Starting phenix.real_space_refine on Mon Sep 14 19:07:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psv_20465/09_2026/6psv_20465_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psv_20465/09_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_20465/09_2026/6psv_20465_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psv_20465/09_2026/6psv_20465_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6psv_20465/09_2026/6psv_20465.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psv_20465/09_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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.43, 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: 2.91 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: 4.14 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: 8.80 Time building geometry restraints manager: 3.76 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: 43833 2.60 - 5.19: 1101 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: 3798 0.056 - 0.111: 1159 0.111 - 0.167: 188 0.167 - 0.223: 15 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 38.030 Find NCS groups from input model: 0.280 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.012 0.510 33047 Z= 0.552 Angle : 1.045 30.025 45093 Z= 0.620 Chirality : 0.053 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/Z covalent geometry : bond 0.01117 / 0.54 (33035) covalent geometry : angle 1.02066 / 0.62 (45081) hydrogen bonds : bond 0.15861 / 10.67 ( 1326) hydrogen bonds : angle 7.67589 / 5.20 ( 3692) metal coordination : bond 0.16633 / 8.10 ( 11) metal coordination : angle 13.70565 / 10.34 ( 12) Misc. bond : bond 0.00139 / 0.07 ( 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 : 1.294 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: 0.2580 (mpt-90) outliers start: 367 outliers final: 243 residues processed: 842 average time/residue: 0.2120 time to fit residues: 280.7398 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 : 1.119 ------------------------------------------------------------------------------- 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... N 30 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 330 HIS I 463 GLN I 622 ASN I 649 GLN I 659 GLN I 677 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 808 ASN I 824 GLN I 856 ASN I 965 GLN I1010 GLN I1108 ASN I1116 HIS I1134 GLN I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1244 HIS I1257 GLN I1268 GLN J 45 ASN J 80 HIS J 157 GLN ** J 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 294 ASN J 335 GLN 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 464 ASN L 600 HIS Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.177410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.147055 restraints weight = 43191.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146414 restraints weight = 97528.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.147083 restraints weight = 87803.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.147046 restraints weight = 53045.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.147490 restraints weight = 47040.458| |-----------------------------------------------------------------------------| r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 33047 Z= 0.167 Angle : 0.789 12.209 45093 Z= 0.404 Chirality : 0.048 0.315 5168 Planarity : 0.006 0.090 5502 Dihedral : 18.359 127.991 6120 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.33 % Favored : 92.61 % Rotamer: Outliers : 8.32 % Allowed : 24.08 % Favored : 67.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.16 % Twisted Proline : 0.66 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.21 (0.12), residues: 3804 helix: -1.26 (0.12), residues: 1528 sheet: -3.03 (0.21), residues: 421 loop : -2.67 (0.13), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 3 TYR 0.021 0.002 TYR I1018 PHE 0.027 0.002 PHE L 306 TRP 0.021 0.002 TRP L 434 HIS 0.008 0.001 HIS G 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (33035) covalent geometry : angle 0.78538 / 0.40 (45081) hydrogen bonds : bond 0.05630 / 3.75 ( 1326) hydrogen bonds : angle 5.76797 / 3.94 ( 3692) metal coordination : bond 0.00979 / 0.61 ( 11) metal coordination : angle 4.76248 / 3.20 ( 12) Misc. bond : bond 0.00037 / 0.02 ( 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 750 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 272 poor density : 478 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 35 TYR cc_start: 0.7381 (m-80) cc_final: 0.7137 (m-80) REVERT: G 41 ASN cc_start: 0.8993 (t0) cc_final: 0.8690 (t0) REVERT: H 23 HIS cc_start: 0.7358 (t-90) cc_final: 0.7098 (t-170) REVERT: H 86 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7865 (mtpt) REVERT: I 121 GLU cc_start: 0.7141 (tp30) cc_final: 0.6937 (tp30) REVERT: I 385 PHE cc_start: 0.5309 (OUTLIER) cc_final: 0.3943 (p90) REVERT: I 854 ILE cc_start: 0.8585 (mt) cc_final: 0.8321 (mt) REVERT: I 1061 GLN cc_start: 0.8367 (pt0) cc_final: 0.8146 (pt0) REVERT: I 1136 GLN cc_start: 0.7513 (tp40) cc_final: 0.7312 (tp40) REVERT: I 1151 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7950 (tm) REVERT: I 1197 GLU cc_start: 0.7642 (tm-30) cc_final: 0.7355 (tp30) REVERT: I 1200 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7697 (tttp) REVERT: J 18 ASP cc_start: 0.7145 (t0) cc_final: 0.6898 (t0) REVERT: J 50 LYS cc_start: 0.8300 (mttt) cc_final: 0.7878 (mttp) REVERT: J 180 MET cc_start: 0.6886 (mtm) cc_final: 0.6543 (mtm) REVERT: J 217 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6451 (tm) REVERT: J 441 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.8001 (mt) REVERT: J 484 MET cc_start: 0.9270 (mtm) cc_final: 0.8988 (mtm) REVERT: J 521 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7935 (tttm) REVERT: J 528 THR cc_start: 0.8551 (m) cc_final: 0.8345 (p) REVERT: J 532 GLU cc_start: 0.7578 (tt0) cc_final: 0.6931 (tt0) REVERT: J 644 MET cc_start: 0.7841 (ptp) cc_final: 0.7214 (ptp) REVERT: J 655 SER cc_start: 0.7948 (t) cc_final: 0.7689 (p) REVERT: J 731 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.7374 (tpt90) REVERT: J 749 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7975 (mtpp) REVERT: J 802 ASP cc_start: 0.7344 (p0) cc_final: 0.7136 (p0) REVERT: J 849 LEU cc_start: 0.6390 (mm) cc_final: 0.6054 (mt) REVERT: J 868 TRP cc_start: 0.6693 (OUTLIER) cc_final: 0.6260 (t-100) REVERT: J 1353 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8932 (t) REVERT: K 51 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7953 (mt) REVERT: K 69 ARG cc_start: 0.7720 (ttm-80) cc_final: 0.6347 (ttp-110) REVERT: K 74 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5979 (mt-10) REVERT: L 476 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6879 (ptt90) REVERT: L 525 ASP cc_start: 0.7419 (t0) cc_final: 0.7135 (t0) outliers start: 272 outliers final: 159 residues processed: 700 average time/residue: 0.1940 time to fit residues: 220.0212 Evaluate side-chains 566 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 394 time to evaluate : 1.070 ------------------------------------------------------------------------------- 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 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 172 LEU 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 204 GLU Chi-restraints excluded: chain H residue 6 THR 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 86 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 201 LEU Chi-restraints excluded: chain H residue 207 THR 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 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 118 LYS 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 242 VAL Chi-restraints excluded: chain I residue 255 ILE 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 492 MET 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 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 602 GLU Chi-restraints excluded: chain I residue 604 HIS Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 659 GLN Chi-restraints excluded: chain I residue 690 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 766 ASN 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 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 1083 GLU Chi-restraints excluded: chain I residue 1113 LEU Chi-restraints excluded: chain I residue 1131 MET 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 1186 VAL Chi-restraints excluded: chain I residue 1200 LYS Chi-restraints excluded: chain I residue 1206 THR Chi-restraints excluded: chain I residue 1226 THR 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 1315 MET Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 441 LEU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 503 SER Chi-restraints excluded: chain J residue 521 LYS 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 582 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 731 ARG 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 774 ILE 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 855 ASP Chi-restraints excluded: chain J residue 868 TRP Chi-restraints excluded: chain J residue 872 LEU Chi-restraints excluded: chain J residue 890 THR Chi-restraints excluded: chain J residue 901 ARG Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL 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 1093 THR Chi-restraints excluded: chain J residue 1106 ILE Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1172 LYS Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1235 ASN Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1257 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 1326 GLN Chi-restraints excluded: chain J residue 1337 VAL Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 74 GLU 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 304 THR Chi-restraints excluded: chain L residue 416 VAL Chi-restraints excluded: chain L residue 449 THR Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 489 MET 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 314 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 123 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 333 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 chunk 273 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 260 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 262 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 132 HIS H 132 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN I1108 ASN I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1257 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 GLN J 266 ASN J 504 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.171954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.137725 restraints weight = 43239.