Starting phenix.real_space_refine on Fri Mar 6 16:49:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psv_20465/03_2026/6psv_20465_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psv_20465/03_2026/6psv_20465.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6psv_20465/03_2026/6psv_20465_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psv_20465/03_2026/6psv_20465_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6psv_20465/03_2026/6psv_20465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psv_20465/03_2026/6psv_20465.map" } resolution = 3.5 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= 0.000 sd= 0.007 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 3 6.06 5 P 105 5.49 5 Mg 1 5.21 5 S 136 5.16 5 C 19976 2.51 5 N 5696 2.21 5 O 6414 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.02s 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: 32331 Number of models: 1 Model: "" Number of chains: 14 Chain: "N" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 571 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 4, 'TRANS': 67} Chain: "G" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1761 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 218} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1664 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 10564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10564 Classifications: {'peptide': 1340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 10466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10466 Classifications: {'peptide': 1345} Link IDs: {'CIS': 2, 'PTRANS': 55, 'TRANS': 1287} Chain breaks: 2 Chain: "K" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "L" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3846 Classifications: {'peptide': 474} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 14, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "O" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1128 Classifications: {'DNA': 55} Link IDs: {'rna3p': 54} Chain breaks: 1 Chain: "P" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1020 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "M" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 572 Classifications: {'peptide': 73} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 68} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1, '1N7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 1, ' ZN': 2, '1N7': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'1N7': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'1N7:plan-1': 1} Unresolved non-hydrogen planarities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 281 SG CYS N 37 50.579 54.739 30.098 1.00 53.11 S ATOM 438 SG CYS N 58 51.962 57.203 27.800 1.00 40.93 S ATOM 460 SG CYS N 61 49.500 57.964 30.426 1.00 43.50 S ATOM 15009 SG CYS J 70 77.842 102.200 115.823 1.00 35.44 S ATOM 15023 SG CYS J 72 75.881 105.102 115.833 1.00 36.70 S ATOM 15131 SG CYS J 85 75.065 102.412 118.264 1.00 38.52 S ATOM 15155 SG CYS J 88 73.565 102.763 114.576 1.00 37.51 S ATOM 20843 SG CYS J 814 70.542 40.018 89.557 1.00 26.84 S ATOM 21408 SG CYS J 888 70.378 43.955 88.327 1.00 18.79 S ATOM 21459 SG CYS J 895 73.507 41.742 89.304 1.00 14.85 S ATOM 21480 SG CYS J 898 71.647 40.496 86.308 1.00 16.21 S Time building chain proxies: 6.40, per 1000 atoms: 0.20 Number of scatterers: 32331 At special positions: 0 Unit cell: (159.9, 154.7, 169, 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 3 29.99 S 136 16.00 P 105 15.00 Mg 1 11.99 O 6414 8.00 N 5696 7.00 C 19976 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 72 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 895 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 814 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " Number of angles added : 12 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7116 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 52 sheets defined 42.3% alpha, 13.3% beta 48 base pairs and 84 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'N' and resid 3 through 26 removed outlier: 3.512A pdb=" N SER N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLY N 19 " --> pdb=" O LEU N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 52 Processing helix chain 'N' and resid 58 through 71 Processing helix chain 'G' and resid 34 through 50 Processing helix chain 'G' and resid 77 through 80 Processing helix chain 'G' and resid 81 through 86 Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.020A pdb=" N GLN G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU G 234 " --> pdb=" O ALA G 230 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 4.081A pdb=" N THR H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.584A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 115 No H-bonds generated for 'chain 'H' and resid 113 through 115' Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.575A pdb=" N ARG H 218 " --> pdb=" O GLU H 214 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN H 227 " --> pdb=" O ILE H 223 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU H 228 " --> pdb=" O LEU H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 229 through 231 No H-bonds generated for 'chain 'H' and resid 229 through 231' Processing helix chain 'I' and resid 4 through 8 removed outlier: 3.638A pdb=" N LYS I 8 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 39 removed outlier: 3.655A pdb=" N LEU I 32 " --> pdb=" O LEU I 28 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 57 removed outlier: 3.528A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.446A pdb=" N LEU I 210 " --> pdb=" O ALA I 206 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 225 Processing helix chain 'I' and resid 243 through 247 removed outlier: 3.500A pdb=" N ARG I 247 " --> pdb=" O GLU I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 280 removed outlier: 3.880A pdb=" N ILE I 274 " --> pdb=" O THR I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 288 through 293 Processing helix chain 'I' and resid 318 through 327 Processing helix chain 'I' and resid 345 through 354 removed outlier: 3.870A pdb=" N GLU I 349 " --> pdb=" O PRO I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 358 through 371 Processing helix chain 'I' and resid 377 through 391 removed outlier: 3.596A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER I 391 " --> pdb=" O ASN I 387 " (cutoff:3.500A) Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 438 removed outlier: 4.490A pdb=" N ILE I 425 " --> pdb=" O SER I 421 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ILE I 426 " --> pdb=" O LYS I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 4.153A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 Processing helix chain 'I' and resid 520 through 525 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.756A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 614 removed outlier: 3.720A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ASN I 613 " --> pdb=" O ILE I 609 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TYR I 614 " --> pdb=" O GLU I 610 " (cutoff:3.500A) Processing helix chain 'I' and resid 648 through 650 No H-bonds generated for 'chain 'I' and resid 648 through 650' Processing helix chain 'I' and resid 675 through 686 Processing helix chain 'I' and resid 687 through 689 No H-bonds generated for 'chain 'I' and resid 687 through 689' Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 738 through 741 Processing helix chain 'I' and resid 820 through 825 Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.748A pdb=" N SER I 863 " --> pdb=" O ALA I 860 " (cutoff:3.500A) Processing helix chain 'I' and resid 896 through 906 Processing helix chain 'I' and resid 942 through 981 removed outlier: 4.272A pdb=" N ILE I 966 " --> pdb=" O GLU I 962 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU I 967 " --> pdb=" O GLU I 963 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA I 981 " --> pdb=" O ALA I 977 " (cutoff:3.500A) Processing helix chain 'I' and resid 985 through 990 removed outlier: 3.554A pdb=" N ASP I 990 " --> pdb=" O ALA I 986 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 998 removed outlier: 3.512A pdb=" N LEU I 998 " --> pdb=" O ASP I 995 " (cutoff:3.500A) Processing helix chain 'I' and resid 1006 through 1037 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.244A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1130 Processing helix chain 'I' and resid 1138 through 1151 removed outlier: 3.843A pdb=" N GLU I1143 " --> pdb=" O ALA I1139 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU I1151 " --> pdb=" O ARG I1147 " (cutoff:3.500A) Processing helix chain 'I' and resid 1165 through 1176 removed outlier: 3.721A pdb=" N ARG I1171 " --> pdb=" O GLU I1167 " (cutoff:3.500A) Processing helix chain 'I' and resid 1185 through 1189 removed outlier: 4.021A pdb=" N GLY I1189 " --> pdb=" O VAL I1186 " (cutoff:3.500A) Processing helix chain 'I' and resid 1191 through 1202 removed outlier: 3.619A pdb=" N GLY I1202 " --> pdb=" O LEU I1198 " (cutoff:3.500A) Processing helix chain 'I' and resid 1238 through 1243 removed outlier: 3.788A pdb=" N LYS I1242 " --> pdb=" O LEU I1238 " (cutoff:3.500A) Processing helix chain 'I' and resid 1272 through 1281 removed outlier: 4.207A pdb=" N LEU I1278 " --> pdb=" O GLU I1274 " (cutoff:3.500A) Processing helix chain 'I' and resid 1283 through 1291 removed outlier: 3.529A pdb=" N LEU I1287 " --> pdb=" O ALA I1283 " (cutoff:3.500A) Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.504A pdb=" N TYR I1305 " --> pdb=" O ARG I1301 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS I1306 " --> pdb=" O THR I1302 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1332 removed outlier: 3.547A pdb=" N ASN I1324 " --> pdb=" O PRO I1320 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 removed outlier: 3.678A pdb=" N SER J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 63 Processing helix chain 'J' and resid 94 through 100 removed outlier: 3.566A pdb=" N VAL J 97 " --> pdb=" O GLN J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 127 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 172 Processing helix chain 'J' and resid 180 through 191 removed outlier: 3.518A pdb=" N ILE J 185 " --> pdb=" O GLY J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 194 through 208 Processing helix chain 'J' and resid 212 through 230 Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 264 through 286 Processing helix chain 'J' and resid 288 through 308 removed outlier: 3.642A pdb=" N GLU J 301 " --> pdb=" O ARG J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 342 Processing helix chain 'J' and resid 370 through 377 removed outlier: 3.648A pdb=" N GLU J 375 " --> pdb=" O LYS J 371 " (cutoff:3.500A) Processing helix chain 'J' and resid 377 through 389 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 3.518A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) Processing helix chain 'J' and resid 430 through 432 No H-bonds generated for 'chain 'J' and resid 430 through 432' Processing helix chain 'J' and resid 453 through 458 Processing helix chain 'J' and resid 473 through 483 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 504 through 514 Processing helix chain 'J' and resid 529 through 538 removed outlier: 3.605A pdb=" N ALA J 533 " --> pdb=" O GLY J 529 " (cutoff:3.500A) Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.851A pdb=" N MET J 581 " --> pdb=" O ALA J 577 " (cutoff:3.500A) Processing helix chain 'J' and resid 588 through 592 Processing helix chain 'J' and resid 597 through 613 Processing helix chain 'J' and resid 614 through 634 removed outlier: 4.359A pdb=" N ASP J 622 " --> pdb=" O VAL J 618 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET J 625 " --> pdb=" O ALA J 621 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLY J 628 " --> pdb=" O ILE J 624 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 671 Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.327A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 