( 3334) metal coordination : bond 0.00926 ( 8) metal coordination : angle 4.49224 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 521 time to evaluate : 1.099 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: S 54 LEU cc_start: 0.7018 (OUTLIER) cc_final: 0.6627 (tp) REVERT: S 56 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7600 (mm-30) REVERT: S 88 ARG cc_start: 0.8007 (ttm170) cc_final: 0.7543 (ttm170) REVERT: S 90 LYS cc_start: 0.8385 (mttp) cc_final: 0.7998 (ttmm) REVERT: S 133 MET cc_start: 0.8943 (mmm) cc_final: 0.8576 (mmt) REVERT: S 154 TYR cc_start: 0.7857 (OUTLIER) cc_final: 0.7398 (m-10) REVERT: S 207 ARG cc_start: 0.7277 (mpt-90) cc_final: 0.6247 (tpp80) REVERT: M 9 ASP cc_start: 0.6489 (t70) cc_final: 0.6176 (t70) REVERT: M 13 ASP cc_start: 0.8071 (m-30) cc_final: 0.7632 (m-30) REVERT: M 19 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8398 (mm) REVERT: M 52 ILE cc_start: 0.8450 (OUTLIER) cc_final: 0.8095 (mm) REVERT: M 63 TYR cc_start: 0.8752 (p90) cc_final: 0.8492 (p90) REVERT: M 81 MET cc_start: 0.8598 (mmm) cc_final: 0.8233 (mmm) REVERT: M 127 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8300 (mpp) REVERT: M 153 GLN cc_start: 0.8049 (pp30) cc_final: 0.7674 (pp30) REVERT: M 168 TYR cc_start: 0.7446 (m-80) cc_final: 0.6880 (m-80) REVERT: M 169 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.7961 (t80) REVERT: M 190 LEU cc_start: 0.7014 (tp) cc_final: 0.6752 (tp) REVERT: M 193 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7409 (tm-30) REVERT: Z 92 MET cc_start: 0.8327 (mtt) cc_final: 0.8078 (mtt) REVERT: Z 149 MET cc_start: 0.3626 (ttt) cc_final: 0.3323 (mmp) REVERT: Z 230 ARG cc_start: 0.7344 (tmt-80) cc_final: 0.5483 (mtt90) REVERT: Z 295 GLU cc_start: 0.6350 (OUTLIER) cc_final: 0.6012 (pp20) REVERT: Z 401 GLN cc_start: 0.8584 (tm-30) cc_final: 0.8343 (pp30) REVERT: Z 457 GLU cc_start: 0.8967 (tt0) cc_final: 0.8547 (tp30) REVERT: Z 472 MET cc_start: 0.8425 (ptp) cc_final: 0.8114 (ptt) REVERT: Z 541 GLU cc_start: 0.8379 (tp30) cc_final: 0.7987 (tp30) REVERT: Z 569 ARG cc_start: 0.8206 (mpp80) cc_final: 0.7758 (mtt90) REVERT: A 77 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7055 (mp0) REVERT: A 128 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8647 (mtmm) REVERT: B 80 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.9095 (tp) REVERT: B 133 TYR cc_start: 0.7300 (t80) cc_final: 0.6648 (t80) REVERT: B 221 ARG cc_start: 0.8978 (ttm170) cc_final: 0.8712 (mtm110) REVERT: C 35 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8061 (t80) REVERT: C 87 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8379 (tp30) REVERT: C 135 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8358 (ttm) REVERT: C 185 ASP cc_start: 0.7051 (p0) cc_final: 0.6716 (p0) REVERT: C 394 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6542 (pp20) REVERT: C 405 MET cc_start: 0.7982 (ttp) cc_final: 0.7741 (ptp) REVERT: C 442 LYS cc_start: 0.7754 (mppt) cc_final: 0.6355 (tptp) REVERT: C 457 ARG cc_start: 0.8693 (ttp-170) cc_final: 0.8047 (ttp-110) REVERT: C 556 THR cc_start: 0.9350 (p) cc_final: 0.9072 (p) REVERT: C 634 GLU cc_start: 0.8231 (tp30) cc_final: 0.7792 (tp30) REVERT: C 720 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8127 (pt) REVERT: C 803 MET cc_start: 0.8824 (tpp) cc_final: 0.8511 (tpp) REVERT: C 852 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8809 (mt) REVERT: C 1182 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8699 (mm) REVERT: C 1242 MET cc_start: 0.8976 (tmm) cc_final: 0.8643 (tmm) REVERT: C 1256 HIS cc_start: 0.7829 (t70) cc_final: 0.7475 (t70) REVERT: C 1286 GLU cc_start: 0.8559 (mp0) cc_final: 0.8353 (mp0) REVERT: C 1351 PHE cc_start: 0.8075 (m-80) cc_final: 0.7274 (m-80) REVERT: D 100 MET cc_start: 0.7760 (mtt) cc_final: 0.7502 (mtt) REVERT: D 135 LYS cc_start: 0.8920 (mttt) cc_final: 0.8626 (mtpt) REVERT: D 165 GLU cc_start: 0.7994 (mm-30) cc_final: 0.7297 (mm-30) REVERT: D 195 GLU cc_start: 0.8333 (tp30) cc_final: 0.7905 (tp30) REVERT: D 279 LYS cc_start: 0.8594 (tttt) cc_final: 0.8154 (mmtt) REVERT: D 403 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7204 (mm-30) REVERT: D 608 ARG cc_start: 0.8952 (ttm170) cc_final: 0.8562 (ttm170) REVERT: D 786 LYS cc_start: 0.8451 (OUTLIER) cc_final: 0.7984 (tmmt) REVERT: D 796 ARG cc_start: 0.9048 (mtm-85) cc_final: 0.8380 (mtm-85) REVERT: D 849 LYS cc_start: 0.7220 (mttt) cc_final: 0.6858 (tmtt) REVERT: D 926 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8166 (pp) REVERT: D 1132 PHE cc_start: 0.8644 (m-80) cc_final: 0.8443 (m-80) REVERT: D 1269 GLU cc_start: 0.7780 (tp30) cc_final: 0.7462 (tm-30) REVERT: D 1279 LYS cc_start: 0.8305 (tptm) cc_final: 0.7868 (tptp) REVERT: E 10 LEU cc_start: 0.9055 (mm) cc_final: 0.8780 (mm) outliers start: 185 outliers final: 121 residues processed: 657 average time/residue: 0.1775 time to fit residues: 187.9693 Evaluate side-chains 621 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 482 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 295 GLU Chi-restraints excluded: chain Z residue 353 SER Chi-restraints excluded: chain Z residue 358 TYR Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 450 HIS Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 542 VAL Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 566 THR Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 761 SER Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 929 THR Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 350 ARG Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 926 LEU Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1297 ILE Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 110 optimal weight: 9.9990 chunk 263 optimal weight: 0.8980 chunk 235 optimal weight: 5.9990 chunk 188 optimal weight: 0.1980 chunk 245 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 300 optimal weight: 4.9990 chunk 309 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 182 ASN ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 467 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 631 HIS C1122 ASN ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.148961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.111671 restraints weight = 55626.698| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.75 r_work: 0.3259 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 31054 Z= 0.136 Angle : 0.615 10.745 42289 Z= 0.325 Chirality : 0.043 0.180 4927 Planarity : 0.004 0.063 5167 Dihedral : 15.216 86.167 5005 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.76 % Allowed : 27.48 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.24 (0.13), residues: 3715 helix: -0.03 (0.14), residues: 1484 sheet: -1.84 (0.25), residues: 390 loop : -2.74 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 257 TYR 0.021 0.001 TYR Z 385 PHE 0.025 0.001 PHE Z 200 TRP 0.010 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 364 Details of bonding type rmsd covalent geometry : bond 0.00311 (31046) covalent geometry : angle 0.61142 (42277) hydrogen bonds : bond 0.04004 ( 1194) hydrogen bonds : angle 4.67242 ( 3334) metal coordination : bond 0.00600 ( 8) metal coordination : angle 3.95292 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 547 time to evaluate : 0.910 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: S 24 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7828 (mm-30) REVERT: S 54 LEU cc_start: 0.6841 (OUTLIER) cc_final: 0.5820 (mt) REVERT: S 56 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7560 (mm-30) REVERT: S 88 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7549 (ttm170) REVERT: S 90 LYS cc_start: 0.8390 (mttp) cc_final: 0.7981 (ttmm) REVERT: S 133 MET cc_start: 0.8891 (mmm) cc_final: 0.8568 (mmt) REVERT: S 154 TYR cc_start: 0.7741 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: S 207 ARG cc_start: 0.7316 (mpt-90) cc_final: 0.6290 (tpp80) REVERT: M 9 ASP cc_start: 0.6284 (t70) cc_final: 0.5918 (t70) REVERT: M 13 ASP cc_start: 0.8027 (m-30) cc_final: 0.7484 (m-30) REVERT: M 52 ILE cc_start: 0.8384 (mm) cc_final: 0.7820 (mp) REVERT: M 63 TYR cc_start: 0.8679 (p90) cc_final: 0.8439 (p90) REVERT: M 127 MET cc_start: 0.8776 (mpp) cc_final: 0.8300 (mpp) REVERT: M 153 GLN cc_start: 0.8008 (pp30) cc_final: 0.7692 (pp30) REVERT: M 168 TYR cc_start: 0.7479 (m-80) cc_final: 0.6860 (m-80) REVERT: M 169 PHE cc_start: 0.8325 (OUTLIER) cc_final: 0.7982 (t80) REVERT: M 193 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7396 (tm-30) REVERT: Z 92 MET cc_start: 0.8320 (mtt) cc_final: 0.8049 (mtt) REVERT: Z 136 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7959 (tp30) REVERT: Z 143 GLU cc_start: 0.6981 (OUTLIER) cc_final: 0.6609 (tt0) REVERT: Z 230 ARG cc_start: 0.7387 (tmt-80) cc_final: 0.5446 (mtt90) REVERT: Z 245 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8166 (mm) REVERT: Z 295 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5919 (pp20) REVERT: Z 298 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7666 (mt) REVERT: Z 401 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8343 (pp30) REVERT: Z 457 GLU cc_start: 0.8933 (tt0) cc_final: 0.8581 (tp30) REVERT: Z 472 MET cc_start: 0.8486 (ptp) cc_final: 0.8202 (ptt) REVERT: Z 476 ILE cc_start: 0.5655 (OUTLIER) cc_final: 0.5182 (pt) REVERT: Z 541 GLU cc_start: 0.8357 (tp30) cc_final: 0.7962 (tp30) REVERT: Z 569 ARG cc_start: 0.8036 (mpp80) cc_final: 0.7593 (mtt90) REVERT: A 77 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7117 (mp0) REVERT: A 128 LYS cc_start: 0.8824 (mmtt) cc_final: 0.8602 (mtmm) REVERT: B 80 ILE cc_start: 0.9317 (OUTLIER) cc_final: 0.9028 (tp) REVERT: B 133 TYR cc_start: 0.7369 (t80) cc_final: 0.6697 (t80) REVERT: B 221 ARG cc_start: 0.8920 (ttm170) cc_final: 0.8685 (mtm110) REVERT: C 3 TYR cc_start: 0.6380 (OUTLIER) cc_final: 0.6140 (m-10) REVERT: C 35 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8074 (t80) REVERT: C 87 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8352 (tp30) REVERT: C 135 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8285 (ttm) REVERT: C 394 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6470 (pp20) REVERT: C 405 MET cc_start: 0.7950 (ttp) cc_final: 0.7660 (ptp) REVERT: C 442 LYS cc_start: 0.7756 (mppt) cc_final: 0.6177 (tptp) REVERT: C 457 ARG cc_start: 0.8767 (ttp-170) cc_final: 0.8324 (ttm110) REVERT: C 556 THR cc_start: 0.9355 (p) cc_final: 0.9108 (p) REVERT: C 634 GLU cc_start: 0.8159 (tp30) cc_final: 0.7733 (tp30) REVERT: C 720 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8080 (pt) REVERT: C 803 MET cc_start: 0.8699 (tpp) cc_final: 0.8474 (tpp) REVERT: C 852 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8770 (mt) REVERT: C 1182 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8709 (mm) REVERT: C 1189 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8115 (ttmt) REVERT: C 1241 TYR cc_start: 0.8201 (OUTLIER) cc_final: 0.6724 (m-80) REVERT: C 1242 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8606 (tmm) REVERT: C 1350 ASP cc_start: 0.8361 (p0) cc_final: 0.7955 (t0) REVERT: C 1351 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7455 (m-80) REVERT: D 37 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8511 (mtmm) REVERT: D 100 MET cc_start: 0.7669 (mtt) cc_final: 0.7427 (mtt) REVERT: D 135 LYS cc_start: 0.8906 (mttt) cc_final: 0.8614 (mtpt) REVERT: D 165 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7252 (mm-30) REVERT: D 195 GLU cc_start: 0.8308 (tp30) cc_final: 0.7839 (tp30) REVERT: D 219 LEU cc_start: 0.8829 (mm) cc_final: 0.8580 (tp) REVERT: D 279 LYS cc_start: 0.8616 (tttt) cc_final: 0.8081 (mmtt) REVERT: D 310 ARG cc_start: 0.6931 (ptm-80) cc_final: 0.6610 (ptm160) REVERT: D 397 ARG cc_start: 0.8492 (tpp80) cc_final: 0.8203 (mmm-85) REVERT: D 403 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7240 (mm-30) REVERT: D 651 LYS cc_start: 0.8836 (tptt) cc_final: 0.8331 (mmtt) REVERT: D 782 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.8188 (m-30) REVERT: D 796 ARG cc_start: 0.8971 (mtm-85) cc_final: 0.8353 (mtm-85) REVERT: D 818 MET cc_start: 0.8058 (mmt) cc_final: 0.7743 (mmt) REVERT: D 849 LYS cc_start: 0.7228 (mttt) cc_final: 0.6828 (tmtt) REVERT: D 1132 PHE cc_start: 0.8578 (m-80) cc_final: 0.8297 (m-80) REVERT: D 1133 GLU cc_start: 0.7538 (tp30) cc_final: 0.7045 (mm-30) REVERT: D 1136 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7211 (tmm-80) REVERT: D 1269 GLU cc_start: 0.7750 (tp30) cc_final: 0.7422 (tm-30) REVERT: D 1279 LYS cc_start: 0.8304 (tptm) cc_final: 0.7867 (tptp) outliers start: 175 outliers final: 121 residues processed: 679 average time/residue: 0.1744 time to fit residues: 190.8476 Evaluate side-chains 641 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 494 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 182 ASN Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 295 GLU Chi-restraints excluded: chain Z residue 298 ILE Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 450 HIS Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 73 TYR Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 730 VAL Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 897 LEU Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1145 THR Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain D residue 16 ASP Chi-restraints excluded: chain D residue 37 LYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1231 MET Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1287 GLU Chi-restraints excluded: chain D residue 1297 ILE Chi-restraints excluded: chain D residue 1325 ILE Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 114 optimal weight: 3.9990 chunk 338 optimal weight: 7.9990 chunk 358 optimal weight: 7.9990 chunk 360 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 289 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 308 optimal weight: 9.9990 chunk 336 optimal weight: 0.9980 chunk 271 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 44 ASN M 182 ASN ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN D 388 HIS ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.146496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108759 restraints weight = 55908.404| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.86 r_work: 0.3210 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31054 Z= 0.227 Angle : 0.680 11.403 42289 Z= 0.357 Chirality : 0.045 0.183 4927 Planarity : 0.005 0.062 5167 Dihedral : 15.248 85.777 4994 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.12 % Favored : 88.88 % Rotamer: Outliers : 6.88 % Allowed : 26.95 % Favored : 66.