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.131607 restraints weight = 45043.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.132730 restraints weight = 58415.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.133286 restraints weight = 41363.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.133502 restraints weight = 35247.903| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.144 33047 Z= 0.307 Angle : 0.833 12.594 45093 Z= 0.427 Chirality : 0.051 0.310 5168 Planarity : 0.006 0.078 5502 Dihedral : 18.090 128.730 5858 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.89 % Favored : 91.06 % Rotamer: Outliers : 8.97 % Allowed : 25.58 % Favored : 65.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.93 (0.12), residues: 3804 helix: -0.96 (0.12), residues: 1533 sheet: -2.80 (0.21), residues: 442 loop : -2.59 (0.13), residues: 1829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 529 TYR 0.029 0.002 TYR J1186 PHE 0.021 0.002 PHE I 225 TRP 0.020 0.002 TRP L 326 HIS 0.009 0.002 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.31 (33035) covalent geometry : angle 0.83018 / 0.43 (45081) hydrogen bonds : bond 0.05725 / 3.85 ( 1326) hydrogen bonds : angle 5.58747 / 3.82 ( 3692) metal coordination : bond 0.01083 / 0.77 ( 11) metal coordination : angle 4.33402 / 3.28 ( 12) Misc. bond : bond 0.00163 / 0.09 ( 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 698 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 293 poor density : 405 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 48 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.4898 (tmt90) REVERT: H 23 HIS cc_start: 0.7473 (t-90) cc_final: 0.7210 (t-170) REVERT: H 77 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8319 (t0) REVERT: H 86 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8175 (mtpt) REVERT: H 142 MET cc_start: 0.7287 (ptt) cc_final: 0.7012 (ptt) REVERT: I 211 ARG cc_start: 0.5611 (mmm160) cc_final: 0.5212 (mmm160) REVERT: I 385 PHE cc_start: 0.5593 (OUTLIER) cc_final: 0.4162 (p90) REVERT: I 503 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7742 (mtmt) REVERT: I 573 ASN cc_start: 0.8160 (m-40) cc_final: 0.7905 (m-40) REVERT: I 854 ILE cc_start: 0.8608 (mt) cc_final: 0.8354 (mt) REVERT: I 1136 GLN cc_start: 0.7684 (tp40) cc_final: 0.7478 (tp40) REVERT: I 1197 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7452 (tp30) REVERT: I 1200 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7737 (tttp) REVERT: J 50 LYS cc_start: 0.8479 (mttt) cc_final: 0.7976 (mttp) REVERT: J 148 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6966 (tt0) REVERT: J 180 MET cc_start: 0.6966 (mtm) cc_final: 0.6603 (mtm) REVERT: J 217 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6553 (tm) REVERT: J 311 ARG cc_start: 0.6523 (tpt90) cc_final: 0.6263 (tpt90) REVERT: J 325 LYS cc_start: 0.7913 (tttt) cc_final: 0.7695 (tttp) REVERT: J 443 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6675 (pp20) REVERT: J 532 GLU cc_start: 0.7885 (tt0) cc_final: 0.7259 (tt0) REVERT: J 655 SER cc_start: 0.7947 (t) cc_final: 0.7567 (p) REVERT: J 747 MET cc_start: 0.8679 (mmm) cc_final: 0.8479 (mmt) REVERT: J 749 LYS cc_start: 0.8311 (mtmt) cc_final: 0.7956 (mtpp) REVERT: J 756 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: J 849 LEU cc_start: 0.6255 (mm) cc_final: 0.5820 (mt) REVERT: J 868 TRP cc_start: 0.6941 (OUTLIER) cc_final: 0.6336 (t-100) REVERT: J 925 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7481 (tm-30) REVERT: J 995 TYR cc_start: 0.7022 (m-80) cc_final: 0.6807 (m-10) REVERT: J 1244 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7617 (mm110) REVERT: K 51 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7676 (mt) REVERT: K 74 GLU cc_start: 0.6076 (OUTLIER) cc_final: 0.5745 (mt-10) REVERT: L 110 LEU cc_start: 0.6225 (OUTLIER) cc_final: 0.5890 (pp) REVERT: L 158 LEU cc_start: -0.0286 (OUTLIER) cc_final: -0.0972 (tp) REVERT: L 277 MET cc_start: 0.5210 (tmm) cc_final: 0.4447 (tmm) REVERT: L 403 ASP cc_start: 0.7401 (OUTLIER) cc_final: 0.6975 (t0) REVERT: L 470 MET cc_start: 0.7437 (mtp) cc_final: 0.7233 (mtp) outliers start: 293 outliers final: 210 residues processed: 645 average time/residue: 0.1962 time to fit residues: 206.7851 Evaluate side-chains 597 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 227 poor density : 370 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 48 ARG Chi-restraints excluded: chain G residue 19 VAL Chi-restraints excluded: chain G residue 23 HIS Chi-restraints excluded: chain G residue 56 VAL Chi-restraints excluded: chain G residue 75 GLN Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 140 ILE 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 188 GLU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 99 ILE 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 4 SER 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 47 TYR Chi-restraints excluded: chain I residue 59 ILE Chi-restraints excluded: chain I residue 82 VAL Chi-restraints excluded: chain I residue 83 GLN Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 118 LYS Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 242 VAL Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 360 LEU Chi-restraints excluded: chain I residue 385 PHE Chi-restraints excluded: chain I residue 428 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 492 MET 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 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 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 607 SER Chi-restraints excluded: chain I residue 609 ILE Chi-restraints excluded: chain I residue 638 SER Chi-restraints excluded: chain I residue 657 THR Chi-restraints excluded: chain I residue 684 ASN Chi-restraints excluded: chain I residue 690 VAL Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 723 VAL Chi-restraints excluded: chain I residue 745 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 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 829 THR Chi-restraints excluded: chain I residue 842 ASP Chi-restraints excluded: chain I residue 878 THR Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 915 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 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 978 VAL Chi-restraints excluded: chain I residue 998 LEU 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 1083 GLU Chi-restraints excluded: chain I residue 1092 THR Chi-restraints excluded: chain I residue 1108 ASN Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1132 LEU Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 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 1200 LYS 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 1240 ASP Chi-restraints excluded: chain I residue 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1339 LEU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 65 VAL Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 392 THR Chi-restraints excluded: chain J residue 401 VAL Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 449 LEU Chi-restraints excluded: chain J residue 487 THR Chi-restraints excluded: chain J residue 503 SER 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 582 ILE Chi-restraints excluded: chain J residue 591 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 641 ILE 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 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 756 GLU Chi-restraints excluded: chain J residue 760 THR Chi-restraints excluded: chain J residue 774 ILE Chi-restraints excluded: chain J residue 776 THR 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 844 THR 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 901 ARG Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 925 GLU Chi-restraints excluded: chain J residue 963 VAL Chi-restraints excluded: chain J residue 997 VAL 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 1024 THR Chi-restraints excluded: chain J residue 1063 ASP 