728 removed outlier: 3.706A pdb=" N ALA J 726 " --> pdb=" O ILE J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 768 through 787 removed outlier: 3.503A pdb=" N SER J 775 " --> pdb=" O GLN J 771 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU J 783 " --> pdb=" O ALA J 779 " (cutoff:3.500A) Processing helix chain 'J' and resid 789 through 804 removed outlier: 3.659A pdb=" N SER J 793 " --> pdb=" O LYS J 789 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY J 794 " --> pdb=" O THR J 790 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N TYR J 795 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ARG J 798 " --> pdb=" O GLY J 794 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 Processing helix chain 'J' and resid 865 through 875 removed outlier: 3.831A pdb=" N ASN J 875 " --> pdb=" O LEU J 871 " (cutoff:3.500A) Processing helix chain 'J' and resid 896 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 926 through 929 Processing helix chain 'J' and resid 1138 through 1146 Processing helix chain 'J' and resid 1216 through 1224 Processing helix chain 'J' and resid 1225 through 1245 removed outlier: 3.820A pdb=" N ARG J1231 " --> pdb=" O HIS J1227 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN J1235 " --> pdb=" O ARG J1231 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN J1244 " --> pdb=" O VAL J1240 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.535A pdb=" N GLU J1254 " --> pdb=" O ASP J1250 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL J1255 " --> pdb=" O LYS J1251 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE J1256 " --> pdb=" O HIS J1252 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN J1259 " --> pdb=" O VAL J1255 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 3.754A pdb=" N ASN J1289 " --> pdb=" O VAL J1285 " (cutoff:3.500A) Processing helix chain 'J' and resid 1310 through 1315 removed outlier: 3.691A pdb=" N ALA J1315 " --> pdb=" O LYS J1311 " (cutoff:3.500A) Processing helix chain 'J' and resid 1319 through 1326 removed outlier: 4.185A pdb=" N PHE J1325 " --> pdb=" O SER J1321 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN J1326 " --> pdb=" O ALA J1322 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.630A pdb=" N ALA J1335 " --> pdb=" O VAL J1331 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL J1337 " --> pdb=" O THR J1333 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1353 removed outlier: 3.563A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1373 removed outlier: 4.277A pdb=" N ALA J1364 " --> pdb=" O GLY J1360 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR J1365 " --> pdb=" O THR J1361 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 13 Processing helix chain 'K' and resid 17 through 32 Processing helix chain 'K' and resid 45 through 56 Processing helix chain 'K' and resid 61 through 76 Processing helix chain 'L' and resid 96 through 107 Processing helix chain 'L' and resid 114 through 136 Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.818A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 157 through 161 removed outlier: 3.860A pdb=" N LEU L 161 " --> pdb=" O LEU L 158 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 233 removed outlier: 3.503A pdb=" N ALA L 217 " --> pdb=" O ASP L 213 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP L 233 " --> pdb=" O VAL L 229 " (cutoff:3.500A) Processing helix chain 'L' and resid 244 through 256 removed outlier: 3.595A pdb=" N GLU L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) Processing helix chain 'L' and resid 257 through 259 No H-bonds generated for 'chain 'L' and resid 257 through 259' Processing helix chain 'L' and resid 262 through 289 Processing helix chain 'L' and resid 298 through 307 Processing helix chain 'L' and resid 326 through 330 Processing helix chain 'L' and resid 333 through 352 Processing helix chain 'L' and resid 354 through 392 removed outlier: 5.183A pdb=" N ARG L 385 " --> pdb=" O GLU L 381 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N LEU L 386 " --> pdb=" O ALA L 382 " (cutoff:3.500A) Processing helix chain 'L' and resid 400 through 418 removed outlier: 4.033A pdb=" N ASP L 417 " --> pdb=" O MET L 413 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS L 418 " --> pdb=" O LYS L 414 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.509A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 446 removed outlier: 3.721A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.579A pdb=" N ARG L 468 " --> pdb=" O ASN L 464 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN L 469 " --> pdb=" O ARG L 465 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 492 through 501 Processing helix chain 'L' and resid 518 through 523 removed outlier: 3.503A pdb=" N ASP L 521 " --> pdb=" O HIS L 518 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE L 522 " --> pdb=" O LEU L 519 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE L 523 " --> pdb=" O GLY L 520 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 518 through 523' Processing helix chain 'L' and resid 530 through 551 removed outlier: 3.508A pdb=" N ALA L 535 " --> pdb=" O PRO L 531 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY L 550 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 578 Processing helix chain 'L' and resid 583 through 600 removed outlier: 3.789A pdb=" N ILE L 587 " --> pdb=" O THR L 583 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS L 593 " --> pdb=" O GLN L 589 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N HIS L 600 " --> pdb=" O ARG L 596 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 611 removed outlier: 3.608A pdb=" N LEU L 611 " --> pdb=" O LEU L 607 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 254 Processing helix chain 'M' and resid 263 through 274 Processing helix chain 'M' and resid 277 through 282 Processing helix chain 'M' and resid 285 through 291 Processing helix chain 'M' and resid 296 through 309 removed outlier: 3.590A pdb=" N LEU M 300 " --> pdb=" O GLY M 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 13 through 17 removed outlier: 4.218A pdb=" N THR G 27 " --> pdb=" O VAL G 14 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE G 16 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LYS G 25 " --> pdb=" O ILE G 16 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N HIS G 23 " --> pdb=" O THR G 207 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N THR G 207 " --> pdb=" O HIS G 23 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS G 25 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N MET G 205 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N THR G 27 " --> pdb=" O ILE G 203 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE G 203 " --> pdb=" O THR G 27 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS G 200 " --> pdb=" O VAL G 187 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL G 187 " --> pdb=" O LYS G 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL G 202 " --> pdb=" O TYR G 185 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N TYR G 185 " --> pdb=" O VAL G 202 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 115 through 116 removed outlier: 4.569A pdb=" N THR G 101 " --> pdb=" O THR G 116 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ARG G 143 " --> pdb=" O VAL G 59 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N VAL G 59 " --> pdb=" O ARG G 143 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LYS G 145 " --> pdb=" O THR G 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA4, first strand: chain 'G' and resid 108 through 111 Processing sheet with id=AA5, first strand: chain 'H' and resid 23 through 31 removed outlier: 6.275A pdb=" N HIS H 23 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR H 207 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 23 through 31 removed outlier: 6.275A pdb=" N HIS H 23 " --> pdb=" O THR H 207 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N THR H 207 " --> pdb=" O HIS H 23 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LYS H 25 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N MET H 205 " --> pdb=" O LYS H 25 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR H 27 " --> pdb=" O ILE H 203 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE H 203 " --> pdb=" O THR H 27 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU H 29 " --> pdb=" O LEU H 201 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU H 201 " --> pdb=" O GLU H 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 54 through 61 removed outlier: 5.561A pdb=" N VAL H 56 " --> pdb=" O GLN H 147 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLN H 147 " --> pdb=" O VAL H 56 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AA9, first strand: chain 'H' and resid 109 through 111 Processing sheet with id=AB1, first strand: chain 'H' and resid 152 through 153 Processing sheet with id=AB2, first strand: chain 'I' and resid 13 through 14 removed outlier: 6.698A pdb=" N LYS I 13 " --> pdb=" O ALA I1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.402A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU I 102 " --> pdb=" O ILE I 117 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ILE I 117 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 5.402A pdb=" N SER I 66 " --> pdb=" O TYR I 105 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR I 105 " --> pdb=" O SER I 66 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LEU I 68 " --> pdb=" O VAL I 103 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N VAL I 103 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N TYR I 70 " --> pdb=" O ARG I 101 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG I 101 " --> pdb=" O TYR I 70 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER I 72 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 136 through 137 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 454 removed outlier: 6.647A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 154 through 158 Processing sheet with id=AB8, first strand: chain 'I' and resid 187 through 188 Processing sheet with id=AB9, first strand: chain 'I' and resid 284 through 286 removed outlier: 5.308A pdb=" N ILE I 229 " --> pdb=" O GLU I 240 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.716A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 296 through 297 removed outlier: 3.916A pdb=" N MET I 315 " --> pdb=" O VAL I 297 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.498A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC5, first strand: chain 'I' and resid 633 through 636 Processing sheet with id=AC6, first strand: chain 'I' and resid 716 through 717 removed outlier: 6.550A pdb=" N ALA I 716 " --> pdb=" O LEU I 783 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 749 through 752 removed outlier: 6.099A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 757 through 758 Processing sheet with id=AC9, first strand: chain 'I' and resid 798 through 804 removed outlier: 4.299A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 798 through 804 removed outlier: 4.299A pdb=" N THR I1226 " --> pdb=" O PHE I 804 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 816 through 819 removed outlier: 7.400A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE I1079 " --> pdb=" O ILE I 816 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL I 818 " --> pdb=" O ILE I1079 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 846 through 847 removed outlier: 6.219A pdb=" N THR I 830 " --> pdb=" O LYS I1057 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS I1057 " --> pdb=" O THR I 830 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS I 832 " --> pdb=" O ALA I1055 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA I1055 " --> pdb=" O HIS I 832 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLN I 834 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR I1053 " --> pdb=" O GLN I 834 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU I 836 " --> pdb=" O LYS