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.31 (0.13), residues: 3715 helix: -0.11 (0.13), residues: 1482 sheet: -1.84 (0.25), residues: 397 loop : -2.76 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 67 TYR 0.018 0.002 TYR Z 385 PHE 0.027 0.002 PHE M 196 TRP 0.009 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 566 Details of bonding type rmsd covalent geometry : bond 0.00536 (31046) covalent geometry : angle 0.67683 (42277) hydrogen bonds : bond 0.04542 ( 1194) hydrogen bonds : angle 4.80257 ( 3334) metal coordination : bond 0.01047 ( 8) metal coordination : angle 4.21677 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 209 poor density : 513 time to evaluate : 1.059 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: S 54 LEU cc_start: 0.6990 (OUTLIER) cc_final: 0.6568 (tp) REVERT: S 88 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7687 (ttm170) REVERT: S 90 LYS cc_start: 0.8405 (mttp) cc_final: 0.8022 (ttmm) REVERT: S 133 MET cc_start: 0.8916 (mmm) cc_final: 0.8534 (mmt) REVERT: S 154 TYR cc_start: 0.7870 (OUTLIER) cc_final: 0.7501 (m-10) REVERT: S 207 ARG cc_start: 0.7264 (mpt-90) cc_final: 0.6223 (tpp80) REVERT: M 9 ASP cc_start: 0.6287 (t70) cc_final: 0.5861 (t70) REVERT: M 13 ASP cc_start: 0.8067 (m-30) cc_final: 0.7528 (m-30) REVERT: M 19 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8430 (mm) REVERT: M 52 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8077 (mm) REVERT: M 81 MET cc_start: 0.8485 (mmm) cc_final: 0.8126 (mmm) REVERT: M 153 GLN cc_start: 0.8089 (pp30) cc_final: 0.7717 (pp30) REVERT: M 168 TYR cc_start: 0.7500 (m-80) cc_final: 0.6846 (m-80) REVERT: M 169 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8157 (t80) REVERT: M 193 GLU cc_start: 0.7817 (OUTLIER) cc_final: 0.7463 (tm-30) REVERT: Z 136 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7918 (tp30) REVERT: Z 143 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.6483 (tt0) REVERT: Z 230 ARG cc_start: 0.7293 (tmt-80) cc_final: 0.5459 (mtt90) REVERT: Z 245 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8200 (mm) REVERT: Z 298 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7649 (mm) REVERT: Z 457 GLU cc_start: 0.8957 (tt0) cc_final: 0.8559 (tp30) REVERT: Z 472 MET cc_start: 0.8526 (ptp) cc_final: 0.8226 (ptt) REVERT: Z 506 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7152 (mtp85) REVERT: Z 541 GLU cc_start: 0.8378 (tp30) cc_final: 0.7962 (tp30) REVERT: Z 569 ARG cc_start: 0.8211 (mpp80) cc_final: 0.7760 (mtt90) REVERT: A 77 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: A 128 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8624 (mtmm) REVERT: B 4 GLU cc_start: 0.6827 (mp0) cc_final: 0.6538 (mp0) REVERT: B 80 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9042 (tp) REVERT: B 133 TYR cc_start: 0.7230 (t80) cc_final: 0.6627 (t80) REVERT: B 221 ARG cc_start: 0.8959 (ttm170) cc_final: 0.8682 (mtm110) REVERT: C 3 TYR cc_start: 0.6475 (OUTLIER) cc_final: 0.6211 (m-10) REVERT: C 35 TYR cc_start: 0.9044 (OUTLIER) cc_final: 0.8071 (t80) REVERT: C 87 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8411 (tp30) REVERT: C 135 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8327 (ttm) REVERT: C 185 ASP cc_start: 0.7140 (p0) cc_final: 0.6927 (p0) REVERT: C 394 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6522 (pp20) REVERT: C 405 MET cc_start: 0.8009 (ttp) cc_final: 0.7738 (ptp) REVERT: C 442 LYS cc_start: 0.7729 (mppt) cc_final: 0.6269 (tptp) REVERT: C 457 ARG cc_start: 0.8721 (ttp-170) cc_final: 0.8228 (ttm110) REVERT: C 556 THR cc_start: 0.9370 (p) cc_final: 0.9127 (p) REVERT: C 634 GLU cc_start: 0.8260 (tp30) cc_final: 0.7804 (tp30) REVERT: C 720 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8088 (pt) REVERT: C 803 MET cc_start: 0.8720 (tpp) cc_final: 0.8343 (tpp) REVERT: C 852 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8866 (mt) REVERT: C 1182 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8734 (mm) REVERT: C 1189 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8154 (ttmt) REVERT: C 1242 MET cc_start: 0.9043 (OUTLIER) cc_final: 0.8735 (tmm) REVERT: C 1271 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7602 (mt) REVERT: C 1338 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8807 (tp) REVERT: C 1351 PHE cc_start: 0.8051 (m-80) cc_final: 0.7241 (m-80) REVERT: D 100 MET cc_start: 0.7750 (mtt) cc_final: 0.7496 (mtt) REVERT: D 135 LYS cc_start: 0.8927 (mttt) cc_final: 0.8644 (mtpt) REVERT: D 165 GLU cc_start: 0.8060 (mm-30) cc_final: 0.7397 (mm-30) REVERT: D 195 GLU cc_start: 0.8377 (tp30) cc_final: 0.7885 (tp30) REVERT: D 219 LEU cc_start: 0.8869 (mm) cc_final: 0.8620 (tp) REVERT: D 279 LYS cc_start: 0.8571 (tttt) cc_final: 0.8108 (mmtt) REVERT: D 403 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7293 (mm-30) REVERT: D 651 LYS cc_start: 0.8876 (tptt) cc_final: 0.8626 (tptt) REVERT: D 786 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.7872 (tmmt) REVERT: D 818 MET cc_start: 0.8089 (mmt) cc_final: 0.7736 (mmt) REVERT: D 849 LYS cc_start: 0.7212 (mttt) cc_final: 0.6849 (tmtt) REVERT: D 1132 PHE cc_start: 0.8608 (m-80) cc_final: 0.8270 (m-80) REVERT: D 1133 GLU cc_start: 0.7673 (tp30) cc_final: 0.7173 (mm-30) REVERT: D 1266 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8002 (mm-30) REVERT: D 1269 GLU cc_start: 0.7750 (tp30) cc_final: 0.7430 (tm-30) REVERT: D 1279 LYS cc_start: 0.8309 (tptm) cc_final: 0.7841 (tptp) outliers start: 209 outliers final: 155 residues processed: 669 average time/residue: 0.1693 time to fit residues: 184.5139 Evaluate side-chains 672 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 493 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 99 ASP Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain S residue 159 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 298 ILE Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 344 ILE Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 450 HIS Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 506 ARG Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 639 CYS Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 710 ILE Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1145 THR Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1338 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 192 ILE Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 324 SER Chi-restraints excluded: chain D residue 327 ASP Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1231 MET Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1297 ILE Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 328 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 208 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 109 optimal weight: 20.0000 chunk 197 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 467 HIS C1122 ASN ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.146884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110194 restraints weight = 55768.781| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.83 r_work: 0.3225 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31054 Z= 0.204 Angle : 0.672 11.333 42289 Z= 0.353 Chirality : 0.044 0.180 4927 Planarity : 0.004 0.062 5167 Dihedral : 15.229 86.292 4994 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.69 % Favored : 89.31 % Rotamer: Outliers : 6.98 % Allowed : 27.28 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.13), residues: 3715 helix: -0.05 (0.13), residues: 1476 sheet: -1.75 (0.25), residues: 395 loop : -2.74 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 67 TYR 0.016 0.001 TYR C1136 PHE 0.031 0.002 PHE M 196 TRP 0.009 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 566 Details of bonding type rmsd covalent geometry : bond 0.00480 (31046) covalent geometry : angle 0.66858 (42277) hydrogen bonds : bond 0.04466 ( 1194) hydrogen bonds : angle 4.77648 ( 3334) metal coordination : bond 0.00919 ( 8) metal coordination : angle 4.08491 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 212 poor density : 518 time to evaluate : 0.910 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: S 54 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6512 (tp) REVERT: S 88 ARG cc_start: 0.8128 (ttm170) cc_final: 