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 1172 LYS Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1223 LEU Chi-restraints excluded: chain J residue 1235 ASN Chi-restraints excluded: chain J residue 1244 GLN Chi-restraints excluded: chain J residue 1246 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1272 SER 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 J residue 1337 VAL Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 158 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 322 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 457 ILE Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 467 SER Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 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: 2.9990 chunk 35 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 39 optimal weight: 0.0060 chunk 333 optimal weight: 5.9990 chunk 209 optimal weight: 0.9980 chunk 364 optimal weight: 0.0470 chunk 237 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.5494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 23 HIS H 132 HIS H 186 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 387 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1220 GLN ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS J 716 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 545 HIS ** M 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.146357 restraints weight = 42891.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.145279 restraints weight = 96309.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.146240 restraints weight = 85549.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.146180 restraints weight = 53716.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.146695 restraints weight = 48480.173| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33047 Z= 0.139 Angle : 0.694 12.017 45093 Z= 0.358 Chirality : 0.046 0.275 5168 Planarity : 0.005 0.070 5502 Dihedral : 17.625 124.205 5835 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.94 % Favored : 92.98 % Rotamer: Outliers : 7.25 % Allowed : 27.17 % Favored : 65.58 % 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: -2.35 (0.13), residues: 3804 helix: -0.39 (0.13), residues: 1519 sheet: -2.61 (0.22), residues: 417 loop : -2.32 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1284 TYR 0.022 0.002 TYR J1186 PHE 0.019 0.002 PHE I 225 TRP 0.022 0.001 TRP L 326 HIS 0.006 0.001 HIS G 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (33035) covalent geometry : angle 0.69254 / 0.36 (45081) hydrogen bonds : bond 0.04841 / 3.23 ( 1326) hydrogen bonds : angle 5.16029 / 3.54 ( 3692) metal coordination : bond 0.00279 / 0.19 ( 11) metal coordination : angle 3.20185 / 2.34 ( 12) Misc. bond : bond 0.00062 / 0.03 ( 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 654 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 237 poor density : 417 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: N 49 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7967 (ttp-110) REVERT: G 41 ASN cc_start: 0.9060 (t0) cc_final: 0.8756 (t0) REVERT: G 231 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.8110 (t80) REVERT: H 13 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7720 (pp) REVERT: H 23 HIS cc_start: 0.7229 (t-90) cc_final: 0.7005 (t-170) REVERT: I 47 TYR cc_start: 0.7341 (OUTLIER) cc_final: 0.6952 (p90) REVERT: I 85 CYS cc_start: 0.8160 (OUTLIER) cc_final: 0.7898 (m) REVERT: I 213 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6422 (mt) REVERT: I 503 LYS cc_start: 0.7896 (mtmm) cc_final: 0.7495 (mtmt) REVERT: I 573 ASN cc_start: 0.7943 (m-40) cc_final: 0.7729 (m110) REVERT: I 711 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8277 (t0) REVERT: I 854 ILE cc_start: 0.8285 (mt) cc_final: 0.8080 (mt) REVERT: I 1136 GLN cc_start: 0.7375 (tp40) cc_final: 0.7175 (tp40) REVERT: I 1143 GLU cc_start: 0.7750 (pp20) cc_final: 0.7453 (pp20) REVERT: J 99 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.7322 (mtp85) REVERT: J 148 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6257 (tm-30) REVERT: J 180 MET cc_start: 0.6963 (mtm) cc_final: 0.6635 (mtm) REVERT: J 325 LYS cc_start: 0.7766 (tttt) cc_final: 0.7486 (mmtt) REVERT: J 503 SER cc_start: 0.7856 (OUTLIER) cc_final: 0.7374 (t) REVERT: J 532 GLU cc_start: 0.7532 (tt0) cc_final: 0.7132 (tt0) REVERT: J 582 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8250 (mt) REVERT: J 641 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7585 (tp) REVERT: J 655 SER cc_start: 0.7919 (t) cc_final: 0.7718 (p) REVERT: J 731 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7409 (tpt90) REVERT: J 756 GLU cc_start: 0.7638 (pt0) cc_final: 0.6924 (tt0) REVERT: J 849 LEU cc_start: 0.6201 (mm) cc_final: 0.5859 (mt) REVERT: J 868 TRP cc_start: 0.6778 (OUTLIER) cc_final: 0.6323 (t-100) REVERT: J 925 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7502 (tm-30) REVERT: K 51 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7860 (mt) REVERT: K 74 GLU cc_start: 0.6109 (OUTLIER) cc_final: 0.5441 (mt-10) REVERT: L 277 MET cc_start: 0.4046 (tmm) cc_final: 0.3761 (tmm) REVERT: L 403 ASP cc_start: 0.7235 (OUTLIER) cc_final: 0.6809 (t0) REVERT: L 470 MET cc_start: 0.7393 (mtp) cc_final: 0.7156 (mtp) REVERT: L 523 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8670 (mm) REVERT: M 284 ARG cc_start: 0.2946 (OUTLIER) cc_final: 0.1861 (mtt180) outliers start: 237 outliers final: 156 residues processed: 603 average time/residue: 0.2039 time to fit residues: 200.0180 Evaluate side-chains 534 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 360 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 172 LEU 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 231 PHE Chi-restraints excluded: chain H residue 6 THR Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 83 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 21 VAL 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 91 THR 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 194 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 228 VAL Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 385 PHE 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 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 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 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 616 ILE Chi-restraints excluded: chain I residue 638 SER Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 711 ASP 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 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 946 LEU Chi-restraints excluded: chain I residue 951 MET 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 1029 LEU Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1107 MET Chi-restraints excluded: chain I residue 1131 MET 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 1226 THR 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 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1337 ILE Chi-restraints excluded: chain I residue 1340 GLU Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 70 CYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 200 GLN 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 503 SER 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 582 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 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 731 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 776 THR Chi-restraints excluded: chain J residue 801 VAL Chi-restraints excluded: chain J residue 839 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 901 ARG Chi-restraints excluded: chain J residue 963 VAL 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 1024 THR Chi-restraints excluded: chain J residue 1086 ASN Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1095 MET Chi-restraints excluded: chain J residue 1113 VAL 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 1246 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1261 LEU Chi-restraints excluded: chain J residue 1272 SER 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 K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain K residue 74 GLU Chi-restraints excluded: chain L residue 98 VAL 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 322 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 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 523 ILE Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 275 ILE Chi-restraints excluded: chain M residue 281 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 347 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 380 optimal weight: 40.0000 chunk 247 optimal weight: 3.9990 chunk 164 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 207 optimal weight: 0.0570 chunk 311 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 313 optimal weight: 0.7980 overall best weight: 1.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 677 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.177745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.144924 restraints weight = 43160.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.139376 restraints weight = 41773.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.140434 restraints weight = 59932.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.141267 restraints weight = 41064.