I1051 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LYS I1051 " --> pdb=" O LEU I 836 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS I 838 " --> pdb=" O ILE I1049 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE I1049 " --> pdb=" O CYS I 838 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER I 840 " --> pdb=" O LEU I1047 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP I 930 " --> pdb=" O TYR I1053 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA I1055 " --> pdb=" O VAL I 928 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL I 928 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 882 through 884 removed outlier: 6.619A pdb=" N LEU I 918 " --> pdb=" O LEU I 883 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 887 through 888 Processing sheet with id=AD6, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD7, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 7.396A pdb=" N ILE J 447 " --> pdb=" O ARG J 352 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL J 354 " --> pdb=" O ILE J 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 1268 through 1269 Processing sheet with id=AD9, first strand: chain 'I' and resid 1335 through 1337 Processing sheet with id=AE1, first strand: chain 'J' and resid 103 through 112 removed outlier: 3.541A pdb=" N LEU J 107 " --> pdb=" O THR J 240 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 9.893A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 9.636A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 144 through 145 Processing sheet with id=AE3, first strand: chain 'J' and resid 252 through 254 removed outlier: 6.074A pdb=" N PHE J 260 " --> pdb=" O ILE L 505 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 526 through 527 removed outlier: 7.011A pdb=" N LEU J 527 " --> pdb=" O ARG J 551 " (cutoff:3.500A) removed outlier: 9.185A pdb=" N THR J 553 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE6, first strand: chain 'J' and resid 746 through 748 removed outlier: 4.671A pdb=" N MET J 747 " --> pdb=" O ILE J 755 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 809 through 811 Processing sheet with id=AE8, first strand: chain 'J' and resid 821 through 822 Processing sheet with id=AE9, first strand: chain 'J' and resid 848 through 849 removed outlier: 6.845A pdb=" N VAL J 848 " --> pdb=" O LEU J 857 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 991 through 996 removed outlier: 3.858A pdb=" N GLU J 981 " --> pdb=" O SER J 961 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER J 961 " --> pdb=" O GLU J 981 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'J' and resid 965 through 967 Processing sheet with id=AF3, first strand: chain 'J' and resid 1098 through 1100 Processing sheet with id=AF4, first strand: chain 'J' and resid 1046 through 1048 removed outlier: 3.686A pdb=" N VAL J1060 " --> pdb=" O THR J1047 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU J1059 " --> pdb=" O VAL J1107 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 1089 through 1090 removed outlier: 3.717A pdb=" N ILE J1090 " --> pdb=" O THR J1093 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'J' and resid 1162 through 1165 removed outlier: 3.922A pdb=" N TYR J1186 " --> pdb=" O ILE J1177 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'J' and resid 1279 through 1281 1228 hydrogen bonds defined for protein. 3468 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 224 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 84 stacking parallelities Total time for adding SS restraints: 7.32 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10526 1.34 - 1.46: 7293 1.46 - 1.59: 14750 1.59 - 1.71: 222 1.71 - 1.84: 244 Bond restraints: 33035 Sorted by residual: bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.838 -0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.837 -0.305 2.00e-02 2.50e+03 2.32e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.830 -0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C19 1N7 N 102 " pdb=" C3 1N7 N 102 " ideal model delta sigma weight residual 1.532 1.820 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C3 1N7 L 701 " pdb=" C4 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.731 -0.199 2.00e-02 2.50e+03 9.94e+01 ... (remaining 33030 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.60: 43890 2.60 - 5.19: 1044 5.19 - 7.79: 119 7.79 - 10.38: 21 10.38 - 12.98: 7 Bond angle restraints: 45081 Sorted by residual: angle pdb=" N ASP I 516 " pdb=" CA ASP I 516 " pdb=" C ASP I 516 " ideal model delta sigma weight residual 109.96 99.93 10.03 1.50e+00 4.44e-01 4.47e+01 angle pdb=" C ILE I1096 " pdb=" N VAL I1097 " pdb=" CA VAL I1097 " ideal model delta sigma weight residual 122.96 117.39 5.57 9.50e-01 1.11e+00 3.44e+01 angle pdb=" C GLN H 194 " pdb=" N ARG H 195 " pdb=" CA ARG H 195 " ideal model delta sigma weight residual 121.70 131.55 -9.85 1.80e+00 3.09e-01 2.99e+01 angle pdb=" N GLY I 449 " pdb=" CA GLY I 449 " pdb=" C GLY I 449 " ideal model delta sigma weight residual 115.61 106.36 9.25 1.74e+00 3.30e-01 2.83e+01 angle pdb=" N VAL I1275 " pdb=" CA VAL I1275 " pdb=" C VAL I1275 " ideal model delta sigma weight residual 111.81 107.30 4.51 8.60e-01 1.35e+00 2.75e+01 ... (remaining 45076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.47: 17919 25.47 - 50.94: 2001 50.94 - 76.42: 363 76.42 - 101.89: 32 101.89 - 127.36: 4 Dihedral angle restraints: 20319 sinusoidal: 9285 harmonic: 11034 Sorted by residual: dihedral pdb=" CA LEU L 110 " pdb=" C LEU L 110 " pdb=" N LEU L 111 " pdb=" CA LEU L 111 " ideal model delta harmonic sigma weight residual 180.00 137.35 42.65 0 5.00e+00 4.00e-02 7.28e+01 dihedral pdb=" CA ARG H 12 " pdb=" C ARG H 12 " pdb=" N LEU H 13 " pdb=" CA LEU H 13 " ideal model delta harmonic sigma weight residual 0.00 38.96 -38.96 0 5.00e+00 4.00e-02 6.07e+01 dihedral pdb=" CA ASP I 81 " pdb=" C ASP I 81 " pdb=" N VAL I 82 " pdb=" CA VAL I 82 " ideal model delta harmonic sigma weight residual -180.00 -145.07 -34.93 0 5.00e+00 4.00e-02 4.88e+01 ... (remaining 20316 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3870 0.056 - 0.111: 1110 0.111 - 0.167: 166 0.167 - 0.223: 14 0.223 - 0.279: 8 Chirality restraints: 5168 Sorted by residual: chirality pdb=" C19 1N7 N 102 " pdb=" C18 1N7 N 102 " pdb=" C2 1N7 N 102 " pdb=" C3 1N7 N 102 " both_signs ideal model delta sigma weight residual False -2.53 -2.81 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C15 1N7 J1504 " pdb=" C14 1N7 J1504 " pdb=" C16 1N7 J1504 " pdb=" C2 1N7 J1504 " both_signs ideal model delta sigma weight residual False -2.47 -2.74 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C19 1N7 I1401 " pdb=" C18 1N7 I1401 " pdb=" C2 1N7 I1401 " pdb=" C3 1N7 I1401 " both_signs ideal model delta sigma weight residual False -2.53 -2.79 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 5165 not shown) Planarity restraints: 5502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL I1103 " -0.050 5.00e-02 4.00e+02 7.48e-02 8.94e+00 pdb=" N PRO I1104 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO I1104 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO I1104 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN I 519 " 0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO I 520 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO I 520 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO I 520 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 368 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO J 369 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO J 369 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 369 " -0.033 5.00e-02 4.00e+02 ... (remaining 5499 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 314 2.55 - 3.14: 27998 3.14 - 3.72: 50556 3.72 - 4.31: 72431 4.31 - 4.90: 117582 Nonbonded interactions: 268881 Sorted by model distance: nonbonded pdb=" OD1 ASP J 462 " pdb="MG MG J1501 " model vdw 1.959 2.170 nonbonded pdb=" OH TYR I 301 " pdb=" O ARG I 332 " model vdw 2.019 3.040 nonbonded pdb=" O TRP J 115 " pdb=" OG SER J 119 " model vdw 2.054 3.040 nonbonded pdb=" OG1 THR M 263 " pdb=" OE1 GLU M 302 " model vdw 2.060 3.040 nonbonded pdb=" O LYS I 593 " pdb=" OG1 THR I 600 " model vdw 2.081 3.040 ... (remaining 268876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'G' and ((resid 7 and (name N or name CA or name C or name O or name CB ) \ ) or resid 8 through 11 or (resid 12 and (name N or name CA or name C or name O \ or name CB )) or resid 13 through 94 or (resid 95 and (name N or name CA or name \ C or name O or name CB )) or resid 96 or (resid 97 and (name N or name CA or na \ me C or name O or name CB )) or resid 98 through 158 or resid 171 through 233 or \ (resid 234 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'H' and (resid 7 through 228 or (resid 229 through 230 and (name N or nam \ e CA or name C or name O or name CB )) or resid 231 through 232 or (resid 233 th \ rough 234 and (name N or name CA or name C or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 37.730 Find NCS groups from input model: 0.290 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.011 0.510 33047 Z= 0.516 Angle : 1.026 30.025 45093 Z= 0.568 Chirality : 0.052 0.279 5168 Planarity : 0.005 0.075 5502 Dihedral : 20.031 127.359 13203 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 40.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 11.12 % Favored : 88.75 % Rotamer: Outliers : 11.23 % Allowed : 21.05 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.16 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -4.43 (0.11), residues: 3804 helix: -2.46 (0.10), residues: 1508 sheet: -3.54 (0.20), residues: 436 loop : -3.20 (0.13), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 610 TYR 0.030 0.003 TYR I 605 PHE 0.025 0.003 PHE H 35 TRP 0.013 0.002 TRP L 434 HIS 0.011 0.002 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.01105 (33035) covalent geometry : angle 1.00120 (45081) hydrogen bonds : bond 0.15861 ( 1326) hydrogen bonds : angle 7.67589 ( 3692) metal coordination : bond 0.16633 ( 11) metal coordination : angle 13.70565 ( 12) Misc. bond : bond 0.00139 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 367 poor density : 530 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 65 GLN cc_start: 0.8389 (tp40) cc_final: 0.7247 (tm-30) REVERT: G 85 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8552 (mt) REVERT: H 16 ILE cc_start: 0.8549 (OUTLIER) cc_final: 0.8292 (tt) REVERT: H 23 HIS cc_start: 0.7715 (t-90) cc_final: 0.7344 (t-170) REVERT: H 123 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8298 (mm) REVERT: H 188 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: I 121 GLU cc_start: 0.7622 (tp30) cc_final: 0.7380 (tp30) REVERT: I 211 ARG cc_start: 0.6115 (mmm160) cc_final: 0.5755 (mmm160) REVERT: I 225 PHE cc_start: 0.4956 (m-80) cc_final: 0.4631 (m-80) REVERT: I 385 PHE cc_start: 0.5363 (OUTLIER) cc_final: 0.4551 (p90) REVERT: I 407 ARG cc_start: 0.7297 (tpp80) cc_final: 0.6882 (ttm170) REVERT: I 496 LYS cc_start: 0.8504 (mtpp) cc_final: 0.8294 (mmtp) REVERT: I 573 ASN cc_start: 0.8237 (m-40) cc_final: 0.7976 (m-40) REVERT: I 844 LYS cc_start: 0.6641 (pttm) cc_final: 0.6198 (pttp) REVERT: I 955 GLN cc_start: 0.8081 (tp40) cc_final: 0.7732 (tp40) REVERT: I 1180 MET cc_start: 0.9003 (ttt) cc_final: 0.8739 (ttp) REVERT: I 1197 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7449 (tp30) REVERT: J 50 LYS cc_start: 0.8544 (mttt) cc_final: 0.8144 (mttp) REVERT: J 156 ARG cc_start: 0.6484 (ptp-110) cc_final: 0.6253 (ttm170) REVERT: J 164 GLN cc_start: 0.6959 (OUTLIER) cc_final: 0.6755 (pm20) REVERT: J 180 MET cc_start: 0.6707 (mtm) cc_final: 0.6340 (mtm) REVERT: J 314 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.5687 (tpt170) REVERT: J 441 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8264 (mt) REVERT: J 503 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7913 (t) REVERT: J 532 GLU cc_start: 0.7653 (tt0) cc_final: 0.7383 (tt0) REVERT: J 554 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8351 (pt0) REVERT: J 655 SER cc_start: 0.7881 (t) cc_final: 0.7565 (p) REVERT: J 749 LYS cc_start: 0.8291 (mtmt) cc_final: 0.8052 (mtpp) REVERT: J 756 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7131 (tt0) REVERT: J 802 ASP cc_start: 0.7431 (p0) cc_final: 0.7221 (p0) REVERT: J 955 LYS cc_start: 0.6264 (tmtt) cc_final: 0.4838 (ttmt) REVERT: J 995 TYR cc_start: 0.7098 (m-80) cc_final: 0.6874 (m-10) REVERT: J 1015 GLU cc_start: 0.3041 (OUTLIER) cc_final: 0.1435 (mm-30) REVERT: J 1148 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6306 (mtt90) REVERT: J 1203 ARG cc_start: 0.6481 (ttp80) cc_final: 0.6197 (tmt-80) REVERT: J 1244 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7295 (mm110) REVERT: J 1355 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8106 (ptm160) REVERT: K 51 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7571 (mt) REVERT: L 113 ARG cc_start: 0.6763 (tpt90) cc_final: 0.6484 (tpt-90) REVERT: L 114 GLU cc_start: 0.7447 (pm20) cc_final: 0.7241 (pm20) REVERT: L 256 PHE cc_start: 0.5262 (m-10) cc_final: 0.5006 (m-80) REVERT: L 470 MET cc_start: 0.7484 (mtp) cc_final: 0.7141 (mtp) REVERT: L 476 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7023 (ptt90) REVERT: L 524 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7430 (pp20) REVERT: L 548 LEU cc_start: 0.7352 (mt) cc_final: 0.7126 (mt) REVERT: M 284 ARG cc_start: 0.2794 (OUTLIER) cc_final: 0.2581 (mpt-90) outliers start: 367 outliers final: 243 residues processed: 842 average time/residue: 0.2301 time to fit residues: 303.5877 Evaluate side-chains 657 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 262 poor density : 395 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 10 SER Chi-restraints excluded: chain N residue 12 THR Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 20 ILE Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 42 ASN Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 129 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 140 ILE Chi-restraints excluded: chain G residue 147 GLN Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 210 THR Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 78 ILE Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 111 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 123 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain H residue 210 THR Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain H residue 224 LEU Chi-restraints excluded: chain I residue 4 SER Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 23 ASP Chi-restraints excluded: chain I residue 29 SER Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 130 MET Chi-restraints excluded: chain I residue 155 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 348 SER Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain I residue 425 ILE Chi-restraints excluded: chain I residue 428 VAL Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 539 THR Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 561 ILE Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 684 ASN Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 697 LYS Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 741 MET Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 819 SER Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 873 ILE Chi-restraints excluded: chain I residue 902 LEU Chi-restraints excluded: chain I residue 915 ASP Chi-restraints excluded: chain I residue 925 SER Chi-restraints excluded: chain I residue 939 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 984 VAL Chi-restraints excluded: chain I residue 1003 THR Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1036 ILE Chi-restraints excluded: chain I residue 1058 ARG Chi-restraints excluded: chain I residue 1079 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1115 THR Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1182 ILE Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1204 LEU Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1227 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1241 ASP Chi-restraints excluded: chain I residue 1253 LEU Chi-restraints excluded: chain I residue 1254 VAL Chi-restraints excluded: chain I residue 1255 THR Chi-restraints excluded: chain I residue 1308 ILE Chi-restraints excluded: chain I residue 1309 VAL Chi-restraints excluded: chain I residue 1327 LEU Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 67 ASP Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 114 ILE Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 164 GLN Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 205 LEU Chi-restraints excluded: chain J residue 230 SER Chi-restraints excluded: chain J residue 240 THR Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 278 ARG Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 314 ARG Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 386 GLU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 499 ILE Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 517 CYS Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 536 LEU Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 550 VAL Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 554 GLU Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 582 ILE Chi-restraints excluded: chain J residue 601 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 674 THR Chi-restraints excluded: chain J residue 678 ARG Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 762 ASN Chi-restraints excluded: chain J residue 768 ASN Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 775 SER Chi-restraints excluded: chain J residue 786 THR Chi-restraints excluded: chain J residue 789 LYS Chi-restraints excluded: chain J residue 797 THR Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 878 ASP Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 960 LEU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 982 LEU Chi-restraints excluded: chain J residue 997 VAL Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1015 GLU Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1041 ILE Chi-restraints excluded: chain J residue 1046 ILE Chi-restraints excluded: chain J residue 1089 LEU Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1094 ASP Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1116 SER Chi-restraints excluded: chain J residue 1135 THR Chi-restraints excluded: chain J residue 1148 ARG Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1210 ILE Chi-restraints excluded: chain J residue 1226 VAL Chi-restraints excluded: chain J residue 1235 ASN Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1272 SER Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1306 LEU Chi-restraints excluded: chain J residue 1310 THR Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1324 SER Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain J residue 1355 ARG Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 36 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 249 ILE Chi-restraints excluded: chain L residue 261 LEU Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 335 GLU Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 442 SER Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 487 MET Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 524 GLU Chi-restraints excluded: chain L residue 598 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 197 optimal weight: 0.0980 chunk 388 optimal weight: 0.0470 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 30 HIS G 23 HIS G 117 HIS H 84 ASN H 128 HIS H 132 HIS H 186 ASN I 46 GLN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN I 314 ASN I 387 ASN I 463 GLN I 622 ASN I 649 GLN I 677 ASN I 808 ASN I 856 ASN I 965 GLN I1010 GLN I1108 ASN I1116 HIS I1134 GLN I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN J 45 ASN ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 294 ASN J 341 ASN J 488 ASN J 680 ASN J 861 ASN J 875 ASN J 979 ASN J1023 HIS J1126 GLN J1295 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 GLN K 62 GLN L 129 GLN L 309 ASN L 464 ASN L 600 HIS Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.179801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.149618 restraints weight = 43419.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.149386 restraints weight = 96567.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.150098 restraints weight = 83818.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.149910 restraints weight = 53395.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.150461 restraints weight = 45925.668| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 33047 Z= 0.144 Angle : 0.700 11.233 45093 Z= 0.360 Chirality : 0.045 0.323 5168 Planarity : 0.005 0.089 5502 Dihedral : 17.762 128.471 6120 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.52 % Favored : 93.43 % Rotamer: Outliers : 7.13 % Allowed : 24.02 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.89 (0.12), residues: 3804 helix: -0.90 (0.12), residues: 1527 sheet: -2.88 (0.22), residues: 404 loop : -2.59 (0.13), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I1106 TYR 0.018 0.002 TYR I1018 PHE 0.032 0.002 PHE L 306 TRP 0.016 0.002 TRP L 434 HIS 0.010 0.001 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00321 (33035) covalent geometry : angle 0.69759 (45081) hydrogen bonds : bond 0.04690 ( 1326) hydrogen bonds : angle 5.28928 ( 3692) metal coordination : bond 0.00485 ( 11) metal coordination : angle 3.61672 ( 12) Misc. bond : bond 0.00025 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 758 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 233 poor density : 525 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7517 (m-80) cc_final: 0.7210 (m-80) REVERT: G 41 ASN cc_start: 0.8951 (t0) cc_final: 0.8710 (t0) REVERT: G 80 GLU cc_start: 0.8080 (tp30) cc_final: 0.7870 (tp30) REVERT: G 134 THR cc_start: 0.9048 (OUTLIER) cc_final: 0.8774 (m) REVERT: G 231 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.8134 (t80) REVERT: H 16 ILE cc_start: 0.8035 (tt) cc_final: 0.7810 (tt) REVERT: H 23 HIS cc_start: 0.7260 (t-90) cc_final: 0.6943 (t-170) REVERT: H 25 LYS cc_start: 0.8466 (ttmt) cc_final: 0.8263 (ttmt) REVERT: H 65 LEU cc_start: 0.4666 (OUTLIER) cc_final: 0.4272 (tp) REVERT: H 86 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7909 (mtpt) REVERT: I 385 PHE cc_start: 0.5153 (OUTLIER) cc_final: 0.3945 (p90) REVERT: I 515 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8531 (ttm) REVERT: I 573 ASN cc_start: 0.7820 (m-40) cc_final: 0.7614 (m110) REVERT: I 589 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8611 (t) REVERT: I 854 ILE cc_start: 0.8437 (mt) cc_final: 0.8114 (mt) REVERT: I 1292 THR cc_start: 0.8795 (m) cc_final: 0.8505 (p) REVERT: J 18 ASP cc_start: 0.7179 (t0) cc_final: 0.6931 (t0) REVERT: J 156 ARG cc_start: 0.5959 (ptp-110) cc_final: 0.5711 (ttm110) REVERT: J 180 MET cc_start: 0.6718 (mtm) cc_final: 0.6318 (mtm) REVERT: J 200 GLN cc_start: 0.7621 (OUTLIER) cc_final: 0.6877 (mt0) REVERT: J 201 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7426 (mt) REVERT: J 307 LEU cc_start: 0.7714 (mt) cc_final: 0.7269 (mp) REVERT: J 311 ARG cc_start: 0.6606 (tpt90) cc_final: 0.6226 (tpt90) REVERT: J 423 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8547 (mp) REVERT: J 503 SER cc_start: 0.7763 (OUTLIER) cc_final: 0.7365 (t) REVERT: J 532 GLU cc_start: 0.7449 (tt0) cc_final: 0.6825 (tt0) REVERT: J 535 ARG cc_start: 0.8269 (ttp80) cc_final: 0.8023 (ttp80) REVERT: J 624 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8735 (tt) REVERT: J 641 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7404 (tp) REVERT: J 667 GLN cc_start: 0.8338 (mt0) cc_final: 0.7992 (mt0) REVERT: J 749 LYS cc_start: 0.8323 (mtmt) cc_final: 0.8041 (mtpp) REVERT: J 756 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.6951 (tt0) REVERT: J 820 ILE cc_start: 0.8641 (pt) cc_final: 0.8441 (pt) REVERT: J 849 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6170 (mt) REVERT: J 863 LEU cc_start: 0.7380 (tp) cc_final: 0.7056 (tp) REVERT: J 865 HIS