0.7607 (ttm170) REVERT: S 90 LYS cc_start: 0.8399 (mttp) cc_final: 0.8010 (ttmm) REVERT: S 92 ARG cc_start: 0.8775 (mtt90) cc_final: 0.8502 (mtm180) REVERT: S 133 MET cc_start: 0.8967 (mmm) cc_final: 0.8682 (mmt) REVERT: S 154 TYR cc_start: 0.7828 (OUTLIER) cc_final: 0.7484 (m-10) REVERT: S 207 ARG cc_start: 0.7228 (mpt-90) cc_final: 0.6244 (tpp80) REVERT: M 9 ASP cc_start: 0.6241 (t70) cc_final: 0.5762 (t70) REVERT: M 13 ASP cc_start: 0.8049 (m-30) cc_final: 0.7564 (m-30) REVERT: M 19 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8396 (mm) REVERT: M 52 ILE cc_start: 0.8472 (OUTLIER) cc_final: 0.8095 (mm) REVERT: M 70 GLU cc_start: 0.8809 (pp20) cc_final: 0.8600 (pp20) REVERT: M 81 MET cc_start: 0.8457 (mmm) cc_final: 0.8223 (mmm) REVERT: M 153 GLN cc_start: 0.8089 (pp30) cc_final: 0.7695 (pp30) REVERT: M 168 TYR cc_start: 0.7350 (m-80) cc_final: 0.6651 (m-80) REVERT: M 169 PHE cc_start: 0.8480 (OUTLIER) cc_final: 0.8263 (t80) REVERT: M 190 LEU cc_start: 0.6989 (tp) cc_final: 0.6741 (tp) REVERT: M 193 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: Z 92 MET cc_start: 0.8327 (mtt) cc_final: 0.8075 (mtt) REVERT: Z 136 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7873 (tp30) REVERT: Z 143 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: Z 230 ARG cc_start: 0.7331 (tmt-80) cc_final: 0.5416 (mtt90) REVERT: Z 245 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8183 (mm) REVERT: Z 366 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8059 (mp) REVERT: Z 457 GLU cc_start: 0.8955 (tt0) cc_final: 0.8553 (tp30) REVERT: Z 472 MET cc_start: 0.8511 (ptp) cc_final: 0.8199 (ptt) REVERT: Z 476 ILE cc_start: 0.5766 (OUTLIER) cc_final: 0.5346 (pt) REVERT: Z 506 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7095 (mtp85) REVERT: Z 541 GLU cc_start: 0.8367 (tp30) cc_final: 0.7938 (tp30) REVERT: Z 569 ARG cc_start: 0.8205 (mpp80) cc_final: 0.7774 (mtt90) REVERT: A 19 ASP cc_start: 0.8676 (t0) cc_final: 0.8332 (t0) REVERT: A 74 ASP cc_start: 0.8710 (m-30) cc_final: 0.7968 (t70) REVERT: A 77 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 128 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8636 (mtmm) REVERT: B 4 GLU cc_start: 0.6787 (mp0) cc_final: 0.6528 (mp0) REVERT: B 80 ILE cc_start: 0.9322 (OUTLIER) cc_final: 0.9028 (tp) REVERT: B 133 TYR cc_start: 0.7322 (t80) cc_final: 0.6703 (t80) REVERT: B 221 ARG cc_start: 0.8971 (ttm170) cc_final: 0.8675 (mtm110) REVERT: C 3 TYR cc_start: 0.6451 (OUTLIER) cc_final: 0.6194 (m-10) REVERT: C 35 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8092 (t80) REVERT: C 87 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8430 (tp30) REVERT: C 135 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8323 (ttm) REVERT: C 185 ASP cc_start: 0.7125 (p0) cc_final: 0.6813 (p0) REVERT: C 394 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6493 (pp20) REVERT: C 405 MET cc_start: 0.8002 (ttp) cc_final: 0.7736 (ptp) REVERT: C 442 LYS cc_start: 0.7729 (mppt) cc_final: 0.6265 (tptp) REVERT: C 457 ARG cc_start: 0.8707 (ttp-170) cc_final: 0.8198 (ttm110) REVERT: C 556 THR cc_start: 0.9376 (p) cc_final: 0.9131 (p) REVERT: C 634 GLU cc_start: 0.8262 (tp30) cc_final: 0.7762 (tp30) REVERT: C 720 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8060 (pt) REVERT: C 803 MET cc_start: 0.8700 (tpp) cc_final: 0.8355 (tpp) REVERT: C 852 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8831 (mt) REVERT: C 1056 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7315 (mt) REVERT: C 1182 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8739 (mm) REVERT: C 1189 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8133 (ttmt) REVERT: C 1241 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: C 1242 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8642 (tmm) REVERT: C 1258 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8726 (ttt180) REVERT: C 1271 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7525 (mt) REVERT: C 1338 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8793 (tp) REVERT: C 1351 PHE cc_start: 0.8068 (m-80) cc_final: 0.7204 (m-80) REVERT: D 100 MET cc_start: 0.7740 (mtt) cc_final: 0.7472 (mtt) REVERT: D 135 LYS cc_start: 0.8917 (mttt) cc_final: 0.8626 (mtpt) REVERT: D 165 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7377 (mm-30) REVERT: D 195 GLU cc_start: 0.8389 (tp30) cc_final: 0.7894 (tp30) REVERT: D 219 LEU cc_start: 0.8846 (mm) cc_final: 0.8591 (tp) REVERT: D 279 LYS cc_start: 0.8566 (tttt) cc_final: 0.8092 (mmtt) REVERT: D 651 LYS cc_start: 0.8891 (tptt) cc_final: 0.8649 (tptt) REVERT: D 786 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7901 (tmmt) REVERT: D 796 ARG cc_start: 0.8985 (mtm-85) cc_final: 0.8156 (mtm-85) REVERT: D 818 MET cc_start: 0.8094 (mmt) cc_final: 0.7691 (mmt) REVERT: D 849 LYS cc_start: 0.7277 (mttt) cc_final: 0.6905 (tmtt) REVERT: D 1132 PHE cc_start: 0.8588 (m-80) cc_final: 0.8263 (m-80) REVERT: D 1133 GLU cc_start: 0.7688 (tp30) cc_final: 0.7226 (mm-30) REVERT: D 1268 ILE cc_start: 0.8898 (mm) cc_final: 0.8629 (mm) REVERT: D 1269 GLU cc_start: 0.7717 (tp30) cc_final: 0.7348 (tm-30) REVERT: D 1279 LYS cc_start: 0.8273 (tptm) cc_final: 0.7736 (mtpp) outliers start: 212 outliers final: 153 residues processed: 679 average time/residue: 0.1698 time to fit residues: 187.8646 Evaluate side-chains 669 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 488 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain S residue 159 ILE Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 52 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 118 THR Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 143 GLU Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 344 ILE Chi-restraints excluded: chain Z residue 366 LEU Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 450 HIS Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 488 ILE Chi-restraints excluded: chain Z residue 506 ARG Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 66 ASN Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 837 GLU Chi-restraints excluded: chain C residue 840 CYS Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 864 LEU Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 1056 LEU Chi-restraints excluded: chain C residue 1061 LEU Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1145 THR Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1338 LEU Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 317 SER Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 398 MET Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 570 THR Chi-restraints excluded: chain D residue 580 ILE Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 748 ASP Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 786 LYS Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 852 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1231 MET Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1295 MET Chi-restraints excluded: chain D residue 1297 ILE Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 31 LEU Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 30 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 chunk 243 optimal weight: 0.9980 chunk 372 optimal weight: 6.9990 chunk 326 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 317 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 overall best weight: 2.