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.141392 restraints weight = 33371.212| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33047 Z= 0.149 Angle : 0.682 11.978 45093 Z= 0.349 Chirality : 0.045 0.271 5168 Planarity : 0.005 0.085 5502 Dihedral : 17.425 125.217 5796 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.60 % Favored : 92.32 % Rotamer: Outliers : 6.82 % Allowed : 27.63 % Favored : 65.54 % 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: -2.08 (0.13), residues: 3804 helix: -0.20 (0.13), residues: 1527 sheet: -2.32 (0.22), residues: 423 loop : -2.18 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 158 TYR 0.030 0.002 TYR J 995 PHE 0.031 0.002 PHE L 302 TRP 0.022 0.001 TRP L 326 HIS 0.007 0.001 HIS J 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (33035) covalent geometry : angle 0.68067 / 0.35 (45081) hydrogen bonds : bond 0.04689 / 3.12 ( 1326) hydrogen bonds : angle 5.01435 / 3.43 ( 3692) metal coordination : bond 0.00449 / 0.31 ( 11) metal coordination : angle 2.77690 / 2.07 ( 12) Misc. bond : bond 0.00042 / 0.02 ( 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 615 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 223 poor density : 392 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: G 41 ASN cc_start: 0.9081 (t0) cc_final: 0.8804 (t0) REVERT: G 231 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7912 (t80) REVERT: H 13 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7644 (pp) REVERT: I 47 TYR cc_start: 0.7375 (OUTLIER) cc_final: 0.6937 (p90) REVERT: I 85 CYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7934 (m) REVERT: I 213 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6176 (mt) REVERT: I 403 MET cc_start: 0.7319 (tmm) cc_final: 0.6959 (tpt) REVERT: I 503 LYS cc_start: 0.8130 (mtmm) cc_final: 0.7761 (mtmt) REVERT: I 573 ASN cc_start: 0.8054 (m-40) cc_final: 0.7796 (m110) REVERT: I 854 ILE cc_start: 0.8286 (mt) cc_final: 0.8076 (mt) REVERT: I 1136 GLN cc_start: 0.7467 (tp40) cc_final: 0.7241 (tp40) REVERT: J 99 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8016 (mtp85) REVERT: J 148 GLU cc_start: 0.7302 (tt0) cc_final: 0.6390 (tm-30) REVERT: J 165 TYR cc_start: 0.6539 (t80) cc_final: 0.6211 (t80) REVERT: J 180 MET cc_start: 0.6917 (mtm) cc_final: 0.6534 (mtm) REVERT: J 200 GLN cc_start: 0.7473 (OUTLIER) cc_final: 0.6623 (mt0) REVERT: J 443 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6764 (pp20) REVERT: J 532 GLU cc_start: 0.7759 (tt0) cc_final: 0.7373 (tt0) REVERT: J 582 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8320 (mt) REVERT: J 655 SER cc_start: 0.8036 (t) cc_final: 0.7708 (p) REVERT: J 756 GLU cc_start: 0.7579 (pt0) cc_final: 0.7217 (tt0) REVERT: J 849 LEU cc_start: 0.6302 (mm) cc_final: 0.5959 (mt) REVERT: J 868 TRP cc_start: 0.6714 (OUTLIER) cc_final: 0.6168 (t-100) REVERT: J 925 GLU cc_start: 0.7966 (tm-30) cc_final: 0.7520 (tm-30) REVERT: K 25 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7877 (ttm170) REVERT: K 51 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7575 (mt) REVERT: L 110 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5667 (pp) REVERT: L 116 GLU cc_start: 0.7791 (pt0) cc_final: 0.7301 (tt0) REVERT: L 297 MET cc_start: -0.0113 (ppp) cc_final: -0.0375 (ppp) REVERT: L 403 ASP cc_start: 0.7300 (OUTLIER) cc_final: 0.7038 (t0) REVERT: L 470 MET cc_start: 0.7571 (mtp) cc_final: 0.7329 (mtp) REVERT: L 523 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8735 (mm) REVERT: M 284 ARG cc_start: 0.2480 (OUTLIER) cc_final: 0.1389 (mtt180) REVERT: M 298 LYS cc_start: 0.0496 (OUTLIER) cc_final: 0.0264 (tptt) REVERT: M 300 LEU cc_start: 0.0318 (OUTLIER) cc_final: -0.0356 (pp) outliers start: 223 outliers final: 165 residues processed: 570 average time/residue: 0.2014 time to fit residues: 186.6661 Evaluate side-chains 543 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 361 time to evaluate : 1.144 ------------------------------------------------------------------------------- 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 75 GLN Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 131 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 172 LEU 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 231 PHE Chi-restraints excluded: chain H residue 13 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 98 VAL 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 157 THR 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 82 VAL Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 91 THR 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 194 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 319 LEU Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 385 PHE 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 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 547 VAL 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 663 VAL Chi-restraints excluded: chain I residue 705 GLU 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 915 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 951 MET 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 1012 GLU 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 1131 MET 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 1160 ASP 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 1226 THR 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 1248 THR Chi-restraints excluded: chain I residue 1250 SER Chi-restraints excluded: chain I residue 1337 ILE 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 70 CYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 83 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 99 ARG Chi-restraints excluded: chain J residue 129 ASP Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 306 LEU Chi-restraints excluded: chain J residue 343 LEU Chi-restraints excluded: chain J residue 443 GLU Chi-restraints excluded: chain J residue 473 THR 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 582 ILE Chi-restraints excluded: chain J residue 612 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 722 ILE Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 801 VAL 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 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 901 ARG Chi-restraints excluded: chain J residue 930 LEU Chi-restraints excluded: chain J residue 963 VAL 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 1024 THR Chi-restraints excluded: chain J residue 1041 ILE 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 1155 ILE 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 1272 SER 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 110 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 322 MET Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 476 ARG 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 275 ILE Chi-restraints excluded: chain M residue 281 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 Chi-restraints excluded: chain M residue 298 LYS Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 214 optimal weight: 0.7980 chunk 185 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 340 optimal weight: 0.4980 chunk 225 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 chunk 163 optimal weight: 0.0980 chunk 286 optimal weight: 3.9990 chunk 318 optimal weight: 0.0370 chunk 231 optimal weight: 0.5980 chunk 372 optimal weight: 50.0000 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS H 66 HIS ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN I 725 GLN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 ASN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 309 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.175713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142135 restraints weight = 43365.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140992 restraints weight = 90924.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.142000 restraints weight = 85233.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.141994 restraints weight = 52932.