cc_start: 0.5240 (m90) cc_final: 0.4377 (m-70) REVERT: J 868 TRP cc_start: 0.6593 (OUTLIER) cc_final: 0.6349 (t-100) REVERT: J 870 ASP cc_start: 0.5672 (m-30) cc_final: 0.5372 (m-30) REVERT: J 925 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7719 (tm-30) REVERT: J 1029 THR cc_start: 0.4858 (OUTLIER) cc_final: 0.4559 (m) REVERT: K 51 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.7828 (mt) REVERT: K 69 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.6136 (ttp-110) REVERT: L 111 LEU cc_start: 0.4433 (OUTLIER) cc_final: 0.4187 (mt) REVERT: L 523 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8737 (mm) REVERT: L 525 ASP cc_start: 0.7328 (t0) cc_final: 0.7123 (t0) REVERT: M 284 ARG cc_start: 0.3022 (OUTLIER) cc_final: 0.1885 (mtt180) REVERT: M 300 LEU cc_start: 0.0743 (OUTLIER) cc_final: -0.0391 (pp) outliers start: 233 outliers final: 107 residues processed: 714 average time/residue: 0.2197 time to fit residues: 249.4195 Evaluate side-chains 530 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 401 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 157 THR Chi-restraints excluded: chain G residue 172 LEU Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 204 GLU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 766 ASN Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 946 LEU Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 1002 LEU Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1113 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1198 LEU Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 201 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 641 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 849 LEU Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1029 THR Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1235 ASN Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1344 LEU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 141 ILE Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 523 ILE Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 123 optimal weight: 0.9980 chunk 276 optimal weight: 7.9990 chunk 333 optimal weight: 9.9990 chunk 235 optimal weight: 1.9990 chunk 273 optimal weight: 7.9990 chunk 69 optimal weight: 0.3980 chunk 260 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 262 optimal weight: 0.0070 chunk 21 optimal weight: 0.0000 chunk 27 optimal weight: 5.9990 overall best weight: 0.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN I1061 GLN I1108 ASN I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 335 GLN ** J 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1244 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.181983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.152035 restraints weight = 43427.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.151237 restraints weight = 98173.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.151952 restraints weight = 86980.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151829 restraints weight = 54066.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.152335 restraints weight = 48265.359| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33047 Z= 0.123 Angle : 0.632 11.338 45093 Z= 0.325 Chirality : 0.043 0.287 5168 Planarity : 0.005 0.068 5502 Dihedral : 17.050 131.460 5789 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.31 % Favored : 93.64 % Rotamer: Outliers : 5.08 % Allowed : 26.56 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.05 (0.13), residues: 3804 helix: -0.15 (0.13), residues: 1549 sheet: -2.44 (0.22), residues: 420 loop : -2.18 (0.14), residues: 1835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 281 TYR 0.018 0.001 TYR I1018 PHE 0.021 0.002 PHE L 302 TRP 0.016 0.001 TRP L 326 HIS 0.005 0.001 HIS G 160 Details of bonding type rmsd covalent geometry : bond 0.00269 (33035) covalent geometry : angle 0.63094 (45081) hydrogen bonds : bond 0.04201 ( 1326) hydrogen bonds : angle 4.80596 ( 3692) metal coordination : bond 0.00305 ( 11) metal coordination : angle 2.33979 ( 12) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 461 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7190 (m-80) cc_final: 0.6575 (m-80) REVERT: G 80 GLU cc_start: 0.8017 (tp30) cc_final: 0.7787 (tp30) REVERT: H 13 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7738 (pp) REVERT: H 16 ILE cc_start: 0.7899 (tt) cc_final: 0.7645 (tt) REVERT: H 23 HIS cc_start: 0.7283 (t-90) cc_final: 0.7046 (t-170) REVERT: H 65 LEU cc_start: 0.4564 (OUTLIER) cc_final: 0.4183 (tp) REVERT: I 47 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.6309 (p90) REVERT: I 83 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6726 (mp10) REVERT: I 85 CYS cc_start: 0.7350 (OUTLIER) cc_final: 0.7131 (t) REVERT: I 116 ASP cc_start: 0.3976 (OUTLIER) cc_final: 0.3660 (m-30) REVERT: I 515 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8516 (ttm) REVERT: I 589 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8412 (m) REVERT: I 915 ASP cc_start: 0.7007 (t0) cc_final: 0.6724 (t70) REVERT: I 1220 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8190 (tt0) REVERT: J 18 ASP cc_start: 0.7045 (t0) cc_final: 0.6840 (t0) REVERT: J 148 GLU cc_start: 0.7109 (tt0) cc_final: 0.6506 (tm-30) REVERT: J 151 MET cc_start: 0.4420 (tpt) cc_final: 0.4061 (tpt) REVERT: J 156 ARG cc_start: 0.5806 (ptp-110) cc_final: 0.5383 (ttp-110) REVERT: J 200 GLN cc_start: 0.6849 (OUTLIER) cc_final: 0.6562 (mt0) REVERT: J 343 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8301 (mm) REVERT: J 479 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8166 (mt-10) REVERT: J 698 MET cc_start: 0.8223 (tpp) cc_final: 0.7886 (mmm) REVERT: J 731 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7373 (tpt90) REVERT: J 756 GLU cc_start: 0.7485 (pt0) cc_final: 0.6955 (tt0) REVERT: J 822 MET cc_start: 0.7221 (tpp) cc_final: 0.6778 (ttm) REVERT: J 849 LEU cc_start: 0.6469 (mm) cc_final: 0.6099 (mt) REVERT: J 863 LEU cc_start: 0.7012 (tp) cc_final: 0.6575 (tp) REVERT: J 865 HIS cc_start: 0.5260 (m90) cc_final: 0.4807 (m170) REVERT: J 925 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7561 (tm-30) REVERT: K 51 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7840 (mt) REVERT: K 65 ASP cc_start: 0.6470 (t0) cc_final: 0.6255 (t0) REVERT: L 110 LEU cc_start: 0.5574 (OUTLIER) cc_final: 0.5366 (pp) REVERT: L 111 LEU cc_start: 0.4142 (OUTLIER) cc_final: 0.3799 (mt) REVERT: L 525 ASP cc_start: 0.7156 (t0) cc_final: 0.6939 (t0) REVERT: M 252 ILE cc_start: 0.2495 (OUTLIER) cc_final: 0.2156 (pt) REVERT: M 284 ARG cc_start: 0.3163 (OUTLIER) cc_final: 0.2227 (mtt90) outliers start: 166 outliers final: 89 residues processed: 594 average time/residue: 0.2182 time to fit residues: 207.1479 Evaluate side-chains 474 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 368 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 36 GLN Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1113 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1220 GLN Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 486 SER Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 731 ARG Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1002 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1235 ASN Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 252 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 165 optimal weight: 4.9990 chunk 39 optimal weight: 0.1980 chunk 333 optimal weight: 5.9990 chunk 209 optimal weight: 0.7980 chunk 364 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 143 optimal weight: 0.3980 chunk 180 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 66 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 824 GLN I 856 ASN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1136 GLN J 504 GLN J 805 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.180963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.150243 restraints weight = 43073.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.149290 restraints weight = 96042.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.150201 restraints weight = 87280.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.150099 restraints weight = 54559.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.150512 restraints weight = 48349.162| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33047 Z= 0.120 Angle : 0.611 11.112 45093 Z= 0.313 Chirality : 0.042 0.251 5168 Planarity : 0.004 0.079 5502 Dihedral : 16.764 131.554 5741 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.98 % Rotamer: Outliers : 5.39 % Allowed : 26.38 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.56 (0.13), residues: 3804 helix: 0.28 (0.13), residues: 1537 sheet: -2.08 (0.24), residues: 408 loop : -1.94 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 363 TYR 0.017 0.001 TYR I1018 PHE 0.017 0.001 PHE L 302 TRP 0.009 0.001 TRP L 326 HIS 0.004 0.001 HIS G 160 Details of bonding type rmsd covalent geometry : bond 0.00270 (33035) covalent geometry : angle 0.61055 (45081) hydrogen bonds : bond 0.03977 ( 1326) hydrogen bonds : angle 4.59378 ( 3692) metal coordination : bond 0.00351 ( 11) metal coordination : angle 1.96853 ( 12) Misc. bond : bond 0.00045 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 418 time to evaluate : 1.264 Fit side-chains REVERT: N 35 TYR cc_start: 0.7354 (m-80) cc_final: 0.6693 (m-80) REVERT: G 107 ILE cc_start: 0.8314 (mp) cc_final: 0.8058 (mt) REVERT: H 13 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7765 (pp) REVERT: H 16 ILE cc_start: 0.7989 (tt) cc_final: 0.7652 (tt) REVERT: H 65 LEU cc_start: 0.4486 (OUTLIER) cc_final: 0.4198 (tp) REVERT: I 47 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.6532 (p90) REVERT: I 116 ASP cc_start: 0.4069 (OUTLIER) cc_final: 0.3733 (m-30) REVERT: I 163 LYS cc_start: 0.7158 (mmtm) cc_final: 0.6513 (pttp) REVERT: I 589 THR cc_start: 0.8730 (OUTLIER) cc_final: 0.8285 (m) REVERT: I 641 GLU cc_start: 0.7205 (pm20) cc_final: 0.6937 (mp0) REVERT: I 705 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8318 (mp0) REVERT: I 915 ASP cc_start: 0.6696 (t0) cc_final: 0.6489 (t70) REVERT: I 1037 THR cc_start: 0.6793 (m) cc_final: 0.6494 (p) REVERT: I 1292 THR cc_start: 0.8785 (m) cc_final: 0.8548 (p) REVERT: J 18 ASP cc_start: 0.7084 (t0) cc_final: 0.6790 (t0) REVERT: J 148 GLU cc_start: 0.6864 (tt0) cc_final: 0.6355 (tm-30) REVERT: J 151 MET cc_start: 0.4343 (tpt) cc_final: 0.3754 (mtp) REVERT: J 156 ARG cc_start: 0.5831 (ptp-110) cc_final: 0.5456 (ttp-110) REVERT: J 317 THR cc_start: 0.7018 (m) cc_final: 0.6764 (t) REVERT: J 330 MET cc_start: 0.6494 (mtp) cc_final: 0.6150 (mtm) REVERT: J 423 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8619 (mp) REVERT: J 441 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7876 (mt) REVERT: J 698 MET cc_start: 0.8142 (tpp) cc_final: 0.7918 (mmm) REVERT: J 731 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.7342 (tpt90) REVERT: J 822 MET cc_start: 0.7331 (tpp) cc_final: 0.7002 (ttm) REVERT: J 849 LEU cc_start: 0.6234 (mm) cc_final: 0.5887 (mt) REVERT: J 925 GLU cc_start: 0.7893 (tm-30) cc_final: 0.7582 (tm-30) REVERT: J 1057 SER cc_start: 0.3479 (OUTLIER) cc_final: 0.3068 (p) REVERT: K 51 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7971 (mt) REVERT: L 111 LEU cc_start: 0.3865 (OUTLIER) cc_final: 0.3568 (mt) REVERT: L 276 MET cc_start: 0.4555 (tpp) cc_final: 0.3965 (tpp) REVERT: L 277 MET cc_start: 0.3972 (tmm) cc_final: 0.3632 (tmm) REVERT: L 279 ARG cc_start: 0.5695 (ttp80) cc_final: 0.5099 (ttm110) REVERT: L 297 MET cc_start: 0.0867 (ppp) cc_final: -0.0082 (ptm) REVERT: L 525 ASP cc_start: 0.7141 (t0) cc_final: 0.6935 (t0) REVERT: M 284 ARG cc_start: 0.3352 (OUTLIER) cc_final: 0.2510 (mtt90) outliers start: 176 outliers final: 112 residues processed: 553 average time/residue: 0.2104 time to fit residues: 189.8955 Evaluate side-chains 492 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 367 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 521 LEU Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1113 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 423 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 661 VAL Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 731 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 855 ASP Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1291 GLU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 347 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 380 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 chunk 164 optimal weight: 0.0470 chunk 0 optimal weight: 10.0000 chunk 207 optimal weight: 4.9990 chunk 311 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 313 optimal weight: 7.