Starting phenix.real_space_refine on Mon Sep 14 18:14:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psu_20464/09_2026/6psu_20464_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psu_20464/09_2026/6psu_20464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6psu_20464/09_2026/6psu_20464_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psu_20464/09_2026/6psu_20464_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6psu_20464/09_2026/6psu_20464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psu_20464/09_2026/6psu_20464.map" } resolution = 3.9 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= 0.006 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 79 5.49 5 Mg 1 5.21 5 S 139 5.16 5 C 19952 2.51 5 N 5657 2.21 5 O 6336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 128 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: 32167 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: 1775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1775 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 220} 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: 1668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1668 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PTRANS': 8, 'TRANS': 206} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 10567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1340, 10567 Classifications: {'peptide': 1340} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 55, 'TRANS': 1282} Chain: "J" Number of atoms: 10433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1344, 10433 Classifications: {'peptide': 1344} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 55, 'TRANS': 1288} Chain breaks: 2 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "K" Number of atoms: 577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 577 Classifications: {'peptide': 72} Link IDs: {'PTRANS': 2, 'TRANS': 69} Chain: "L" Number of atoms: 4277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4277 Classifications: {'peptide': 529} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 513} Chain breaks: 5 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "O" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 863 Classifications: {'DNA': 42} Link IDs: {'rna3p': 41} Chain: "P" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 752 Classifications: {'DNA': 37} Link IDs: {'rna3p': 36} 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 56.648 57.288 28.905 1.00 53.14 S ATOM 301 SG CYS N 40 53.785 57.214 26.133 1.00 53.44 S ATOM 438 SG CYS N 58 57.291 59.428 26.238 1.00 43.23 S ATOM 460 SG CYS N 61 54.572 60.028 29.290 1.00 46.39 S ATOM 15030 SG CYS J 70 81.007 103.049 115.872 1.00 33.05 S ATOM 15152 SG CYS J 85 77.287 103.313 118.934 1.00 41.74 S ATOM 15176 SG CYS J 88 77.317 102.976 115.479 1.00 32.14 S ATOM 21411 SG CYS J 888 74.490 44.471 88.473 1.00 23.95 S ATOM 21483 SG CYS J 898 76.204 41.720 86.848 1.00 11.77 S Time building chain proxies: 7.08, per 1000 atoms: 0.22 Number of scatterers: 32167 At special positions: 0 Unit cell: (163.8, 157.3, 170.3, 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 139 16.00 P 79 15.00 Mg 1 11.99 O 6336 8.00 N 5657 7.00 C 19952 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.19 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN J1502 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 88 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 70 " pdb="ZN ZN J1502 " - pdb=" SG CYS J 85 " pdb=" ZN J1503 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 888 " pdb="ZN ZN J1503 " - pdb=" SG CYS J 898 " pdb=" ZN N 101 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 40 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 58 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 37 " pdb="ZN ZN N 101 " - pdb=" SG CYS N 61 " Number of angles added : 6 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7206 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 46 sheets defined 43.0% alpha, 9.3% beta 33 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 4.24 Creating SS restraints... Processing helix chain 'N' and resid 3 through 26 removed outlier: 4.568A pdb=" N SER N 10 " --> pdb=" O ASP N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 52 removed outlier: 3.669A pdb=" N PHE N 52 " --> pdb=" O ARG N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 71 removed outlier: 3.866A pdb=" N HIS N 71 " --> pdb=" O