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.142641 restraints weight = 48099.876| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3271 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= 0.123 Angle : 0.650 11.760 45093 Z= 0.334 Chirality : 0.044 0.267 5168 Planarity : 0.005 0.079 5502 Dihedral : 17.233 124.716 5781 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.34 % Favored : 93.56 % Rotamer: Outliers : 5.88 % Allowed : 28.86 % Favored : 65.27 % 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: -1.74 (0.13), residues: 3804 helix: 0.06 (0.13), residues: 1540 sheet: -2.11 (0.23), residues: 437 loop : -1.99 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J1284 TYR 0.036 0.002 TYR J 995 PHE 0.019 0.001 PHE L 302 TRP 0.017 0.001 TRP L 326 HIS 0.007 0.001 HIS H 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (33035) covalent geometry : angle 0.64864 / 0.33 (45081) hydrogen bonds : bond 0.04387 / 2.90 ( 1326) hydrogen bonds : angle 4.77967 / 3.27 ( 3692) metal coordination : bond 0.00289 / 0.19 ( 11) metal coordination : angle 2.42412 / 1.67 ( 12) Misc. bond : bond 0.00030 / 0.02 ( 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 611 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 192 poor density : 419 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8872 (t0) cc_final: 0.8654 (t0) REVERT: G 231 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.8032 (t80) REVERT: H 65 LEU cc_start: 0.4451 (OUTLIER) cc_final: 0.4131 (tp) REVERT: H 71 LYS cc_start: 0.6289 (tptp) cc_final: 0.5672 (mmmt) REVERT: H 75 GLN cc_start: 0.7316 (pm20) cc_final: 0.7016 (pt0) REVERT: H 77 ASP cc_start: 0.8395 (OUTLIER) cc_final: 0.8176 (t0) REVERT: I 47 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6789 (p90) REVERT: I 83 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6615 (mp10) REVERT: I 85 CYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7853 (m) REVERT: I 163 LYS cc_start: 0.7170 (mptt) cc_final: 0.6561 (pttp) REVERT: I 503 LYS cc_start: 0.8127 (mtmm) cc_final: 0.7710 (mtmt) REVERT: I 711 ASP cc_start: 0.8433 (OUTLIER) cc_final: 0.8225 (t0) REVERT: I 854 ILE cc_start: 0.8336 (mt) cc_final: 0.8108 (mt) REVERT: I 1136 GLN cc_start: 0.7300 (tp40) cc_final: 0.6953 (tp-100) REVERT: J 148 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6318 (tm-30) REVERT: J 180 MET cc_start: 0.6777 (mtm) cc_final: 0.6378 (mtm) REVERT: J 188 LEU cc_start: 0.7990 (tp) cc_final: 0.7773 (tp) REVERT: J 532 GLU cc_start: 0.7569 (tt0) cc_final: 0.7133 (tt0) REVERT: J 582 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8217 (mt) REVERT: J 655 SER cc_start: 0.8039 (t) cc_final: 0.7816 (p) REVERT: J 756 GLU cc_start: 0.7533 (pt0) cc_final: 0.7225 (tt0) REVERT: J 849 LEU cc_start: 0.6390 (mm) cc_final: 0.5987 (mt) REVERT: J 868 TRP cc_start: 0.6679 (OUTLIER) cc_final: 0.6209 (t-100) REVERT: J 925 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7508 (tm-30) REVERT: K 25 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7979 (ttm170) REVERT: K 51 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7507 (mt) REVERT: K 69 ARG cc_start: 0.7449 (ttm-80) cc_final: 0.6109 (ttp-110) REVERT: L 277 MET cc_start: 0.4172 (tmm) cc_final: 0.3600 (tmm) REVERT: L 403 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6993 (t0) REVERT: L 470 MET cc_start: 0.7436 (mtp) cc_final: 0.7188 (mtp) REVERT: L 523 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8725 (mm) REVERT: L 561 MET cc_start: 0.6714 (mpt) cc_final: 0.6171 (mpt) REVERT: M 284 ARG cc_start: 0.2965 (OUTLIER) cc_final: 0.2064 (mtt180) REVERT: M 300 LEU cc_start: 0.0294 (OUTLIER) cc_final: -0.0264 (pp) outliers start: 192 outliers final: 129 residues processed: 569 average time/residue: 0.2111 time to fit residues: 194.1483 Evaluate side-chains 514 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 370 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU 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 144 ILE 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 203 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 83 LEU Chi-restraints excluded: chain H residue 86 LYS 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 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 61 SER 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 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 385 PHE 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 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL 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 638 SER Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 705 GLU Chi-restraints excluded: chain I residue 711 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 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 951 MET Chi-restraints excluded: chain I residue 953 LEU Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 978 VAL 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 1113 LEU Chi-restraints excluded: chain I residue 1131 MET 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 1240 ASP 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 70 CYS Chi-restraints excluded: chain J residue 78 LEU Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL 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 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 582 ILE Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 672 LEU Chi-restraints excluded: chain J residue 701 LEU Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 746 LEU 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 1024 THR 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 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 K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 132 CYS Chi-restraints excluded: chain L residue 250 LEU Chi-restraints excluded: chain L residue 262 VAL Chi-restraints excluded: chain L residue 304 THR Chi-restraints excluded: chain L residue 322 MET Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS Chi-restraints excluded: chain L residue 523 ILE Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 281 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 Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 372 optimal weight: 50.0000 chunk 233 optimal weight: 2.9990 chunk 169 optimal weight: 0.9990 chunk 46 optimal weight: 0.0870 chunk 305 optimal weight: 0.7980 chunk 290 optimal weight: 30.0000 chunk 27 optimal weight: 5.9990 chunk 140 optimal weight: 0.0000 chunk 287 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 271 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.175408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.140269 restraints weight = 43469.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.139022 restraints weight = 84350.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140072 restraints weight = 82369.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140189 restraints weight = 50754.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140878 restraints weight = 45664.577| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3477 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= 0.122 Angle : 0.648 11.377 45093 Z= 0.331 Chirality : 0.044 0.254 5168 Planarity : 0.005 0.089 5502 Dihedral : 17.065 124.614 5754 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.55 % Favored : 93.35 % Rotamer: Outliers : 5.69 % Allowed : 28.82 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.97 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.49 (0.13), residues: 3804 helix: 0.25 (0.13), residues: 1537 sheet: -1.91 (0.24), residues: 421 loop : -1.84 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 322 TYR 0.019 0.001 TYR J 995 PHE 0.029 0.001 PHE L 302 TRP 0.018 0.001 TRP L 326 HIS 0.005 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (33035) covalent geometry : angle 0.64648 / 0.33 (45081) hydrogen bonds : bond 0.04284 / 2.82 ( 1326) hydrogen bonds : angle 4.69515 / 3.21 ( 3692) metal coordination : bond 0.00287 / 0.18 ( 11) metal coordination : angle 2.36791 / 1.56 ( 12) Misc. bond : bond 0.00032 / 0.02 ( 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 573 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 186 poor density : 387 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8878 (t0) cc_final: 0.8662 (t0) REVERT: G 231 PHE cc_start: 0.8379 (OUTLIER) cc_final: 0.7958 (t80) REVERT: H 65 LEU cc_start: 0.4477 (OUTLIER) cc_final: 0.4184 (tp) REVERT: H 71 LYS cc_start: 0.6262 (tptp) cc_final: 0.5654 (mmmt) REVERT: H 75 GLN cc_start: 0.7257 (pm20) cc_final: 0.6936 (pt0) REVERT: H 77 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8197 (t0) REVERT: H 86 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7197 (mtmt) REVERT: I 47 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.6695 (p90) REVERT: I 85 CYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7839 (m) REVERT: I 163 LYS cc_start: 0.7272 (mptt) cc_final: 0.6536 (pttp) REVERT: I 503 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7758 (mtmt) REVERT: I 711 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8248 (t0) REVERT: I 854 ILE cc_start: 0.8319 (mt) cc_final: 0.8077 (mt) REVERT: I 1136 GLN cc_start: 0.7191 (tp40) cc_final: 0.6804 (tp-100) REVERT: I 1292 THR cc_start: 0.8890 (m) cc_final: 0.8567 (p) REVERT: J 133 ARG cc_start: 0.7705 (mmm160) cc_final: 0.7244 (mmm160) REVERT: J 148 GLU cc_start: 0.7358 (tt0) cc_final: 0.6630 (tm-30) REVERT: J 582 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.8235 (mt) REVERT: J 655 SER cc_start: 0.8093 (t) cc_final: 0.7839 (p) REVERT: J 698 MET cc_start: 0.8430 (tpp) cc_final: 0.7829 (mmm) REVERT: J 756 GLU cc_start: 0.7517 (pt0) cc_final: 0.7238 (tt0) REVERT: J 863 LEU cc_start: 0.7304 (tp) cc_final: 0.6841 (tp) REVERT: J 868 TRP cc_start: 0.6622 (OUTLIER) cc_final: 0.6205 (t-100) REVERT: J 925 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7499 (tm-30) REVERT: J 1276 GLU cc_start: 0.5925 (OUTLIER) cc_final: 0.5443 (tt0) REVERT: K 25 ARG cc_start: 0.8272 (ttp80) cc_final: 0.7931 (ttm170) REVERT: K 51 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7641 (mt) REVERT: L 277 MET cc_start: 0.4391 (tmm) cc_final: 0.3794 (tmm) REVERT: L 403 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.6999 (t0) REVERT: L 470 MET cc_start: 0.7467 (mtp) cc_final: 0.7263 (mtp) REVERT: L 523 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8867 (mm) REVERT: L 561 MET cc_start: 0.6755 (mpt) cc_final: 0.6477 (mpt) REVERT: M 284 ARG cc_start: 0.2898 (OUTLIER) cc_final: 0.2000 (mtt90) REVERT: M 300 LEU cc_start: 0.0338 (OUTLIER) cc_final: -0.0171 (pp) outliers start: 186 outliers final: 141 residues processed: 537 average time/residue: 0.2020 time to fit residues: 176.9986 Evaluate