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 23 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 620 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.180546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.147425 restraints weight = 43398.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142532 restraints weight = 50328.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.144094 restraints weight = 70720.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144680 restraints weight = 45528.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145392 restraints weight = 33981.829| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 33047 Z= 0.115 Angle : 0.599 11.286 45093 Z= 0.305 Chirality : 0.041 0.255 5168 Planarity : 0.004 0.081 5502 Dihedral : 16.603 131.632 5728 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.02 % Favored : 93.95 % Rotamer: Outliers : 5.42 % Allowed : 26.10 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.24 (0.14), residues: 3804 helix: 0.52 (0.13), residues: 1540 sheet: -1.74 (0.24), residues: 414 loop : -1.78 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 529 TYR 0.017 0.001 TYR I1018 PHE 0.017 0.001 PHE I 225 TRP 0.006 0.001 TRP L 315 HIS 0.006 0.001 HIS H 23 Details of bonding type rmsd covalent geometry : bond 0.00259 (33035) covalent geometry : angle 0.59795 (45081) hydrogen bonds : bond 0.03837 ( 1326) hydrogen bonds : angle 4.45730 ( 3692) metal coordination : bond 0.00336 ( 11) metal coordination : angle 1.75267 ( 12) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 412 time to evaluate : 1.193 Fit side-chains revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7521 (m-80) cc_final: 0.6476 (m-80) REVERT: G 12 ARG cc_start: 0.7085 (ttm-80) cc_final: 0.6726 (tpp-160) REVERT: G 107 ILE cc_start: 0.8305 (mp) cc_final: 0.8076 (mt) REVERT: G 231 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7735 (t80) REVERT: H 13 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7400 (pp) REVERT: H 16 ILE cc_start: 0.8084 (tt) cc_final: 0.7695 (tt) REVERT: H 65 LEU cc_start: 0.4528 (OUTLIER) cc_final: 0.4304 (tp) REVERT: H 188 GLU cc_start: 0.7397 (OUTLIER) cc_final: 0.7193 (mt-10) REVERT: I 47 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6459 (p90) REVERT: I 81 ASP cc_start: 0.5015 (OUTLIER) cc_final: 0.4680 (p0) REVERT: I 116 ASP cc_start: 0.4425 (OUTLIER) cc_final: 0.4085 (m-30) REVERT: I 163 LYS cc_start: 0.7098 (mmtm) cc_final: 0.6361 (pttp) REVERT: I 572 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8876 (mt) REVERT: I 589 THR cc_start: 0.8698 (OUTLIER) cc_final: 0.8326 (m) REVERT: I 663 VAL cc_start: 0.8918 (OUTLIER) cc_final: 0.8666 (t) REVERT: I 705 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8358 (mp0) REVERT: I 915 ASP cc_start: 0.6625 (t0) cc_final: 0.6368 (t70) REVERT: I 946 LEU cc_start: 0.7943 (tp) cc_final: 0.7618 (mp) REVERT: I 1020 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6771 (tm-30) REVERT: I 1037 THR cc_start: 0.6936 (m) cc_final: 0.6567 (p) REVERT: I 1292 THR cc_start: 0.8811 (m) cc_final: 0.8529 (p) REVERT: J 18 ASP cc_start: 0.7189 (t0) cc_final: 0.6888 (t0) REVERT: J 148 GLU cc_start: 0.7094 (tt0) cc_final: 0.6451 (tm-30) REVERT: J 151 MET cc_start: 0.4268 (tpt) cc_final: 0.3641 (mtp) REVERT: J 156 ARG cc_start: 0.6171 (ptp-110) cc_final: 0.5514 (ttp-110) REVERT: J 317 THR cc_start: 0.6745 (m) cc_final: 0.6468 (t) REVERT: J 330 MET cc_start: 0.6634 (mtp) cc_final: 0.6388 (mtm) REVERT: J 441 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7947 (mt) REVERT: J 731 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7404 (tpt90) REVERT: J 785 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.7008 (t0) REVERT: J 849 LEU cc_start: 0.6129 (mm) cc_final: 0.5752 (mt) REVERT: J 925 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7587 (tm-30) REVERT: J 1057 SER cc_start: 0.3180 (OUTLIER) cc_final: 0.2803 (p) REVERT: J 1203 ARG cc_start: 0.5707 (tmt-80) cc_final: 0.5362 (tmt-80) REVERT: J 1276 GLU cc_start: 0.6285 (OUTLIER) cc_final: 0.5777 (tt0) REVERT: K 29 GLN cc_start: 0.7495 (tt0) cc_final: 0.6743 (tp40) REVERT: K 51 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7932 (mt) REVERT: K 69 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6001 (ttp-110) REVERT: L 111 LEU cc_start: 0.3714 (OUTLIER) cc_final: 0.3455 (mt) REVERT: L 276 MET cc_start: 0.4522 (tpp) cc_final: 0.3594 (tpp) REVERT: L 277 MET cc_start: 0.4732 (tmm) cc_final: 0.4214 (tmm) REVERT: L 279 ARG cc_start: 0.5483 (ttp80) cc_final: 0.4481 (ttm110) REVERT: L 297 MET cc_start: 0.0857 (ppp) cc_final: 0.0468 (ppp) REVERT: L 525 ASP cc_start: 0.7290 (t0) cc_final: 0.7060 (t0) REVERT: M 284 ARG cc_start: 0.3029 (OUTLIER) cc_final: 0.2146 (mtt90) outliers start: 177 outliers final: 115 residues processed: 548 average time/residue: 0.2067 time to fit residues: 183.9017 Evaluate side-chains 516 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 382 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 207 THR Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 589 THR Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1113 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 731 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 456 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 214 optimal weight: 8.9990 chunk 185 optimal weight: 2.9990 chunk 271 optimal weight: 6.9990 chunk 340 optimal weight: 0.9990 chunk 225 optimal weight: 4.9990 chunk 227 optimal weight: 0.6980 chunk 163 optimal weight: 0.0370 chunk 286 optimal weight: 2.9990 chunk 318 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 372 optimal weight: 20.0000 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 23 HIS H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 659 GLN I 725 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 832 HIS I 856 ASN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 716 GLN J 720 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.178568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.145396 restraints weight = 43257.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.139868 restraints weight = 43220.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.140708 restraints weight = 67547.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.141515 restraints weight = 46313.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141795 restraints weight = 36841.414| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33047 Z= 0.149 Angle : 0.626 11.391 45093 Z= 0.320 Chirality : 0.043 0.226 5168 Planarity : 0.004 0.081 5502 Dihedral : 16.581 130.708 5716 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.57 % Favored : 93.40 % Rotamer: Outliers : 5.51 % Allowed : 26.07 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.14), residues: 3804 helix: 0.53 (0.13), residues: 1542 sheet: -1.56 (0.25), residues: 398 loop : -1.72 (0.14), residues: 1864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 978 TYR 0.022 0.002 TYR J 144 PHE 0.023 0.002 PHE J 17 TRP 0.006 0.001 TRP J 409 HIS 0.005 0.001 HIS J 777 Details of bonding type rmsd covalent geometry : bond 0.00349 (33035) covalent geometry : angle 0.62524 (45081) hydrogen bonds : bond 0.04009 ( 1326) hydrogen bonds : angle 4.45950 ( 3692) metal coordination : bond 0.00572 ( 11) metal coordination : angle 1.87190 ( 12) Misc. bond : bond 0.00058 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 388 time to evaluate : 1.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7602 (m-80) cc_final: 0.6540 (m-80) REVERT: G 107 ILE cc_start: 0.8395 (mp) cc_final: 0.8162 (mt) REVERT: H 65 LEU cc_start: 0.4482 (OUTLIER) cc_final: 0.4216 (tp) REVERT: H 188 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7409 (pt0) REVERT: I 47 TYR cc_start: 0.6843 (OUTLIER) cc_final: 0.6225 (p90) REVERT: I 81 ASP cc_start: 0.5035 (OUTLIER) cc_final: 0.4803 (p0) REVERT: I 116 ASP cc_start: 0.4487 (OUTLIER) cc_final: 0.4140 (m-30) REVERT: I 542 ARG cc_start: 0.6502 (ttt180) cc_final: 0.6100 (mtp180) REVERT: I 572 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8831 (mt) REVERT: I 663 VAL cc_start: 0.8900 (OUTLIER) cc_final: 0.8663 (t) REVERT: I 705 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8305 (mp0) REVERT: I 749 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7937 (t70) REVERT: I 946 LEU cc_start: 0.7908 (tp) cc_final: 0.7699 (mt) REVERT: I 1020 GLU cc_start: 0.7332 (tm-30) cc_final: 0.6822 (tm-30) REVERT: I 1108 ASN cc_start: 0.9057 (OUTLIER) cc_final: 0.8806 (p0) REVERT: I 1292 THR cc_start: 0.8869 (m) cc_final: 0.8587 (p) REVERT: J 18 ASP cc_start: 0.7193 (t0) cc_final: 0.6942 (t0) REVERT: J 148 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6501 (tm-30) REVERT: J 151 MET cc_start: 0.4123 (tpt) cc_final: 0.3546 (mtp) REVERT: J 156 ARG cc_start: 0.6394 (ptp-110) cc_final: 0.5776 (ttp-110) REVERT: J 317 THR cc_start: 0.6869 (m) cc_final: 0.6593 (t) REVERT: J 618 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8307 (t) REVERT: J 624 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8611 (tt) REVERT: J 731 ARG cc_start: 0.7717 (OUTLIER) cc_final: 0.7443 (tpt90) REVERT: J 802 ASP cc_start: 0.7549 (p0) cc_final: 0.7173 (p0) REVERT: J 863 LEU cc_start: 0.6845 (tp) cc_final: 0.6501 (tp) REVERT: J 868 TRP cc_start: 0.6849 (OUTLIER) cc_final: 0.5549 (t-100) REVERT: J 925 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7567 (tm-30) REVERT: J 1057 SER cc_start: 0.2845 (OUTLIER) cc_final: 0.2557 (p) REVERT: J 1276 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5849 (tt0) REVERT: J 1325 PHE cc_start: 0.7609 (t80) cc_final: 0.7134 (t80) REVERT: K 51 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7906 (mt) REVERT: K 69 ARG cc_start: 0.7301 (ttm-80) cc_final: 0.5932 (ttp-110) REVERT: L 111 LEU cc_start: 0.3796 (OUTLIER) cc_final: 0.3438 (mt) REVERT: L 124 GLU cc_start: 0.6433 (tp30) cc_final: 0.6107 (tp30) REVERT: L 276 MET cc_start: 0.4588 (tpp) cc_final: 0.3511 (tpp) REVERT: L 279 ARG cc_start: 0.5510 (ttp80) cc_final: 0.4471 (ttm110) REVERT: L 297 MET cc_start: 0.0938 (ppp) cc_final: 0.0531 (ppp) REVERT: L 489 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7043 (mpm) REVERT: M 284 ARG cc_start: 0.2908 (OUTLIER) cc_final: 0.2029 (mtt90) outliers start: 180 outliers final: 125 residues processed: 524 average time/residue: 0.2008 time to fit residues: 173.1194 Evaluate side-chains 515 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 369 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 641 GLU Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1108 ASN Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 569 LEU Chi-restraints excluded: chain J residue 618 VAL Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 731 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1328 THR Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 372 optimal weight: 20.0000 chunk 233 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 chunk 305 optimal weight: 0.7980 chunk 290 optimal weight: 30.0000 chunk 27 optimal weight: 4.9990 chunk 140 optimal weight: 0.9990 chunk 287 optimal weight: 4.9990 chunk 211 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** G 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 227 GLN L 271 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.181880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.149048 restraints weight = 43023.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143311 restraints weight = 46324.