ARG N 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 50 removed outlier: 3.576A pdb=" N THR G 38 " --> pdb=" O GLY G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 Processing helix chain 'G' and resid 113 through 115 No H-bonds generated for 'chain 'G' and resid 113 through 115' Processing helix chain 'G' and resid 154 through 159 Processing helix chain 'G' and resid 212 through 234 removed outlier: 4.439A pdb=" N ALA G 230 " --> pdb=" O GLU G 226 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 50 removed outlier: 3.752A pdb=" N ALA H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER H 50 " --> pdb=" O ILE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 87 removed outlier: 3.800A pdb=" N GLY H 87 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 154 through 158 removed outlier: 3.588A pdb=" N ARG H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 228 removed outlier: 3.547A pdb=" N THR H 222 " --> pdb=" O ARG H 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU H 224 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 3.536A 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 10 removed outlier: 3.654A pdb=" N LYS I 9 " --> pdb=" O TYR I 5 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG I 10 " --> pdb=" O THR I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 36 Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.836A pdb=" N ALA I 52 " --> pdb=" O GLY I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 89 Processing helix chain 'I' and resid 206 through 213 removed outlier: 4.312A 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 270 through 281 Processing helix chain 'I' and resid 318 through 329 removed outlier: 3.663A pdb=" N SER I 328 " --> pdb=" O LYS I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 354 Processing helix chain 'I' and resid 359 through 371 Processing helix chain 'I' and resid 377 through 390 removed outlier: 3.899A pdb=" N PHE I 389 " --> pdb=" O PHE I 385 " (cutoff:3.500A) Processing helix chain 'I' and resid 391 through 395 Processing helix chain 'I' and resid 398 through 409 Processing helix chain 'I' and resid 421 through 437 removed outlier: 4.068A pdb=" N VAL I 428 " --> pdb=" O ASP I 424 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 481 removed outlier: 3.639A pdb=" N VAL I 466 " --> pdb=" O ASN I 462 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY I 467 " --> pdb=" O GLN I 463 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA I 474 " --> pdb=" O ARG I 470 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU I 481 " --> pdb=" O GLU I 477 " (cutoff:3.500A) Processing helix chain 'I' and resid 495 through 508 removed outlier: 3.521A pdb=" N SER I 499 " --> pdb=" O ALA I 495 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER I 508 " --> pdb=" O GLU I 504 " (cutoff:3.500A) Processing helix chain 'I' and resid 519 through 527 Processing helix chain 'I' and resid 551 through 555 removed outlier: 3.755A pdb=" N TYR I 555 " --> pdb=" O PRO I 552 " (cutoff:3.500A) Processing helix chain 'I' and resid 608 through 612 removed outlier: 4.556A pdb=" N GLY I 612 " --> pdb=" O ALA I 608 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 608 through 612' 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 657 through 661 removed outlier: 3.890A pdb=" N VAL I 660 " --> pdb=" O THR I 657 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL I 661 " --> pdb=" O GLN I 658 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 657 through 661' Processing helix chain 'I' and resid 664 through 668 removed outlier: 3.762A pdb=" N LEU I 667 " --> pdb=" O GLY I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 670 through 674 Processing helix chain 'I' and resid 675 through 687 Processing helix chain 'I' and resid 704 through 711 Processing helix chain 'I' and resid 819 through 825 removed outlier: 3.710A pdb=" N VAL I 823 " --> pdb=" O SER I 819 " (cutoff:3.500A) Processing helix chain 'I' and resid 858 through 863 removed outlier: 3.585A pdb=" N SER I 863 " --> pdb=" O GLU I 859 " (cutoff:3.500A) Processing helix chain 'I' and resid 899 through 906 Processing helix chain 'I' and resid 942 through 979 Processing helix chain 'I' and resid 987 through 992 removed outlier: 3.824A pdb=" N LEU I 992 " --> pdb=" O LYS I 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 993 through 997 Processing helix chain 'I' and resid 1005 