side-chains 523 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 367 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU 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 74 VAL Chi-restraints excluded: chain G residue 83 LEU Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 231 PHE Chi-restraints excluded: chain H residue 9 LEU Chi-restraints excluded: chain H residue 31 LEU Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 46 ILE Chi-restraints excluded: chain H residue 54 CYS Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 86 LYS Chi-restraints excluded: chain H residue 98 VAL 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 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 85 CYS 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 194 LEU Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 385 PHE 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 521 LEU Chi-restraints excluded: chain I residue 538 LEU Chi-restraints excluded: chain I residue 547 VAL 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 711 ASP Chi-restraints excluded: chain I residue 745 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 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 915 ASP 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 978 VAL 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 1131 MET 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 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 1240 ASP 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 78 LEU Chi-restraints excluded: chain J residue 80 HIS 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 200 GLN Chi-restraints excluded: chain J residue 217 LEU 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 486 SER 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 582 ILE 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 722 ILE Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 801 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 1024 THR 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 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 1291 GLU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 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 306 PHE Chi-restraints excluded: chain L residue 322 MET Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG Chi-restraints excluded: chain L residue 489 MET Chi-restraints excluded: chain L residue 502 LYS 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 288 GLU Chi-restraints excluded: chain M residue 292 THR Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 125 optimal weight: 6.9990 chunk 144 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 177 optimal weight: 3.9990 chunk 285 optimal weight: 8.9990 chunk 93 optimal weight: 9.9990 chunk 361 optimal weight: 0.0870 chunk 256 optimal weight: 0.3980 chunk 192 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 271 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.174731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.140343 restraints weight = 43630.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.139420 restraints weight = 91316.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140522 restraints weight = 87138.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.140552 restraints weight = 53456.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.141427 restraints weight = 47311.405| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 33047 Z= 0.132 Angle : 0.649 11.390 45093 Z= 0.331 Chirality : 0.043 0.249 5168 Planarity : 0.005 0.080 5502 Dihedral : 16.974 124.282 5749 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.68 % Favored : 93.22 % Rotamer: Outliers : 5.66 % Allowed : 28.98 % Favored : 65.36 % 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: -1.34 (0.13), residues: 3804 helix: 0.38 (0.13), residues: 1534 sheet: -1.80 (0.24), residues: 409 loop : -1.78 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 322 TYR 0.019 0.001 TYR I1018 PHE 0.025 0.001 PHE L 302 TRP 0.017 0.001 TRP L 326 HIS 0.004 0.001 HIS G 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (33035) covalent geometry : angle 0.64787 / 0.33 (45081) hydrogen bonds : bond 0.04237 / 2.79 ( 1326) hydrogen bonds : angle 4.61217 / 3.14 ( 3692) metal coordination : bond 0.00379 / 0.25 ( 11) metal coordination : angle 2.18158 / 1.43 ( 12) Misc. bond : bond 0.00041 / 0.02 ( 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 566 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 381 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8944 (t0) cc_final: 0.8660 (t0) REVERT: G 231 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7960 (t80) REVERT: H 65 LEU cc_start: 0.4477 (OUTLIER) cc_final: 0.4181 (tp) REVERT: H 71 LYS cc_start: 0.6151 (tptp) cc_final: 0.5611 (mmmt) REVERT: H 75 GLN cc_start: 0.7262 (pm20) cc_final: 0.6934 (pt0) REVERT: H 86 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7294 (mtmt) REVERT: I 47 TYR cc_start: 0.7133 (OUTLIER) cc_final: 0.6762 (p90) REVERT: I 85 CYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7843 (m) REVERT: I 163 LYS cc_start: 0.7261 (mptt) cc_final: 0.6511 (pttp) REVERT: I 503 LYS cc_start: 0.8175 (mtmm) cc_final: 0.7775 (mtmt) REVERT: I 637 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8507 (ptt-90) REVERT: I 711 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8263 (t0) REVERT: I 854 ILE cc_start: 0.8195 (mt) cc_final: 0.7946 (mt) REVERT: I 1136 GLN cc_start: 0.7208 (tp40) cc_final: 0.6861 (tp-100) REVERT: I 1292 THR cc_start: 0.8851 (m) cc_final: 0.8534 (p) REVERT: J 133 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7319 (tpt-90) REVERT: J 148 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6613 (tm-30) REVERT: J 200 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6788 (pp30) REVERT: J 587 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8767 (mp) REVERT: J 655 SER cc_start: 0.8102 (t) cc_final: 0.7777 (p) REVERT: J 698 MET cc_start: 0.8377 (tpp) cc_final: 0.7737 (mmm) REVERT: J 757 THR cc_start: 0.9124 (t) cc_final: 0.8921 (p) REVERT: J 863 LEU cc_start: 0.6989 (tp) cc_final: 0.6674 (tp) REVERT: J 868 TRP cc_start: 0.6659 (OUTLIER) cc_final: 0.6222 (t-100) REVERT: J 925 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7515 (tm-30) REVERT: J 1276 GLU cc_start: 0.5934 (OUTLIER) cc_final: 0.5438 (tt0) REVERT: K 25 ARG cc_start: 0.8248 (ttp80) cc_final: 0.7920 (ttm170) REVERT: K 51 LEU cc_start: 0.7918 (OUTLIER) cc_final: 0.7665 (mt) REVERT: L 277 MET cc_start: 0.4084 (tmm) cc_final: 0.3573 (tmm) REVERT: L 403 ASP cc_start: 0.7257 (OUTLIER) cc_final: 0.6987 (t0) REVERT: L 470 MET cc_start: 0.7470 (mtp) cc_final: 0.7259 (mtp) REVERT: L 561 MET cc_start: 0.6770 (mpt) cc_final: 0.6543 (mpt) REVERT: M 284 ARG cc_start: 0.3181 (OUTLIER) cc_final: 0.2174 (mtt90) REVERT: M 300 LEU cc_start: 0.0133 (OUTLIER) cc_final: -0.0217 (pp) outliers start: 185 outliers final: 145 residues processed: 525 average time/residue: 0.1968 time to fit residues: 167.6633 Evaluate side-chains 528 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 367 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU 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 131 CYS Chi-restraints excluded: chain G residue 144 ILE Chi-restraints excluded: chain G residue 173 VAL Chi-restraints excluded: chain G residue 188 GLU Chi-restraints excluded: chain G residue 203 ILE 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 54 CYS 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 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU 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 61 SER Chi-restraints excluded: chain I residue 85 CYS Chi-restraints excluded: chain I residue 104 ILE Chi-restraints excluded: chain I residue 167 SER Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU Chi-restraints excluded: chain I residue 285 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 385 PHE 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 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 538 LEU Chi-restraints excluded: chain I residue 547 VAL 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 637 ARG Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 711 ASP Chi-restraints excluded: chain I residue 745 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 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 915 ASP 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 978 VAL 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 1131 MET Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1160 ASP 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 1240 ASP 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 56 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 217 LEU 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 486 SER 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 582 ILE Chi-restraints excluded: chain J residue 587 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 722 ILE Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 801 VAL 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 930 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 997 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 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 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 1291 GLU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain J residue 1353 VAL Chi-restraints excluded: chain K residue 51 LEU Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 132 CYS 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 304 THR Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain L residue 322 MET Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG 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 275 ILE 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 Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 272 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 126 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 315 optimal weight: 1.9990 chunk 285 optimal weight: 5.9990 chunk 71 optimal weight: 7.9990 chunk 209 optimal weight: 0.7980 chunk 149 optimal weight: 6.