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144754 restraints weight = 60219.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145385 restraints weight = 40536.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145496 restraints weight = 34788.214| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33047 Z= 0.119 Angle : 0.600 11.324 45093 Z= 0.307 Chirality : 0.041 0.196 5168 Planarity : 0.004 0.084 5502 Dihedral : 16.496 130.670 5714 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.18 % Favored : 93.80 % Rotamer: Outliers : 5.29 % Allowed : 26.71 % Favored : 67.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3804 helix: 0.65 (0.13), residues: 1554 sheet: -1.42 (0.25), residues: 392 loop : -1.63 (0.14), residues: 1858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 978 TYR 0.028 0.001 TYR J 144 PHE 0.037 0.001 PHE I 186 TRP 0.006 0.001 TRP J1193 HIS 0.003 0.001 HIS J 430 Details of bonding type rmsd covalent geometry : bond 0.00271 (33035) covalent geometry : angle 0.59899 (45081) hydrogen bonds : bond 0.03822 ( 1326) hydrogen bonds : angle 4.36348 ( 3692) metal coordination : bond 0.00398 ( 11) metal coordination : angle 1.71641 ( 12) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 391 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7525 (m-80) cc_final: 0.6285 (m-80) REVERT: N 62 GLN cc_start: 0.8184 (tp40) cc_final: 0.7974 (tp40) REVERT: G 231 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.7881 (t80) REVERT: H 65 LEU cc_start: 0.4396 (OUTLIER) cc_final: 0.4140 (tp) REVERT: H 104 LYS cc_start: 0.6888 (tmtt) cc_final: 0.6240 (tptm) REVERT: H 188 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7228 (mt-10) REVERT: I 47 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.6563 (p90) REVERT: I 81 ASP cc_start: 0.5021 (OUTLIER) cc_final: 0.4718 (p0) REVERT: I 116 ASP cc_start: 0.4268 (OUTLIER) cc_final: 0.3962 (m-30) REVERT: I 225 PHE cc_start: 0.5668 (m-80) cc_final: 0.5400 (m-80) REVERT: I 483 ASP cc_start: 0.2654 (OUTLIER) cc_final: 0.2345 (m-30) REVERT: I 572 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8792 (mt) REVERT: I 663 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8686 (t) REVERT: I 705 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: I 946 LEU cc_start: 0.8020 (tp) cc_final: 0.7747 (mp) REVERT: I 1020 GLU cc_start: 0.7401 (tm-30) cc_final: 0.6910 (tm-30) REVERT: I 1108 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8812 (p0) REVERT: I 1292 THR cc_start: 0.8792 (m) cc_final: 0.8545 (p) REVERT: J 18 ASP cc_start: 0.7180 (t0) cc_final: 0.6929 (t0) REVERT: J 148 GLU cc_start: 0.7102 (OUTLIER) cc_final: 0.6458 (tm-30) REVERT: J 151 MET cc_start: 0.3995 (tpt) cc_final: 0.3632 (mtp) REVERT: J 156 ARG cc_start: 0.6276 (ptp-110) cc_final: 0.5651 (ttp-110) REVERT: J 317 THR cc_start: 0.6750 (m) cc_final: 0.6427 (t) REVERT: J 581 MET cc_start: 0.7612 (mtp) cc_final: 0.7395 (mtp) REVERT: J 614 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7777 (tt) REVERT: J 624 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8526 (tt) REVERT: J 731 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7364 (tpt90) REVERT: J 863 LEU cc_start: 0.6708 (tp) cc_final: 0.6401 (tp) REVERT: J 868 TRP cc_start: 0.6958 (OUTLIER) cc_final: 0.5658 (t-100) REVERT: J 925 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7652 (tm-30) REVERT: J 1057 SER cc_start: 0.2839 (OUTLIER) cc_final: 0.2574 (p) REVERT: J 1276 GLU cc_start: 0.6292 (OUTLIER) cc_final: 0.5770 (tt0) REVERT: K 51 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7935 (mt) REVERT: K 69 ARG cc_start: 0.7365 (ttm-80) cc_final: 0.6028 (ttp-110) REVERT: L 124 GLU cc_start: 0.6398 (tp30) cc_final: 0.6074 (tp30) REVERT: L 276 MET cc_start: 0.4809 (tpp) cc_final: 0.4175 (tpp) REVERT: L 279 ARG cc_start: 0.5467 (ttp80) cc_final: 0.4378 (ttm110) REVERT: L 297 MET cc_start: 0.0811 (ppp) cc_final: 0.0463 (ppp) REVERT: L 403 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.6704 (t0) REVERT: L 489 MET cc_start: 0.7486 (OUTLIER) cc_final: 0.6991 (mpm) REVERT: M 284 ARG cc_start: 0.2741 (OUTLIER) cc_final: 0.2053 (mtt180) outliers start: 173 outliers final: 128 residues processed: 521 average time/residue: 0.2020 time to fit residues: 172.6533 Evaluate side-chains 524 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 374 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 17 MET Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 483 ASP Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1108 ASN Chi-restraints excluded: chain I residue 1113 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 50 LYS Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 614 LEU Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 731 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 111 LEU Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 273 MET Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 125 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 177 optimal weight: 0.0070 chunk 285 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 361 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 192 optimal weight: 9.9990 chunk 267 optimal weight: 0.9980 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1108 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN L 545 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.180425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.148335 restraints weight = 43101.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.142738 restraints weight = 42311.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.143752 restraints weight = 59800.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.144483 restraints weight = 41619.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144656 restraints weight = 34549.368| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33047 Z= 0.122 Angle : 0.599 11.357 45093 Z= 0.306 Chirality : 0.041 0.174 5168 Planarity : 0.004 0.082 5502 Dihedral : 16.309 130.622 5712 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.26 % Favored : 93.72 % Rotamer: Outliers : 5.45 % Allowed : 26.65 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3804 helix: 0.74 (0.13), residues: 1556 sheet: -1.37 (0.26), residues: 387 loop : -1.59 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 978 TYR 0.036 0.002 TYR J 144 PHE 0.032 0.001 PHE I 186 TRP 0.006 0.001 TRP L 315 HIS 0.008 0.001 HIS L 545 Details of bonding type rmsd covalent geometry : bond 0.00280 (33035) covalent geometry : angle 0.59867 (45081) hydrogen bonds : bond 0.03790 ( 1326) hydrogen bonds : angle 4.30863 ( 3692) metal coordination : bond 0.00434 ( 11) metal coordination : angle 1.69629 ( 12) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 178 poor density : 396 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7509 (m-80) cc_final: 0.6527 (m-80) REVERT: G 231 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7951 (t80) REVERT: H 65 LEU cc_start: 0.4428 (OUTLIER) cc_final: 0.4172 (tp) REVERT: H 188 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: I 47 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.6507 (p90) REVERT: I 81 ASP cc_start: 0.5027 (OUTLIER) cc_final: 0.4728 (p0) REVERT: I 116 ASP cc_start: 0.3966 (OUTLIER) cc_final: 0.3734 (m-30) REVERT: I 336 LEU cc_start: 0.6105 (pp) cc_final: 0.5073 (mm) REVERT: I 572 ILE cc_start: 0.8936 (OUTLIER) cc_final: 0.8732 (mt) REVERT: I 663 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8695 (t) REVERT: I 749 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7841 (t70) REVERT: I 946 LEU cc_start: 0.8019 (tp) cc_final: 0.7756 (mp) REVERT: I 976 ARG cc_start: 0.8151 (ttp-110) cc_final: 0.7674 (mtp-110) REVERT: I 1020 GLU cc_start: 0.7134 (tm-30) cc_final: 0.6647 (tm-30) REVERT: I 1292 THR cc_start: 0.8746 (m) cc_final: 0.8438 (p) REVERT: J 18 ASP cc_start: 0.7125 (t0) cc_final: 0.6847 (t0) REVERT: J 148 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: J 151 MET cc_start: 0.3799 (tpt) cc_final: 0.3597 (mtp) REVERT: J 156 ARG cc_start: 0.6223 (ptp-110) cc_final: 0.5679 (ttp-110) REVERT: J 213 LYS cc_start: 0.6579 (mtpt) cc_final: 0.5657 (tttp) REVERT: J 317 THR cc_start: 0.6591 (m) cc_final: 0.6276 (t) REVERT: J 581 MET cc_start: 0.7587 (mtp) cc_final: 0.7298 (mtp) REVERT: J 624 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8505 (tt) REVERT: J 731 ARG cc_start: 0.7653 (OUTLIER) cc_final: 0.7386 (tpt90) REVERT: J 785 ASP cc_start: 0.7469 (OUTLIER) cc_final: 0.7030 (t0) REVERT: J 863 LEU cc_start: 0.6850 (tp) cc_final: 0.6506 (tp) REVERT: J 868 TRP cc_start: 0.6974 (OUTLIER) cc_final: 0.5715 (t-100) REVERT: J 925 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7657 (tm-30) REVERT: J 1057 SER cc_start: 0.2884 (OUTLIER) cc_final: 0.2627 (p) REVERT: J 1276 GLU cc_start: 0.6361 (OUTLIER) cc_final: 0.5833 (tt0) REVERT: K 51 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.8024 (mt) REVERT: K 69 ARG cc_start: 0.7177 (ttm-80) cc_final: 0.5864 (ttp-110) REVERT: L 276 MET cc_start: 0.4689 (tpp) cc_final: 0.4333 (tpp) REVERT: L 297 MET cc_start: 0.0780 (ppp) cc_final: 0.0452 (ppp) REVERT: L 403 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6687 (t0) REVERT: L 489 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.6970 (mpm) REVERT: M 284 ARG cc_start: 0.2709 (OUTLIER) cc_final: 0.2112 (mtt180) outliers start: 178 outliers final: 135 residues processed: 530 average time/residue: 0.2070 time to fit residues: 178.6393 Evaluate side-chains 523 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 368 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 287 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 515 MET Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 572 ILE Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 664 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 731 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 272 optimal weight: 5.9990 chunk 313 optimal weight: 0.6980 chunk 310 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 315 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 209 optimal weight: 0.6980 chunk 149 optimal weight: 0.9990 chunk 198 optimal weight: 0.0370 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN H 103 ASN H 186 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.182318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.149941 restraints weight = 42923.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144478 restraints weight = 42293.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.145010 restraints weight = 56479.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.146809 restraints weight = 41742.