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 128 GLN ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN C1122 ASN ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.148642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111348 restraints weight = 55688.842| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.74 r_work: 0.3255 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31054 Z= 0.149 Angle : 0.646 12.128 42289 Z= 0.339 Chirality : 0.043 0.174 4927 Planarity : 0.004 0.063 5167 Dihedral : 15.127 85.628 4994 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 6.12 % Allowed : 28.17 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.13), residues: 3715 helix: 0.09 (0.14), residues: 1488 sheet: -1.59 (0.26), residues: 390 loop : -2.65 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 257 TYR 0.017 0.001 TYR Z 197 PHE 0.035 0.001 PHE M 196 TRP 0.011 0.001 TRP C 183 HIS 0.004 0.001 HIS Z 364 Details of bonding type rmsd covalent geometry : bond 0.00346 (31046) covalent geometry : angle 0.64334 (42277) hydrogen bonds : bond 0.04058 ( 1194) hydrogen bonds : angle 4.64930 ( 3334) metal coordination : bond 0.00639 ( 8) metal coordination : angle 3.76838 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 521 time to evaluate : 0.817 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: S 54 LEU cc_start: 0.6739 (OUTLIER) cc_final: 0.5652 (mt) REVERT: S 88 ARG cc_start: 0.8079 (ttm170) cc_final: 0.7680 (ttm170) REVERT: S 90 LYS cc_start: 0.8366 (mttp) cc_final: 0.8008 (ttmm) REVERT: S 133 MET cc_start: 0.8949 (mmm) cc_final: 0.8655 (mmt) REVERT: S 154 TYR cc_start: 0.7669 (OUTLIER) cc_final: 0.7410 (m-10) REVERT: S 207 ARG cc_start: 0.7230 (mpt-90) cc_final: 0.6238 (tpp80) REVERT: M 9 ASP cc_start: 0.6282 (t70) cc_final: 0.5872 (t70) REVERT: M 13 ASP cc_start: 0.8023 (m-30) cc_final: 0.7516 (m-30) REVERT: M 70 GLU cc_start: 0.8831 (pp20) cc_final: 0.8528 (pp20) REVERT: M 81 MET cc_start: 0.8421 (mmm) cc_final: 0.8205 (mmm) REVERT: M 127 MET cc_start: 0.8702 (mpp) cc_final: 0.8286 (mpp) REVERT: M 153 GLN cc_start: 0.8059 (pp30) cc_final: 0.7726 (pp30) REVERT: M 168 TYR cc_start: 0.7420 (m-80) cc_final: 0.6738 (m-80) REVERT: M 169 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.8259 (t80) REVERT: M 190 LEU cc_start: 0.6973 (tp) cc_final: 0.6718 (tp) REVERT: M 193 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7378 (tm-30) REVERT: Z 92 MET cc_start: 0.8335 (mtt) cc_final: 0.8100 (mtt) REVERT: Z 136 GLU cc_start: 0.8225 (tm-30) cc_final: 0.7945 (tp30) REVERT: Z 143 GLU cc_start: 0.6898 (pp20) cc_final: 0.6447 (tt0) REVERT: Z 230 ARG cc_start: 0.7331 (tmt-80) cc_final: 0.5395 (mtt90) REVERT: Z 245 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8170 (mm) REVERT: Z 256 LYS cc_start: 0.8517 (mttt) cc_final: 0.7662 (tptt) REVERT: Z 315 MET cc_start: 0.8804 (tpp) cc_final: 0.8336 (tpp) REVERT: Z 401 GLN cc_start: 0.8305 (pp30) cc_final: 0.8072 (pp30) REVERT: Z 457 GLU cc_start: 0.8927 (tt0) cc_final: 0.8587 (tp30) REVERT: Z 472 MET cc_start: 0.8505 (ptp) cc_final: 0.8217 (ptt) REVERT: Z 476 ILE cc_start: 0.5697 (OUTLIER) cc_final: 0.5242 (pt) REVERT: Z 506 ARG cc_start: 0.7538 (OUTLIER) cc_final: 0.7023 (mtp85) REVERT: Z 533 MET cc_start: 0.8221 (tpp) cc_final: 0.7999 (tpp) REVERT: Z 541 GLU cc_start: 0.8366 (tp30) cc_final: 0.7905 (tp30) REVERT: Z 569 ARG cc_start: 0.8162 (mpp80) cc_final: 0.7608 (mtt90) REVERT: A 74 ASP cc_start: 0.8683 (m-30) cc_final: 0.7982 (t70) REVERT: A 77 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7201 (mp0) REVERT: B 4 GLU cc_start: 0.6733 (mp0) cc_final: 0.6487 (mp0) REVERT: B 80 ILE cc_start: 0.9330 (OUTLIER) cc_final: 0.9040 (tp) REVERT: B 133 TYR cc_start: 0.7300 (t80) cc_final: 0.6702 (t80) REVERT: B 221 ARG cc_start: 0.8919 (ttm170) cc_final: 0.8624 (mtm110) REVERT: C 3 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.6116 (m-10) REVERT: C 35 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.8021 (t80) REVERT: C 87 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8368 (tp30) REVERT: C 135 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8295 (ttm) REVERT: C 185 ASP cc_start: 0.7101 (p0) cc_final: 0.6834 (p0) REVERT: C 394 GLU cc_start: 0.6992 (OUTLIER) cc_final: 0.6542 (pp20) REVERT: C 405 MET cc_start: 0.7964 (ttp) cc_final: 0.7700 (ptp) REVERT: C 442 LYS cc_start: 0.7731 (mppt) cc_final: 0.6298 (tptp) REVERT: C 556 THR cc_start: 0.9388 (p) cc_final: 0.9133 (p) REVERT: C 609 LEU cc_start: 0.8982 (tp) cc_final: 0.8581 (mm) REVERT: C 634 GLU cc_start: 0.8175 (tp30) cc_final: 0.7712 (tp30) REVERT: C 720 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8004 (pt) REVERT: C 803 MET cc_start: 0.8686 (tpp) cc_final: 0.8372 (tpp) REVERT: C 852 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8754 (mt) REVERT: C 1182 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8748 (mm) REVERT: C 1189 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.8083 (ttmt) REVERT: C 1241 TYR cc_start: 0.8283 (OUTLIER) cc_final: 0.6518 (m-80) REVERT: C 1242 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.8500 (tmm) REVERT: C 1258 ARG cc_start: 0.9068 (OUTLIER) cc_final: 0.8764 (ttt180) REVERT: C 1271 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7418 (mt) REVERT: C 1350 ASP cc_start: 0.8287 (p0) cc_final: 0.7902 (t0) REVERT: C 1351 PHE cc_start: 0.8100 (m-80) cc_final: 0.7569 (m-80) REVERT: D 100 MET cc_start: 0.7708 (mtt) cc_final: 0.7424 (mtt) REVERT: D 135 LYS cc_start: 0.8912 (mttt) cc_final: 0.8606 (mtpt) REVERT: D 195 GLU cc_start: 0.8338 (tp30) cc_final: 0.7829 (tp30) REVERT: D 219 LEU cc_start: 0.8843 (mm) cc_final: 0.8589 (tp) REVERT: D 279 LYS cc_start: 0.8548 (tttt) cc_final: 0.8041 (mmtt) REVERT: D 310 ARG cc_start: 0.6981 (ptm-80) cc_final: 0.6709 (ptt180) REVERT: D 651 LYS cc_start: 0.8869 (tptt) cc_final: 0.8596 (tptt) REVERT: D 657 LYS cc_start: 0.7956 (mmmt) cc_final: 0.6993 (ptmt) REVERT: D 796 ARG cc_start: 0.8964 (mtm-85) cc_final: 0.8129 (mtm-85) REVERT: D 818 MET cc_start: 0.8066 (mmt) cc_final: 0.7668 (mmt) REVERT: D 849 LYS cc_start: 0.7229 (mttt) cc_final: 0.6808 (tmtt) REVERT: D 1132 PHE cc_start: 0.8573 (m-80) cc_final: 0.8248 (m-80) REVERT: D 1133 GLU cc_start: 0.7617 (tp30) cc_final: 0.7240 (mm-30) REVERT: D 1136 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7192 (tmm-80) REVERT: D 1266 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7832 (mm-30) REVERT: D 1268 ILE cc_start: 0.8883 (OUTLIER) cc_final: 0.8600 (mm) REVERT: D 1269 GLU cc_start: 0.7694 (tp30) cc_final: 0.7316 (tm-30) REVERT: D 1279 LYS cc_start: 0.8220 (tptm) cc_final: 0.7768 (mtpp) REVERT: E 10 LEU cc_start: 0.8919 (mt) cc_final: 0.8710 (mm) outliers start: 186 outliers final: 139 residues processed: 668 average time/residue: 0.1745 time to fit residues: 190.5317 Evaluate side-chains 669 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 507 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 29 THR Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 68 LEU Chi-restraints excluded: chain S residue 130 LEU Chi-restraints excluded: chain S residue 154 TYR Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 32 SER Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 169 PHE Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 99 ASP Chi-restraints excluded: chain Z residue 118 THR Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 278 VAL Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 447 ILE Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 506 ARG Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 89 VAL Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 577 SER Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 748 ASN Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 828 ASP Chi-restraints excluded: chain C residue 831 THR Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 1122 ASN Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1166 VAL Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1258 ARG Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1267 THR Chi-restraints excluded: chain C residue 1271 LEU Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 68 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 338 GLN Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 391 THR Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1156 ASP Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1231 MET Chi-restraints excluded: chain D residue 1256 ASP Chi-restraints excluded: chain D residue 1268 ILE Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1295 MET Chi-restraints excluded: chain D residue 1297 ILE Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 306 optimal weight: 5.9990 chunk 239 optimal weight: 0.0370 chunk 334 optimal weight: 10.0000 chunk 373 optimal weight: 0.2980 chunk 238 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 265 optimal weight: 10.0000 chunk 127 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 295 optimal weight: 1.