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 720 ASN J 805 GLN ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 271 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.173473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 97)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.137172 restraints weight = 43397.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.132147 restraints weight = 51026.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.133479 restraints weight = 58532.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.134006 restraints weight = 39497.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.134213 restraints weight = 35792.497| |-----------------------------------------------------------------------------| r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 33047 Z= 0.157 Angle : 0.667 11.893 45093 Z= 0.339 Chirality : 0.044 0.229 5168 Planarity : 0.005 0.070 5502 Dihedral : 16.901 124.183 5744 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.02 % Favored : 92.90 % Rotamer: Outliers : 5.75 % Allowed : 29.10 % Favored : 65.15 % 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: -1.32 (0.13), residues: 3804 helix: 0.39 (0.13), residues: 1533 sheet: -1.74 (0.24), residues: 428 loop : -1.77 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 978 TYR 0.019 0.002 TYR I1018 PHE 0.023 0.001 PHE J 172 TRP 0.017 0.001 TRP L 326 HIS 0.004 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (33035) covalent geometry : angle 0.66558 / 0.34 (45081) hydrogen bonds : bond 0.04336 / 2.86 ( 1326) hydrogen bonds : angle 4.62407 / 3.14 ( 3692) metal coordination : bond 0.00544 / 0.36 ( 11) metal coordination : angle 2.36537 / 1.58 ( 12) Misc. bond : bond 0.00055 / 0.03 ( 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 555 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 188 poor density : 367 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8992 (t0) cc_final: 0.8712 (t0) REVERT: G 231 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7955 (t80) REVERT: H 65 LEU cc_start: 0.4538 (OUTLIER) cc_final: 0.4262 (tp) REVERT: H 71 LYS cc_start: 0.6102 (tptp) cc_final: 0.5609 (mmmt) REVERT: H 75 GLN cc_start: 0.7353 (pm20) cc_final: 0.7028 (pt0) REVERT: H 86 LYS cc_start: 0.8268 (OUTLIER) cc_final: 0.7401 (mtmt) REVERT: H 198 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8417 (mt) REVERT: I 47 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.6924 (p90) REVERT: I 85 CYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7863 (m) REVERT: I 163 LYS cc_start: 0.7186 (mptt) cc_final: 0.6413 (pttp) REVERT: I 503 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7834 (mtmt) REVERT: I 637 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8569 (ptt-90) REVERT: I 711 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8343 (t0) REVERT: I 854 ILE cc_start: 0.8225 (mt) cc_final: 0.8002 (mt) REVERT: I 899 GLU cc_start: 0.8348 (tp30) cc_final: 0.8104 (tp30) REVERT: I 1229 TYR cc_start: 0.8891 (m-80) cc_final: 0.8686 (m-80) REVERT: J 133 ARG cc_start: 0.7724 (mmm160) cc_final: 0.7186 (tpt-90) REVERT: J 148 GLU cc_start: 0.7383 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: J 200 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.6801 (pp30) REVERT: J 532 GLU cc_start: 0.7680 (tt0) cc_final: 0.7245 (tt0) REVERT: J 587 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8771 (mp) REVERT: J 624 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8581 (tt) REVERT: J 655 SER cc_start: 0.8132 (t) cc_final: 0.7794 (p) REVERT: J 698 MET cc_start: 0.8407 (tpp) cc_final: 0.7929 (mmm) REVERT: J 863 LEU cc_start: 0.7136 (tp) cc_final: 0.6826 (tp) REVERT: J 868 TRP cc_start: 0.6744 (OUTLIER) cc_final: 0.6235 (t-100) REVERT: J 925 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7552 (tm-30) REVERT: J 1205 GLU cc_start: 0.6689 (OUTLIER) cc_final: 0.6436 (mm-30) REVERT: J 1276 GLU cc_start: 0.5978 (OUTLIER) cc_final: 0.5506 (tt0) REVERT: K 25 ARG cc_start: 0.8290 (ttp80) cc_final: 0.7938 (ttm170) REVERT: L 403 ASP cc_start: 0.7304 (OUTLIER) cc_final: 0.7039 (t0) REVERT: L 470 MET cc_start: 0.7472 (mtp) cc_final: 0.7255 (mtp) REVERT: L 561 MET cc_start: 0.6713 (mpt) cc_final: 0.6344 (mpt) REVERT: M 278 ILE cc_start: 0.3157 (OUTLIER) cc_final: 0.2680 (mt) REVERT: M 284 ARG cc_start: 0.3019 (OUTLIER) cc_final: 0.2054 (mtt180) REVERT: M 300 LEU cc_start: 0.0223 (OUTLIER) cc_final: -0.0212 (pp) outliers start: 188 outliers final: 149 residues processed: 512 average time/residue: 0.1993 time to fit residues: 167.5550 Evaluate side-chains 525 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 357 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU 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 131 CYS Chi-restraints excluded: chain G residue 144 ILE 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 203 ILE 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 54 CYS 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 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU 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 61 SER Chi-restraints excluded: chain I residue 85 CYS 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 173 ASN Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU 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 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 538 LEU Chi-restraints excluded: chain I residue 547 VAL 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 637 ARG Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 711 ASP Chi-restraints excluded: chain I residue 745 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 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 915 ASP 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 978 VAL Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1058 ARG Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1113 LEU Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1160 ASP 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 1240 ASP 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 78 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 200 GLN Chi-restraints excluded: chain J residue 217 LEU 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 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 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 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 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 801 VAL 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 930 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 997 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 1093 THR Chi-restraints excluded: chain J residue 1155 ILE Chi-restraints excluded: chain J residue 1198 VAL Chi-restraints excluded: chain J residue 1205 GLU 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 1276 GLU 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 58 LEU Chi-restraints excluded: chain L residue 132 CYS 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 304 THR Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain L residue 322 MET Chi-restraints excluded: chain L residue 403 ASP Chi-restraints excluded: chain L residue 466 ILE Chi-restraints excluded: chain L residue 476 ARG 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 278 ILE 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 Chi-restraints excluded: chain M residue 300 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 103 optimal weight: 0.0030 chunk 244 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 376 optimal weight: 50.0000 chunk 313 optimal weight: 2.9990 chunk 270 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 124 optimal weight: 0.4980 chunk 375 optimal weight: 40.0000 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 ASN ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 60 ASN L 271 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.173547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138827 restraints weight = 43610.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138089 restraints weight = 89903.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139160 restraints weight = 87289.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.139283 restraints weight = 51873.