through 1038 Processing helix chain 'I' and resid 1101 through 1106 removed outlier: 4.163A pdb=" N SER I1105 " --> pdb=" O LEU I1101 " (cutoff:3.500A) Processing helix chain 'I' and resid 1109 through 1134 removed outlier: 3.516A pdb=" N GLN I1134 " --> pdb=" O ALA I1130 " (cutoff:3.500A) Processing helix chain 'I' and resid 1138 through 1150 Processing helix chain 'I' and resid 1170 through 1175 Processing helix chain 'I' and resid 1191 through 1202 Processing helix chain 'I' and resid 1238 through 1242 Processing helix chain 'I' and resid 1271 through 1281 removed outlier: 3.654A pdb=" N VAL I1275 " --> pdb=" O GLY I1271 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR I1281 " --> pdb=" O ALA I1277 " (cutoff:3.500A) Processing helix chain 'I' and resid 1284 through 1292 Processing helix chain 'I' and resid 1297 through 1310 removed outlier: 3.700A pdb=" N ARG I1301 " --> pdb=" O ASP I1297 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR I1302 " --> pdb=" O VAL I1298 " (cutoff:3.500A) Processing helix chain 'I' and resid 1320 through 1333 removed outlier: 3.889A pdb=" N LEU I1333 " --> pdb=" O GLU I1329 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 34 Processing helix chain 'J' and resid 58 through 63 removed outlier: 3.616A pdb=" N PHE J 62 " --> pdb=" O CYS J 58 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 removed outlier: 3.607A pdb=" N HIS J 80 " --> pdb=" O ARG J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 94 through 100 Processing helix chain 'J' and resid 113 through 118 Processing helix chain 'J' and resid 131 through 140 Processing helix chain 'J' and resid 161 through 170 Processing helix chain 'J' and resid 181 through 192 Processing helix chain 'J' and resid 193 through 207 removed outlier: 4.002A pdb=" N GLU J 197 " --> pdb=" O ASP J 193 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN J 206 " --> pdb=" O ARG J 202 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU J 207 " --> pdb=" O GLU J 203 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 231 removed outlier: 3.925A pdb=" N LYS J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY J 231 " --> pdb=" O PHE J 227 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 236 Processing helix chain 'J' and resid 263 through 286 removed outlier: 4.009A pdb=" N ASP J 267 " --> pdb=" O SER J 263 " (cutoff:3.500A) Processing helix chain 'J' and resid 288 through 308 Processing helix chain 'J' and resid 327 through 331 Processing helix chain 'J' and resid 370 through 377 Processing helix chain 'J' and resid 377 through 388 Processing helix chain 'J' and resid 393 through 404 Processing helix chain 'J' and resid 405 through 416 removed outlier: 4.098A pdb=" N TRP J 409 " --> pdb=" O GLU J 405 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP J 410 " --> pdb=" O ALA J 406 " (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 450 through 458 removed outlier: 3.754A pdb=" N CYS J 454 " --> pdb=" O HIS J 450 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA J 455 " --> pdb=" O PRO J 451 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ALA J 456 " --> pdb=" O LEU J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 473 through 484 Processing helix chain 'J' and resid 485 through 489 Processing helix chain 'J' and resid 505 through 514 Processing helix chain 'J' and resid 529 through 539 Processing helix chain 'J' and resid 574 through 581 removed outlier: 3.863A 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 636 removed outlier: 3.843A pdb=" N GLY J 636 " --> pdb=" O ALA J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 640 through 644 Processing helix chain 'J' and resid 649 through 670 removed outlier: 3.932A pdb=" N ILE J 653 " --> pdb=" O LYS J 649 " (cutoff:3.500A) Processing helix chain 'J' and resid 674 through 703 removed outlier: 4.962A pdb=" N ASN J 680 " --> pdb=" O GLY J 676 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N THR J 703 " --> pdb=" O ASP J 699 " (cutoff:3.500A) Processing helix chain 'J' and resid 722 through 726 Processing helix chain 'J' and resid 733 through 742 Processing helix chain 'J' and resid 768 through 787 removed outlier: 3.638A pdb=" N HIS J 777 " --> pdb=" O PHE J 773 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY J 778 " --> pdb=" O ILE J 774 " (cutoff:3.500A) Processing helix chain 'J' and resid 794 through 805 removed outlier: 4.419A pdb=" N VAL