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.146816 restraints weight = 31174.188| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33047 Z= 0.115 Angle : 0.599 11.392 45093 Z= 0.306 Chirality : 0.041 0.185 5168 Planarity : 0.004 0.084 5502 Dihedral : 16.207 130.735 5706 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.86 % Favored : 94.11 % Rotamer: Outliers : 4.87 % Allowed : 27.51 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3804 helix: 0.88 (0.14), residues: 1549 sheet: -1.31 (0.26), residues: 385 loop : -1.51 (0.14), residues: 1870 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 274 TYR 0.034 0.001 TYR J 144 PHE 0.031 0.001 PHE I 186 TRP 0.007 0.001 TRP L 315 HIS 0.011 0.001 HIS L 600 Details of bonding type rmsd covalent geometry : bond 0.00258 (33035) covalent geometry : angle 0.59822 (45081) hydrogen bonds : bond 0.03695 ( 1326) hydrogen bonds : angle 4.24285 ( 3692) metal coordination : bond 0.00338 ( 11) metal coordination : angle 1.65242 ( 12) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 403 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7515 (m-80) cc_final: 0.6411 (m-80) REVERT: G 231 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7829 (t80) REVERT: H 65 LEU cc_start: 0.4590 (OUTLIER) cc_final: 0.4371 (tp) REVERT: H 188 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7127 (mt-10) REVERT: I 47 TYR cc_start: 0.6831 (OUTLIER) cc_final: 0.6507 (p90) REVERT: I 81 ASP cc_start: 0.5010 (OUTLIER) cc_final: 0.4707 (p0) REVERT: I 663 VAL cc_start: 0.8897 (OUTLIER) cc_final: 0.8690 (t) REVERT: I 749 ASP cc_start: 0.8158 (OUTLIER) cc_final: 0.7874 (t70) REVERT: I 899 GLU cc_start: 0.7986 (tp30) cc_final: 0.7485 (tt0) REVERT: I 946 LEU cc_start: 0.8054 (tp) cc_final: 0.7763 (mp) REVERT: I 951 MET cc_start: 0.7291 (OUTLIER) cc_final: 0.6964 (ttm) REVERT: I 976 ARG cc_start: 0.8027 (ttp-110) cc_final: 0.7570 (mtp-110) REVERT: I 1020 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6552 (tm-30) REVERT: I 1037 THR cc_start: 0.6889 (m) cc_final: 0.6563 (p) REVERT: J 18 ASP cc_start: 0.7077 (t0) cc_final: 0.6866 (t0) REVERT: J 148 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6440 (tm-30) REVERT: J 156 ARG cc_start: 0.6482 (ptp-110) cc_final: 0.5828 (ttp-110) REVERT: J 164 GLN cc_start: 0.6783 (tm-30) cc_final: 0.6154 (tm-30) REVERT: J 213 LYS cc_start: 0.6461 (mtpt) cc_final: 0.5562 (tttp) REVERT: J 317 THR cc_start: 0.6781 (m) cc_final: 0.6502 (t) REVERT: J 581 MET cc_start: 0.7534 (mtp) cc_final: 0.7282 (mtp) REVERT: J 624 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8496 (tt) REVERT: J 672 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8447 (mp) REVERT: J 785 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7041 (t0) REVERT: J 863 LEU cc_start: 0.6807 (tp) cc_final: 0.6538 (tp) REVERT: J 868 TRP cc_start: 0.6912 (OUTLIER) cc_final: 0.5674 (t-100) REVERT: J 925 GLU cc_start: 0.7944 (tm-30) cc_final: 0.7650 (tm-30) REVERT: J 1057 SER cc_start: 0.3133 (OUTLIER) cc_final: 0.2910 (p) REVERT: J 1276 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5852 (tt0) REVERT: K 69 ARG cc_start: 0.7125 (ttm-80) cc_final: 0.5792 (ttp-110) REVERT: L 297 MET cc_start: 0.0602 (ppp) cc_final: 0.0369 (ppp) REVERT: L 403 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.6694 (t0) REVERT: L 489 MET cc_start: 0.7320 (OUTLIER) cc_final: 0.6778 (mpm) REVERT: M 284 ARG cc_start: 0.2554 (OUTLIER) cc_final: 0.2017 (mtt180) outliers start: 159 outliers final: 118 residues processed: 520 average time/residue: 0.2105 time to fit residues: 178.2040 Evaluate side-chains 513 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 377 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 514 PHE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 473 THR Chi-restraints excluded: chain J residue 486 SER Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain L residue 379 MET Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 103 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 48 optimal weight: 0.0020 chunk 376 optimal weight: 10.0000 chunk 313 optimal weight: 2.9990 chunk 270 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN H 103 ASN H 186 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 490 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.180177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.147317 restraints weight = 43324.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.143021 restraints weight = 43586.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143556 restraints weight = 43777.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.143936 restraints weight = 36664.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.143982 restraints weight = 33621.154| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 33047 Z= 0.121 Angle : 0.606 11.916 45093 Z= 0.308 Chirality : 0.041 0.198 5168 Planarity : 0.004 0.082 5502 Dihedral : 16.159 130.651 5704 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.99 % Favored : 93.98 % Rotamer: Outliers : 4.53 % Allowed : 27.85 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3804 helix: 0.92 (0.14), residues: 1539 sheet: -1.29 (0.26), residues: 392 loop : -1.48 (0.14), residues: 1873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 978 TYR 0.023 0.001 TYR J 144 PHE 0.031 0.001 PHE I 186 TRP 0.006 0.001 TRP L 315 HIS 0.003 0.001 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00277 (33035) covalent geometry : angle 0.60521 (45081) hydrogen bonds : bond 0.03725 ( 1326) hydrogen bonds : angle 4.22318 ( 3692) metal coordination : bond 0.00412 ( 11) metal coordination : angle 1.67572 ( 12) Misc. bond : bond 0.00030 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7608 Ramachandran restraints generated. 3804 Oldfield, 0 Emsley, 3804 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 386 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7410 (m-80) cc_final: 0.6461 (m-80) REVERT: G 107 ILE cc_start: 0.8322 (mp) cc_final: 0.8071 (mt) REVERT: G 231 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7921 (t80) REVERT: H 65 LEU cc_start: 0.4537 (OUTLIER) cc_final: 0.4302 (tp) REVERT: H 188 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7099 (mt-10) REVERT: I 47 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6522 (p90) REVERT: I 81 ASP cc_start: 0.5044 (OUTLIER) cc_final: 0.4744 (p0) REVERT: I 158 ASP cc_start: 0.6353 (t0) cc_final: 0.6047 (t70) REVERT: I 211 ARG cc_start: 0.5337 (mmm160) cc_final: 0.4690 (mmp80) REVERT: I 749 ASP cc_start: 0.8099 (OUTLIER) cc_final: 0.7837 (t70) REVERT: I 899 GLU cc_start: 0.7927 (tp30) cc_final: 0.7542 (tt0) REVERT: I 946 LEU cc_start: 0.8009 (tp) cc_final: 0.7768 (mp) REVERT: I 951 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6947 (ttm) REVERT: I 976 ARG cc_start: 0.8060 (ttp-110) cc_final: 0.7651 (mtp-110) REVERT: I 1020 GLU cc_start: 0.7061 (tm-30) cc_final: 0.6544 (tm-30) REVERT: I 1037 THR cc_start: 0.6792 (m) cc_final: 0.6536 (p) REVERT: J 18 ASP cc_start: 0.7041 (t0) cc_final: 0.6823 (t0) REVERT: J 148 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6702 (tm-30) REVERT: J 156 ARG cc_start: 0.6366 (ptp-110) cc_final: 0.5708 (ttp-110) REVERT: J 164 GLN cc_start: 0.6722 (tm-30) cc_final: 0.6101 (tm-30) REVERT: J 213 LYS cc_start: 0.6487 (mtpt) cc_final: 0.5690 (tttp) REVERT: J 317 THR cc_start: 0.6729 (m) cc_final: 0.6495 (t) REVERT: J 581 MET cc_start: 0.7446 (mtp) cc_final: 0.7141 (mtp) REVERT: J 624 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8540 (tt) REVERT: J 785 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7083 (t0) REVERT: J 806 ASP cc_start: 0.6467 (t0) cc_final: 0.6209 (t0) REVERT: J 863 LEU cc_start: 0.6798 (tp) cc_final: 0.6539 (tp) REVERT: J 868 TRP cc_start: 0.6925 (OUTLIER) cc_final: 0.5705 (t-100) REVERT: J 925 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7628 (tm-30) REVERT: J 1057 SER cc_start: 0.3206 (OUTLIER) cc_final: 0.2994 (p) REVERT: J 1276 GLU cc_start: 0.6366 (OUTLIER) cc_final: 0.5851 (tt0) REVERT: J 1325 PHE cc_start: 0.6982 (t80) cc_final: 0.6714 (t80) REVERT: K 42 GLU cc_start: 0.5027 (pt0) cc_final: 0.4660 (pt0) REVERT: L 250 LEU cc_start: 0.2671 (OUTLIER) cc_final: 0.2281 (tp) REVERT: L 277 MET cc_start: 0.4401 (tmm) cc_final: 0.4152 (ttt) REVERT: L 297 MET cc_start: 0.0709 (ppp) cc_final: 0.0078 (ptm) REVERT: L 403 ASP cc_start: 0.7371 (OUTLIER) cc_final: 0.6703 (t0) REVERT: L 489 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6865 (mpm) REVERT: M 284 ARG cc_start: 0.2559 (OUTLIER) cc_final: 0.2094 (mtt180) outliers start: 148 outliers final: 119 residues processed: 495 average time/residue: 0.1998 time to fit residues: 160.6824 Evaluate side-chains 506 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 370 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 15 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain G residue 232 VAL Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 39 ILE Chi-restraints excluded: chain I residue 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 81 ASP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 444 ASP Chi-restraints excluded: chain I residue 456 VAL Chi-restraints excluded: chain I residue 466 VAL Chi-restraints excluded: chain I residue 471 VAL Chi-restraints excluded: chain I residue 472 GLU Chi-restraints excluded: chain I residue 493 ILE Chi-restraints excluded: chain I residue 498 ILE Chi-restraints excluded: chain I residue 563 THR Chi-restraints excluded: chain I residue 582 ASN Chi-restraints excluded: chain I residue 598 VAL Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 616 ILE Chi-restraints excluded: chain I residue 749 ASP Chi-restraints excluded: chain I residue 764 CYS Chi-restraints excluded: chain I residue 765 ILE Chi-restraints excluded: chain I residue 800 MET Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 919 ARG Chi-restraints excluded: chain I residue 924 VAL Chi-restraints excluded: chain I residue 949 GLU Chi-restraints excluded: chain I residue 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1151 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1172 LEU Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1233 LEU Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 486 SER Chi-restraints excluded: chain J residue 505 ASP Chi-restraints excluded: chain J residue 545 HIS Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 553 THR Chi-restraints excluded: chain J residue 557 LYS Chi-restraints excluded: chain J residue 624 ILE Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 785 ASP Chi-restraints excluded: chain J residue 808 VAL Chi-restraints excluded: chain J residue 812 ASP Chi-restraints excluded: chain J residue 818 GLU Chi-restraints excluded: chain J residue 839 VAL Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 865 HIS Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 928 THR Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 1016 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1024 THR Chi-restraints excluded: chain J residue 1057 SER Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1276 GLU Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 224 LEU Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 571 TYR Chi-restraints excluded: chain L residue 607 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 284 ARG Chi-restraints excluded: chain M residue 285 THR Chi-restraints excluded: chain M residue 292 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 252 optimal weight: 1.9990 chunk 283 optimal weight: 1.9990 chunk 282 optimal weight: 0.0470 chunk 245 optimal weight: 1.9990 chunk 253 optimal weight: 0.0970 chunk 300 optimal weight: 1.9990 chunk 198 optimal weight: 5.9990 chunk 380 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 357 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.2282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN G 117 HIS H 103 ASN H 186 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.179618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146993 restraints weight = 43241.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.142989 restraints weight = 41022.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.143352 restraints weight = 42550.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.143734 restraints weight = 36106.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.143836 restraints weight = 32461.238| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33047 Z= 0.134 Angle : 0.628 12.108 45093 Z= 0.319 Chirality : 0.042 0.198 5168 Planarity : 0.004 0.079 5502 Dihedral : 16.146 130.104 5699 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.10 % Favored : 93.87 % Rotamer: Outliers : 4.56 % Allowed : 28.24 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.70 (0.14), residues: 3804 helix: 0.88 (0.14), residues: 1545 sheet: -1.23 (0.26), residues: 408 loop : -1.46 (0.14), residues: 1851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 978 TYR 0.026 0.002 TYR J 995 PHE 0.031 0.001 PHE I 186 TRP 0.005 0.001 TRP L 433 HIS 0.005 0.001 HIS G 117 Details of bonding type rmsd covalent geometry : bond 0.00310 (33035) covalent geometry : angle 0.62748 (45081) hydrogen bonds : bond 0.03837 ( 1326) hydrogen bonds : angle 4.25878 ( 3692) metal coordination : bond 0.00489 ( 11) metal coordination : angle 1.81064 ( 12) Misc. bond : bond 0.00037 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5800.97 seconds wall clock time: 100 minutes 57.80 seconds (6057.80 seconds total)