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.140759 restraints weight = 45621.508| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 33047 Z= 0.158 Angle : 0.750 59.199 45093 Z= 0.403 Chirality : 0.044 0.490 5168 Planarity : 0.005 0.092 5502 Dihedral : 16.881 124.164 5740 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.07 % Favored : 92.82 % Rotamer: Outliers : 5.48 % Allowed : 29.35 % Favored : 65.18 % Cbeta Deviations : 0.03 % 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: -1.30 (0.13), residues: 3804 helix: 0.41 (0.13), residues: 1533 sheet: -1.73 (0.24), residues: 428 loop : -1.77 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 978 TYR 0.020 0.002 TYR J 165 PHE 0.020 0.001 PHE J 172 TRP 0.016 0.001 TRP L 326 HIS 0.003 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (33035) covalent geometry : angle 0.74945 / 0.40 (45081) hydrogen bonds : bond 0.04329 / 2.85 ( 1326) hydrogen bonds : angle 4.62267 / 3.14 ( 3692) metal coordination : bond 0.00433 / 0.29 ( 11) metal coordination : angle 2.34877 / 1.57 ( 12) Misc. bond : bond 0.00042 / 0.02 ( 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: 179 poor density : 355 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 41 ASN cc_start: 0.8958 (t0) cc_final: 0.8672 (t0) REVERT: G 231 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7919 (t80) REVERT: H 65 LEU cc_start: 0.4530 (OUTLIER) cc_final: 0.4243 (tp) REVERT: H 71 LYS cc_start: 0.6143 (tptp) cc_final: 0.5628 (mmmt) REVERT: H 75 GLN cc_start: 0.7305 (pm20) cc_final: 0.6943 (pt0) REVERT: H 86 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7413 (mtmt) REVERT: H 198 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8397 (mt) REVERT: I 47 TYR cc_start: 0.7273 (OUTLIER) cc_final: 0.6905 (p90) REVERT: I 85 CYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7880 (m) REVERT: I 163 LYS cc_start: 0.7148 (mptt) cc_final: 0.6433 (pttp) REVERT: I 503 LYS cc_start: 0.8183 (mtmm) cc_final: 0.7801 (mtmt) REVERT: I 637 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8566 (ptt-90) REVERT: I 711 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8325 (t0) REVERT: I 854 ILE cc_start: 0.8204 (mt) cc_final: 0.7980 (mt) REVERT: I 899 GLU cc_start: 0.8154 (tp30) cc_final: 0.7905 (tp30) REVERT: I 1229 TYR cc_start: 0.8865 (m-80) cc_final: 0.8663 (m-80) REVERT: J 133 ARG cc_start: 0.7744 (mmm160) cc_final: 0.7264 (tpt-90) REVERT: J 148 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6603 (tm-30) REVERT: J 532 GLU cc_start: 0.7676 (tt0) cc_final: 0.7266 (tt0) REVERT: J 587 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8770 (mp) REVERT: J 624 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8549 (tt) REVERT: J 655 SER cc_start: 0.8118 (t) cc_final: 0.7777 (p) REVERT: J 698 MET cc_start: 0.8422 (tpp) cc_final: 0.7951 (mmm) REVERT: J 863 LEU cc_start: 0.7116 (tp) cc_final: 0.6809 (tp) REVERT: J 868 TRP cc_start: 0.6744 (OUTLIER) cc_final: 0.6241 (t-100) REVERT: J 925 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7498 (tm-30) REVERT: J 1276 GLU cc_start: 0.5941 (OUTLIER) cc_final: 0.5476 (tt0) REVERT: K 25 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7912 (ttm170) REVERT: L 403 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.7041 (t0) REVERT: L 470 MET cc_start: 0.7474 (mtp) cc_final: 0.7253 (mtp) REVERT: L 561 MET cc_start: 0.6718 (mpt) cc_final: 0.6477 (mpt) REVERT: M 278 ILE cc_start: 0.3952 (OUTLIER) cc_final: 0.3409 (mt) REVERT: M 284 ARG cc_start: 0.3179 (OUTLIER) cc_final: 0.2220 (mtt180) REVERT: M 300 LEU cc_start: 0.0270 (OUTLIER) cc_final: -0.0138 (pp) REVERT: M 316 MET cc_start: 0.2567 (OUTLIER) cc_final: 0.1150 (tmm) outliers start: 179 outliers final: 154 residues processed: 492 average time/residue: 0.2002 time to fit residues: 160.9578 Evaluate side-chains 524 residues out of total 3282 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 352 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 13 GLU 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 131 CYS Chi-restraints excluded: chain G residue 144 ILE 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 203 ILE 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 54 CYS 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 121 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 157 THR Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 188 GLU Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 201 LEU 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 61 SER Chi-restraints excluded: chain I residue 85 CYS 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 173 ASN Chi-restraints excluded: chain I residue 176 ILE Chi-restraints excluded: chain I residue 194 LEU 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 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 538 LEU Chi-restraints excluded: chain I residue 547 VAL 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 637 ARG Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 711 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 817 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 915 ASP 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 978 VAL Chi-restraints excluded: chain I residue 1011 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1058 ARG Chi-restraints excluded: chain I residue 1082 ILE Chi-restraints excluded: chain I residue 1113 LEU Chi-restraints excluded: chain I residue 1131 MET Chi-restraints excluded: chain I residue 1138 VAL Chi-restraints excluded: chain I residue 1141 LEU Chi-restraints excluded: chain I residue 1159 VAL Chi-restraints excluded: chain I residue 1160 ASP 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 1240 ASP 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 78 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 217 LEU 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 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 582 ILE Chi-restraints excluded: chain J residue 587 LEU Chi-restraints excluded: chain J residue 612 LEU Chi-restraints excluded: chain J residue 624 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 701 LEU Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 722 ILE Chi-restraints excluded: chain J residue 724 MET Chi-restraints excluded: chain J residue 744 ARG Chi-restraints excluded: chain J residue 746 LEU Chi-restraints excluded: chain J residue 751 ASP Chi-restraints excluded: chain J residue 801 VAL 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 930 LEU Chi-restraints excluded: chain J residue 974 VAL Chi-restraints excluded: chain J residue 997 VAL 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 1024 THR 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 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 1291 GLU Chi-restraints excluded: chain J residue 1320 ILE Chi-restraints excluded: chain J residue 1326 GLN Chi-restraints excluded: chain K residue 58 LEU Chi-restraints excluded: chain L residue 132 CYS 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 304 THR Chi-restraints excluded: chain L residue 306 PHE Chi-restraints excluded: chain L residue 322 MET 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 466 ILE Chi-restraints excluded: chain L residue 476 ARG 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 278 ILE 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 Chi-restraints excluded: chain M residue 300 LEU Chi-restraints excluded: chain M residue 316 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 252 optimal weight: 0.0040 chunk 283 optimal weight: 8.9990 chunk 282 optimal weight: 6.9990 chunk 245 optimal weight: 0.5980 chunk 253 optimal weight: 4.9990 chunk 300 optimal weight: 7.9990 chunk 198 optimal weight: 8.9990 chunk 380 optimal weight: 50.0000 chunk 53 optimal weight: 0.7980 chunk 357 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 23 HIS H 103 ASN ** I 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 856 ASN ** I 894 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 271 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.173645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138266 restraints weight = 43538.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.137753 restraints weight = 88855.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138789 restraints weight = 84323.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.138869 restraints weight = 51476.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141032 restraints weight = 44797.056| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.174 33047 Z= 0.159 Angle : 0.746 55.060 45093 Z= 0.404 Chirality : 0.044 0.469 5168 Planarity : 0.005 0.092 5502 Dihedral : 16.881 124.164 5740 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.07 % Favored : 92.82 % Rotamer: Outliers : 5.29 % Allowed : 29.38 % Favored : 65.33 % Cbeta Deviations : 0.03 % 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: -1.30 (0.13), residues: 3804 helix: 0.41 (0.13), residues: 1533 sheet: -1.73 (0.24), residues: 428 loop : -1.77 (0.14), residues: 1843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 978 TYR 0.020 0.002 TYR J 165 PHE 0.020 0.001 PHE J 172 TRP 0.016 0.001 TRP L 326 HIS 0.003 0.001 HIS J 777 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (33035) covalent geometry : angle 0.74552 / 0.40 (45081) hydrogen bonds : bond 0.04329 / 2.85 ( 1326) hydrogen bonds : angle 4.62267 / 3.14 ( 3692) metal coordination : bond 0.00433 / 0.29 ( 11) metal coordination : angle 2.34877 / 1.57 ( 12) Misc. bond : bond 0.00042 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5616.36 seconds wall clock time: 97 minutes 55.94 seconds (5875.94 seconds total)