J 803 " --> pdb=" O ARG J 799 " (cutoff:3.500A) Processing helix chain 'J' and resid 834 through 840 removed outlier: 3.762A pdb=" N ARG J 838 " --> pdb=" O PRO J 834 " (cutoff:3.500A) Processing helix chain 'J' and resid 865 through 876 Processing helix chain 'J' and resid 895 through 900 Processing helix chain 'J' and resid 914 through 925 Processing helix chain 'J' and resid 925 through 930 removed outlier: 4.020A pdb=" N GLN J 929 " --> pdb=" O GLU J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 1138 through 1145 Processing helix chain 'J' and resid 1216 through 1225 removed outlier: 3.585A pdb=" N ILE J1220 " --> pdb=" O ALA J1216 " (cutoff:3.500A) Processing helix chain 'J' and resid 1225 through 1243 removed outlier: 3.502A pdb=" N VAL J1229 " --> pdb=" O GLY J1225 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ASP J1239 " --> pdb=" O ASN J1235 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL J1240 " --> pdb=" O GLU J1236 " (cutoff:3.500A) Processing helix chain 'J' and resid 1250 through 1261 removed outlier: 3.534A pdb=" N VAL J1257 " --> pdb=" O ILE J1253 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN J1259 " --> pdb=" O VAL J1255 " (cutoff:3.500A) Processing helix chain 'J' and resid 1282 through 1295 removed outlier: 4.106A pdb=" N ARG J1290 " --> pdb=" O LYS J1286 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU J1293 " --> pdb=" O ASN J1289 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA J1294 " --> pdb=" O ARG J1290 " (cutoff:3.500A) Processing helix chain 'J' and resid 1308 through 1315 removed outlier: 3.777A pdb=" N LEU J1314 " --> pdb=" O THR J1310 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA J1315 " --> pdb=" O LYS J1311 " (cutoff:3.500A) Processing helix chain 'J' and resid 1327 through 1338 removed outlier: 3.506A pdb=" N GLU J1334 " --> pdb=" O ARG J1330 " (cutoff:3.500A) Processing helix chain 'J' and resid 1346 through 1354 removed outlier: 4.221A pdb=" N ASN J1350 " --> pdb=" O GLY J1346 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL J1351 " --> pdb=" O LEU J1347 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE J1352 " --> pdb=" O LYS J1348 " (cutoff:3.500A) Processing helix chain 'J' and resid 1360 through 1362 No H-bonds generated for 'chain 'J' and resid 1360 through 1362' Processing helix chain 'J' and resid 1363 through 1373 removed outlier: 3.855A pdb=" N ARG J1369 " --> pdb=" O TYR J1365 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 13 Processing helix chain 'K' and resid 17 through 32 removed outlier: 3.647A pdb=" N ARG K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 45 through 55 Processing helix chain 'K' and resid 60 through 73 Processing helix chain 'L' and resid 8 through 20 Processing helix chain 'L' and resid 23 through 30 Processing helix chain 'L' and resid 40 through 49 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 96 through 106 Processing helix chain 'L' and resid 112 through 137 Processing helix chain 'L' and resid 137 through 153 removed outlier: 3.588A pdb=" N ILE L 141 " --> pdb=" O TYR L 137 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 230 removed outlier: 3.927A pdb=" N ALA L 217 " --> pdb=" O ASP L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 231 through 235 removed outlier: 4.455A pdb=" N ILE L 235 " --> pdb=" O ARG L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 245 through 250 removed outlier: 3.721A pdb=" N LEU L 250 " --> pdb=" O GLN L 246 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 258 removed outlier: 3.664A pdb=" N GLN L 258 " --> pdb=" O GLU L 254 " (cutoff:3.500A) Processing helix chain 'L' and resid 262 through 288 removed outlier: 3.906A pdb=" N LEU L 269 " --> pdb=" O GLN L 265 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP L 278 " --> pdb=" O ARG L 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 304 removed outlier: 3.832A pdb=" N PHE L 302 " --> pdb=" O PRO L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 305 through 310 removed outlier: 4.221A pdb=" N ASN L 309 " --> pdb=" O LEU L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 318 through 322 removed outlier: 3.522A pdb=" N ALA L 321 " --> pdb=" O ALA L 318 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 331 removed outlier: 3.811A pdb=" N HIS L 331 " --> pdb=" O GLU L 328 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 352 Processing helix chain 'L' and resid 