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 220 GLN ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 338 GLN ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.151578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114802 restraints weight = 55374.152| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.92 r_work: 0.3290 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31054 Z= 0.119 Angle : 0.626 11.799 42289 Z= 0.328 Chirality : 0.042 0.165 4927 Planarity : 0.004 0.071 5167 Dihedral : 14.967 83.615 4991 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 4.54 % Allowed : 29.81 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.14), residues: 3715 helix: 0.25 (0.14), residues: 1504 sheet: -1.44 (0.25), residues: 394 loop : -2.56 (0.14), residues: 1817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 67 TYR 0.017 0.001 TYR Z 197 PHE 0.032 0.001 PHE M 196 TRP 0.012 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 364 Details of bonding type rmsd covalent geometry : bond 0.00266 (31046) covalent geometry : angle 0.62375 (42277) hydrogen bonds : bond 0.03600 ( 1194) hydrogen bonds : angle 4.49818 ( 3334) metal coordination : bond 0.00414 ( 8) metal coordination : angle 3.32913 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 561 time to evaluate : 1.139 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: S 54 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.5534 (mt) REVERT: S 56 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7449 (mm-30) REVERT: S 88 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7173 (mtt90) REVERT: S 90 LYS cc_start: 0.8481 (mttp) cc_final: 0.8014 (ttmm) REVERT: S 92 ARG cc_start: 0.9044 (mtm180) cc_final: 0.8288 (mtt180) REVERT: S 133 MET cc_start: 0.8880 (mmm) cc_final: 0.8571 (mmt) REVERT: S 207 ARG cc_start: 0.7293 (mpt-90) cc_final: 0.6286 (tpp80) REVERT: M 9 ASP cc_start: 0.5991 (t70) cc_final: 0.5484 (t70) REVERT: M 13 ASP cc_start: 0.7914 (m-30) cc_final: 0.7411 (m-30) REVERT: M 52 ILE cc_start: 0.8364 (mm) cc_final: 0.7774 (mp) REVERT: M 60 PHE cc_start: 0.7971 (p90) cc_final: 0.7465 (p90) REVERT: M 81 MET cc_start: 0.8416 (mmm) cc_final: 0.8204 (mmm) REVERT: M 127 MET cc_start: 0.8680 (mpp) cc_final: 0.8213 (mpp) REVERT: M 153 GLN cc_start: 0.8087 (pp30) cc_final: 0.7775 (pp30) REVERT: M 168 TYR cc_start: 0.7410 (m-80) cc_final: 0.6674 (m-80) REVERT: M 190 LEU cc_start: 0.6915 (tp) cc_final: 0.6678 (tp) REVERT: M 193 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: Z 92 MET cc_start: 0.8322 (mtt) cc_final: 0.8097 (mtt) REVERT: Z 136 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8019 (tp30) REVERT: Z 143 GLU cc_start: 0.6881 (pp20) cc_final: 0.6434 (tt0) REVERT: Z 230 ARG cc_start: 0.7325 (tmt-80) cc_final: 0.5444 (mtt90) REVERT: Z 245 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8163 (mm) REVERT: Z 256 LYS cc_start: 0.8441 (mttt) cc_final: 0.7554 (tptt) REVERT: Z 270 GLN cc_start: 0.6954 (pp30) cc_final: 0.6128 (mp10) REVERT: Z 457 GLU cc_start: 0.8881 (tt0) cc_final: 0.8489 (tp30) REVERT: Z 472 MET cc_start: 0.8505 (ptp) cc_final: 0.8251 (ptt) REVERT: Z 476 ILE cc_start: 0.5546 (OUTLIER) cc_final: 0.5115 (pt) REVERT: Z 503 GLU cc_start: 0.7516 (mp0) cc_final: 0.7228 (mp0) REVERT: Z 506 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7074 (mtp85) REVERT: Z 533 MET cc_start: 0.8216 (tpp) cc_final: 0.8012 (tpp) REVERT: Z 569 ARG cc_start: 0.8072 (mpp80) cc_final: 0.7560 (mtt90) REVERT: A 74 ASP cc_start: 0.8697 (m-30) cc_final: 0.8025 (t70) REVERT: A 77 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7144 (mp0) REVERT: B 4 GLU cc_start: 0.6838 (mp0) cc_final: 0.6582 (mp0) REVERT: B 17 TYR cc_start: 0.7565 (p90) cc_final: 0.7312 (p90) REVERT: B 75 GLU cc_start: 0.8014 (mp0) cc_final: 0.7694 (mm-30) REVERT: B 80 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.9032 (tp) REVERT: B 133 TYR cc_start: 0.7257 (t80) cc_final: 0.6690 (t80) REVERT: B 176 ASP cc_start: 0.7943 (t0) cc_final: 0.7728 (t0) REVERT: B 221 ARG cc_start: 0.8882 (ttm170) cc_final: 0.8615 (mtm110) REVERT: C 3 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.6074 (m-10) REVERT: C 35 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.7971 (t80) REVERT: C 87 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8377 (tp30) REVERT: C 135 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8234 (ttm) REVERT: C 185 ASP cc_start: 0.7106 (p0) cc_final: 0.6845 (p0) REVERT: C 394 GLU cc_start: 0.6963 (OUTLIER) cc_final: 0.6482 (pp20) REVERT: C 405 MET cc_start: 0.7932 (ttp) cc_final: 0.7695 (ptp) REVERT: C 442 LYS cc_start: 0.7723 (mppt) cc_final: 0.6418 (tptp) REVERT: C 457 ARG cc_start: 0.8641 (ttp-170) cc_final: 0.8324 (ttm110) REVERT: C 556 THR cc_start: 0.9391 (p) cc_final: 0.9144 (p) REVERT: C 634 GLU cc_start: 0.8133 (tp30) cc_final: 0.7682 (tp30) REVERT: C 720 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8081 (pt) REVERT: C 852 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8771 (mt) REVERT: C 1182 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8643 (mm) REVERT: C 1189 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8097 (ttmt) REVERT: C 1241 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6938 (m-80) REVERT: C 1242 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8442 (tmm) REVERT: C 1350 ASP cc_start: 0.8272 (p0) cc_final: 0.7965 (t0) REVERT: C 1351 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7375 (m-80) REVERT: D 48 LYS cc_start: 0.8783 (mtpt) cc_final: 0.8374 (mptt) REVERT: D 135 LYS cc_start: 0.8887 (mttt) cc_final: 0.8600 (mtpt) REVERT: D 149 MET cc_start: 0.7742 (tmm) cc_final: 0.7495 (tmm) REVERT: D 165 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7235 (mm-30) REVERT: D 219 LEU cc_start: 0.8815 (mm) cc_final: 0.8571 (tp) REVERT: D 279 LYS cc_start: 0.8566 (tttt) cc_final: 0.8027 (mmtt) REVERT: D 403 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7433 (mt-10) REVERT: D 651 LYS cc_start: 0.8909 (tptt) cc_final: 0.8410 (mmtt) REVERT: D 657 LYS cc_start: 0.7893 (mmmt) cc_final: 0.6986 (ptmt) REVERT: D 782 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.8042 (m-30) REVERT: D 796 ARG cc_start: 0.8910 (mtm-85) cc_final: 0.8222 (mtm-85) REVERT: D 818 MET cc_start: 0.8002 (mmt) cc_final: 0.7631 (mmt) REVERT: D 849 LYS cc_start: 0.7259 (mttt) cc_final: 0.6838 (tmtt) REVERT: D 1132 PHE cc_start: 0.8503 (m-80) cc_final: 0.8215 (m-80) REVERT: D 1133 GLU cc_start: 0.7569 (tp30) cc_final: 0.7125 (mm-30) REVERT: D 1136 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7209 (tmm-80) REVERT: D 1266 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7815 (mm-30) REVERT: D 1269 GLU cc_start: 0.7697 (tp30) cc_final: 0.7369 (tm-30) REVERT: D 1279 LYS cc_start: 0.8218 (tptm) cc_final: 0.7789 (mtpp) REVERT: D 1362 LYS cc_start: 0.8405 (pptt) cc_final: 0.8198 (pptt) REVERT: D 1363 MET cc_start: 0.7673 (mmp) cc_final: 0.7389 (mpp) REVERT: E 7 GLU cc_start: 0.8712 (tp30) cc_final: 0.7886 (tt0) REVERT: E 67 ARG cc_start: 0.8889 (mtp-110) cc_final: 0.8389 (mtp-110) outliers start: 138 outliers final: 101 residues processed: 664 average time/residue: 0.1772 time to fit residues: 190.8467 Evaluate side-chains 652 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 530 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 88 ARG Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain M residue 200 ILE Chi-restraints excluded: chain Z residue 84 THR Chi-restraints excluded: chain Z residue 118 THR Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 308 ILE Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 447 ILE Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 476 ILE Chi-restraints excluded: chain Z residue 506 ARG Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 7 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 888 LYS Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1245 LEU Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 284 ASN Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 466 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 719 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1287 GLU Chi-restraints excluded: chain D residue 1295 MET Chi-restraints excluded: chain D residue 1297 ILE Chi-restraints excluded: chain D residue 1341 ILE Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 96 optimal weight: 8.9990 chunk 28 optimal weight: 6.9990 chunk 320 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 263 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 87 optimal weight: 0.0170 chunk 77 optimal weight: 0.0040 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.2036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 689 GLN ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.151832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.114959 restraints weight = 54920.118| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 3.09 r_work: 0.3281 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31054 Z= 0.122 Angle : 0.632 13.339 42289 Z= 0.329 Chirality : 0.042 0.162 4927 Planarity : 0.004 0.063 5167 Dihedral : 14.852 81.951 4980 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 4.05 % Allowed : 30.70 % Favored : 65.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3715 helix: 0.36 (0.14), residues: 1503 sheet: -1.39 (0.25), residues: 389 loop : -2.47 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 257 TYR 0.022 0.001 TYR Z 385 PHE 0.035 0.001 PHE M 196 TRP 0.011 0.001 TRP C 183 HIS 0.005 0.001 HIS D 102 Details of bonding type rmsd covalent geometry : bond 0.00278 (31046) covalent geometry : angle 0.62989 (42277) hydrogen bonds : bond 0.03563 ( 1194) hydrogen bonds : angle 4.45735 ( 3334) metal coordination : bond 0.00434 ( 8) metal coordination : angle 3.11729 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 540 time to evaluate : 1.134 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: S 54 LEU cc_start: 0.6414 (OUTLIER) cc_final: 0.5299 (mt) REVERT: S 55 MET cc_start: 0.6451 (tpp) cc_final: 0.6133 (mmt) REVERT: S 56 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7452 (mm-30) REVERT: S 88 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7445 (ttm170) REVERT: S 90 LYS cc_start: 0.8468 (mttp) cc_final: 0.8025 (ttmm) REVERT: S 92 ARG cc_start: 0.9000 (mtm180) cc_final: 0.8418 (mtt180) REVERT: S 133 MET cc_start: 0.8907 (mmm) cc_final: 0.8573 (mmt) REVERT: S 207 ARG cc_start: 0.7270 (mpt-90) cc_final: 0.6294 (tpp80) REVERT: M 2 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7430 (tp) REVERT: M 9 ASP cc_start: 0.5987 (t70) cc_final: 0.5608 (t70) REVERT: M 13 ASP cc_start: 0.7893 (m-30) cc_final: 0.7365 (m-30) REVERT: M 52 ILE cc_start: 0.8344 (mm) cc_final: 0.7795 (mp) REVERT: M 60 PHE cc_start: 0.8036 (p90) cc_final: 0.7515 (p90) REVERT: M 153 GLN cc_start: 0.8093 (pp30) cc_final: 0.7772 (pp30) REVERT: M 168 TYR cc_start: 0.7408 (m-80) cc_final: 0.6671 (m-80) REVERT: M 193 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: Z 92 MET cc_start: 0.8361 (mtt) cc_final: 0.8156 (mtt) REVERT: Z 136 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7985 (tp30) REVERT: Z 143 GLU cc_start: 0.6869 (pp20) cc_final: 0.6393 (tt0) REVERT: Z 230 ARG cc_start: 0.7350 (tmt-80) cc_final: 0.5479 (mtt90) REVERT: Z 245 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8134 (mm) REVERT: Z 256 LYS cc_start: 0.8473 (mttt) cc_final: 0.7575 (tptt) REVERT: Z 270 GLN cc_start: 0.6977 (pp30) cc_final: 0.6293 (mm-40) REVERT: Z 315 MET cc_start: 0.8647 (tpp) cc_final: 0.8342 (tpp) REVERT: Z 457 GLU cc_start: 0.8948 (tt0) cc_final: 0.8587 (tp30) REVERT: Z 472 MET cc_start: 0.8484 (ptp) cc_final: 0.8223 (ptt) REVERT: Z 503 GLU cc_start: 0.7470 (mp0) cc_final: 0.7158 (mp0) REVERT: Z 506 ARG cc_start: 0.7447 (tpt-90) cc_final: 0.6995 (mtp85) REVERT: Z 533 MET cc_start: 0.8318 (tpp) cc_final: 0.8076 (tpp) REVERT: Z 541 GLU cc_start: 0.8365 (tp30) cc_final: 0.7923 (tp30) REVERT: Z 569 ARG cc_start: 0.8184 (mpp80) cc_final: 0.7601 (mtt90) REVERT: A 74 ASP cc_start: 0.8690 (m-30) cc_final: 0.7931 (t70) REVERT: A 77 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: B 4 GLU cc_start: 0.6903 (mp0) cc_final: 0.6574 (mp0) REVERT: B 17 TYR cc_start: 0.7569 (p90) cc_final: 0.7309 (p90) REVERT: B 73 CYS cc_start: 0.7936 (p) cc_final: 0.7626 (m) REVERT: B 75 GLU cc_start: 0.8061 (mp0) cc_final: 0.7760 (mm-30) REVERT: B 80 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.8981 (tp) REVERT: B 133 TYR cc_start: 0.7317 (t80) cc_final: 0.7012 (t80) REVERT: B 176 ASP cc_start: 0.7973 (t0) cc_final: 0.7725 (t0) REVERT: B 221 ARG cc_start: 0.8914 (ttm170) cc_final: 0.8572 (mtm110) REVERT: C 3 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.6158 (m-10) REVERT: C 35 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.7950 (t80) REVERT: C 135 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8338 (ttm) REVERT: C 185 ASP cc_start: 0.6996 (p0) cc_final: 0.6714 (p0) REVERT: C 394 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6379 (pp20) REVERT: C 405 MET cc_start: 0.7967 (ttp) cc_final: 0.7637 (ptp) REVERT: C 434 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8569 (mm-30) REVERT: C 442 LYS cc_start: 0.7696 (mppt) cc_final: 0.6347 (tptp) REVERT: C 457 ARG cc_start: 0.8633 (ttp-170) cc_final: 0.8279 (mtm110) REVERT: C 475 GLU cc_start: 0.8689 (pp20) cc_final: 0.8294 (pp20) REVERT: C 556 THR cc_start: 0.9416 (p) cc_final: 0.9166 (p) REVERT: C 634 GLU cc_start: 0.8168 (tp30) cc_final: 0.7649 (tp30) REVERT: C 720 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7928 (pt) REVERT: C 843 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7391 (mtm-85) REVERT: C 852 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8747 (mt) REVERT: C 1182 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8665 (mm) REVERT: C 1189 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8066 (ttmt) REVERT: C 1241 TYR cc_start: 0.8063 (OUTLIER) cc_final: 0.7027 (m-80) REVERT: C 1242 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8351 (tmm) REVERT: C 1350 ASP cc_start: 0.8305 (p0) cc_final: 0.7951 (t0) REVERT: C 1351 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7121 (m-80) REVERT: D 48 LYS cc_start: 0.8807 (mtpt) cc_final: 0.8275 (mptt) REVERT: D 135 LYS cc_start: 0.8849 (mttt) cc_final: 0.8558 (mtpt) REVERT: D 149 MET cc_start: 0.7859 (tmm) cc_final: 0.7596 (tmm) REVERT: D 165 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7319 (mm-30) REVERT: D 219 LEU cc_start: 0.8826 (mm) cc_final: 0.8560 (tp) REVERT: D 279 LYS cc_start: 0.8475 (tttt) cc_final: 0.7948 (mmtt) REVERT: D 403 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7295 (mt-10) REVERT: D 651 LYS cc_start: 0.8868 (tptt) cc_final: 0.8369 (mmtt) REVERT: D 657 LYS cc_start: 0.7883 (mmmt) cc_final: 0.7046 (ptmt) REVERT: D 782 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: D 796 ARG cc_start: 0.8936 (mtm-85) cc_final: 0.8114 (mtm-85) REVERT: D 818 MET cc_start: 0.7897 (mmt) cc_final: 0.7357 (mmt) REVERT: D 849 LYS cc_start: 0.7236 (mttt) cc_final: 0.6811 (tmtt) REVERT: D 1132 PHE cc_start: 0.8469 (m-80) cc_final: 0.8149 (m-80) REVERT: D 1133 GLU cc_start: 0.7642 (tp30) cc_final: 0.7203 (mm-30) REVERT: D 1136 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7198 (tmm-80) REVERT: D 1266 GLU cc_start: 0.8241 (mm-30) cc_final: 0.7797 (mm-30) REVERT: D 1269 GLU cc_start: 0.7685 (tp30) cc_final: 0.7353 (tm-30) REVERT: D 1279 LYS cc_start: 0.8226 (tptm) cc_final: 0.7846 (mtpp) REVERT: D 1363 MET cc_start: 0.7776 (mmp) cc_final: 0.7468 (mpp) REVERT: E 7 GLU cc_start: 0.8757 (tp30) cc_final: 0.7915 (tt0) REVERT: E 53 ARG cc_start: 0.8557 (tpp80) cc_final: 0.8143 (ttm110) REVERT: E 67 ARG cc_start: 0.8905 (mtp-110) cc_final: 0.8380 (mtp-110) outliers start: 123 outliers final: 92 residues processed: 633 average time/residue: 0.1774 time to fit residues: 182.3767 Evaluate side-chains 640 residues out of total 3271 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 528 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 15 SER Chi-restraints excluded: chain S residue 24 GLU Chi-restraints excluded: chain S residue 41 MET Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain S residue 88 ARG Chi-restraints excluded: chain S residue 158 LEU Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 82 PHE Chi-restraints excluded: chain M residue 163 THR Chi-restraints excluded: chain M residue 193 GLU Chi-restraints excluded: chain Z residue 84 THR Chi-restraints excluded: chain Z residue 118 THR Chi-restraints excluded: chain Z residue 134 TYR Chi-restraints excluded: chain Z residue 199 PHE Chi-restraints excluded: chain Z residue 218 LEU Chi-restraints excluded: chain Z residue 219 TYR Chi-restraints excluded: chain Z residue 233 THR Chi-restraints excluded: chain Z residue 235 HIS Chi-restraints excluded: chain Z residue 245 LEU Chi-restraints excluded: chain Z residue 329 ILE Chi-restraints excluded: chain Z residue 392 SER Chi-restraints excluded: chain Z residue 421 ILE Chi-restraints excluded: chain Z residue 447 ILE Chi-restraints excluded: chain Z residue 468 THR Chi-restraints excluded: chain Z residue 512 LEU Chi-restraints excluded: chain Z residue 548 VAL Chi-restraints excluded: chain Z residue 553 ILE Chi-restraints excluded: chain Z residue 557 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 42 ASN Chi-restraints excluded: chain A residue 58 ILE Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 174 PHE Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain C residue 3 TYR Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 35 TYR Chi-restraints excluded: chain C residue 60 PHE Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 419 ASP Chi-restraints excluded: chain C residue 474 VAL Chi-restraints excluded: chain C residue 478 ILE Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 548 PHE Chi-restraints excluded: chain C residue 550 VAL Chi-restraints excluded: chain C residue 562 CYS Chi-restraints excluded: chain C residue 700 LYS Chi-restraints excluded: chain C residue 720 ILE Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 766 CYS Chi-restraints excluded: chain C residue 832 SER Chi-restraints excluded: chain C residue 852 ILE Chi-restraints excluded: chain C residue 856 ILE Chi-restraints excluded: chain C residue 862 SER Chi-restraints excluded: chain C residue 863 SER Chi-restraints excluded: chain C residue 898 THR Chi-restraints excluded: chain C residue 1162 VAL Chi-restraints excluded: chain C residue 1182 LEU Chi-restraints excluded: chain C residue 1189 LYS Chi-restraints excluded: chain C residue 1234 ASP Chi-restraints excluded: chain C residue 1241 TYR Chi-restraints excluded: chain C residue 1242 MET Chi-restraints excluded: chain C residue 1251 VAL Chi-restraints excluded: chain C residue 1266 VAL Chi-restraints excluded: chain C residue 1301 GLU Chi-restraints excluded: chain C residue 1327 MET Chi-restraints excluded: chain C residue 1351 PHE Chi-restraints excluded: chain D residue 32 SER Chi-restraints excluded: chain D residue 56 CYS Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 160 ASP Chi-restraints excluded: chain D residue 225 PHE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 355 VAL Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 471 THR Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 532 SER Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 616 VAL Chi-restraints excluded: chain D residue 782 ASP Chi-restraints excluded: chain D residue 823 VAL Chi-restraints excluded: chain D residue 828 VAL Chi-restraints excluded: chain D residue 846 VAL Chi-restraints excluded: chain D residue 1136 ARG Chi-restraints excluded: chain D residue 1197 VAL Chi-restraints excluded: chain D residue 1203 THR Chi-restraints excluded: chain D residue 1274 LEU Chi-restraints excluded: chain D residue 1295 MET Chi-restraints excluded: chain D residue 1297 ILE Chi-restraints excluded: chain E residue 70 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 379 random chunks: chunk 171 optimal weight: 0.9980 chunk 310 optimal weight: 9.9990 chunk 358 optimal weight: 2.9990 chunk 246 optimal weight: 5.9990 chunk 64 optimal weight: 0.0270 chunk 251 optimal weight: 1.9990 chunk 305 optimal weight: 0.2980 chunk 108 optimal weight: 6.9990 chunk 154 optimal weight: 0.0970 chunk 72 optimal weight: 9.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 557 HIS C 689 GLN ** C1122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1226 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.153647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.116233 restraints weight = 55451.644| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.90 r_work: 0.3318 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31054 Z= 0.116 Angle : 0.630 13.904 42289 Z= 0.326 Chirality : 0.042 0.177 4927 Planarity : 0.004 0.063 5167 Dihedral : 14.728 83.333 4971 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.46 % Allowed : 31.72 % Favored : 64.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.59 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.14), residues: 3715 helix: 0.51 (0.14), residues: 1494 sheet: -1.24 (0.26), residues: 392 loop : -2.39 (0.14), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG Z 528 TYR 0.022 0.001 TYR Z 385 PHE 0.044 0.001 PHE M 196 TRP 0.011 0.001 TRP C 183 HIS 0.005 0.001 HIS Z 364 Details of bonding type rmsd covalent geometry : bond 0.00262 (31046) covalent geometry : angle 0.62834 (42277) hydrogen bonds : bond 0.03329 ( 1194) hydrogen bonds : angle 4.36711 ( 3334) metal coordination : bond 0.00341 ( 8) metal coordination : angle 2.98277 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7526.52 seconds wall clock time: 129 minutes 26.74 seconds (7766.74 seconds total)