354 through 382 removed outlier: 3.679A pdb=" N ALA L 382 " --> pdb=" O GLU L 378 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 391 Processing helix chain 'L' and resid 400 through 417 removed outlier: 3.501A pdb=" N GLY L 411 " --> pdb=" O GLU L 407 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL L 416 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP L 417 " --> pdb=" O MET L 413 " (cutoff:3.500A) Processing helix chain 'L' and resid 420 through 424 removed outlier: 3.981A pdb=" N ARG L 423 " --> pdb=" O GLU L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 426 through 444 removed outlier: 3.633A pdb=" N TYR L 430 " --> pdb=" O LYS L 426 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR L 432 " --> pdb=" O SER L 428 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TRP L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N TRP L 434 " --> pdb=" O TYR L 430 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 475 removed outlier: 3.518A pdb=" N MET L 470 " --> pdb=" O ILE L 466 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU L 473 " --> pdb=" O GLN L 469 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY L 475 " --> pdb=" O LEU L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 479 through 487 Processing helix chain 'L' and resid 493 through 499 removed outlier: 3.865A pdb=" N VAL L 497 " --> pdb=" O LYS L 493 " (cutoff:3.500A) Processing helix chain 'L' and resid 518 through 523 Processing helix chain 'L' and resid 530 through 550 removed outlier: 3.887A pdb=" N SER L 539 " --> pdb=" O ALA L 535 " (cutoff:3.500A) Processing helix chain 'L' and resid 552 through 563 Processing helix chain 'L' and resid 572 through 580 Processing helix chain 'L' and resid 583 through 599 removed outlier: 4.267A pdb=" N ARG L 588 " --> pdb=" O ARG L 584 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 609 removed outlier: 3.872A pdb=" N ARG L 608 " --> pdb=" O SER L 604 " (cutoff:3.500A) Processing helix chain 'M' and resid 250 through 254 removed outlier: 3.609A pdb=" N LEU M 253 " --> pdb=" O ASP M 250 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU M 254 " --> pdb=" O PRO M 251 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 250 through 254' Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 263 through 273 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 310 removed outlier: 3.670A pdb=" N LEU M 300 " --> pdb=" O GLY M 296 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 23 through 25 removed outlier: 6.523A pdb=" N GLU G 204 " --> pdb=" O ILE G 183 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE G 183 " --> pdb=" O GLU G 204 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU G 206 " --> pdb=" O GLU G 181 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 28 through 31 removed outlier: 5.082A pdb=" N GLU G 29 " --> pdb=" O LEU G 201 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU G 201 " --> pdb=" O GLU G 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 97 through 105 removed outlier: 3.540A pdb=" N LYS G 104 " --> pdb=" O ILE G 140 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU G 58 " --> pdb=" O LYS G 145 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N GLN G 147 " --> pdb=" O VAL G 56 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N VAL G 56 " --> pdb=" O GLN G 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'G' and resid 108 through 111 removed outlier: 4.026A pdb=" N GLY G 108 " --> pdb=" O LEU G 133 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 16 through 18 removed outlier: 3.854A pdb=" N GLU H 17 " --> pdb=" O LYS H 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 56 through 60 removed outlier: 6.865A pdb=" N LYS H 145 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL H 59 " --> pdb=" O ARG H 143 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ARG H 143 " --> pdb=" O VAL H 59 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL H 98 " --> pdb=" O VAL H 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 90 through 92 Processing sheet with id=AA9, first strand: chain 'H' and resid 104 through 105 Processing sheet with id=AB1, first strand: chain 'H' and resid 109 through 110 Processing sheet with id=AB2, first strand: chain 'H' and resid 180 through 184 removed outlier: 6.418A pdb=" N GLU H 206 " --> pdb=" O GLU H 181 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE H 183 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLU H 204 " --> pdb=" O ILE H 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.009A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE I 104 " --> pdb=" O LYS I 115 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU I 106 " --> pdb=" O THR I 113 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR I 113 " --> pdb=" O GLU I 106 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 59 through 60 removed outlier: 7.009A pdb=" N LYS I 99 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N TYR I 73 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ARG I 97 " --> pdb=" O TYR I 73 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LEU I 75 " --> pdb=" O PRO I 95 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ALA I 94 " --> pdb=" O GLU I 126 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU I 126 " --> pdb=" O ALA I 94 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LEU I 96 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU I 100 " --> pdb=" O GLN I 120 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 143 through 144 Processing sheet with id=AB6, first strand: chain 'I' and resid 451 through 453 removed outlier: 6.621A pdb=" N SER I 147 " --> pdb=" O SER I 531 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 156 through 158 removed outlier: 3.562A pdb=" N ASP I 158 " --> pdb=" O ASN I 173 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU I 184 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 228 through 231 Processing sheet with id=AB9, first strand: chain 'I' and resid 239 through 240 Processing sheet with id=AC1, first strand: chain 'I' and resid 255 through 257 removed outlier: 6.511A pdb=" N ILE I 255 " --> pdb=" O TYR I 262 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 580 through 581 removed outlier: 5.582A pdb=" N GLU I 602 " --> pdb=" O LYS I 593 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 580 through 581 Processing sheet with id=AC4, first strand: chain 'I' and resid 633 through 637 removed outlier: 3.616A pdb=" N CYS I 636 " --> pdb=" O SER I 643 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 716 through 717 Processing sheet with id=AC6, first strand: chain 'I' and resid 722 through 727 removed outlier: 5.422A pdb=" N VAL I 724 " --> pdb=" O LYS I 735 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N LYS I 735 " --> pdb=" O VAL I 724 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 757 through 759 removed outlier: 3.788A pdb=" N THR I 763 " --> pdb=" O SER I 759 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 789 through 790 removed outlier: 3.507A pdb=" N GLU I 793 " --> pdb=" O ASP I 790 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 1096 through 1098 Processing sheet with id=AD1, first strand: chain 'I' and resid 815 through 817 removed outlier: 7.360A pdb=" N ILE I 816 " --> pdb=" O SER I1077 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'I' and resid 835 through 836 removed outlier: 6.710A pdb=" N TYR I1053 " --> pdb=" O ILE I 929 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR I 927 " --> pdb=" O ALA I1055 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 1087 through 1088 Processing sheet with id=AD4, first strand: chain 'I' and resid 1209 through 1210 Processing sheet with id=AD5, first strand: chain 'I' and resid 1244 through 1246 removed outlier: 3.574A pdb=" N ARG I1246 " --> pdb=" O SER J 350 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER J 350 " --> pdb=" O ARG I1246 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN J 435 " --> pdb=" O LEU J 423 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N CYS J 366 " --> pdb=" O VAL J 440 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ILE J 442 " --> pdb=" O CYS J 366 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU J 368 " --> pdb=" O ILE J 442 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 1335 through 1339 Processing sheet with id=AD7, first strand: chain 'J' and resid 103 through 112 removed outlier: 6.899A pdb=" N THR J 240 " --> pdb=" O LEU J 107 " (cutoff:3.500A) removed outlier: 10.694A pdb=" N SER J 109 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 10.283A pdb=" N ILE J 238 " --> pdb=" O SER J 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 261 through 262 Processing sheet with id=AD9, first strand: chain 'J' and resid 526 through 527 removed outlier: 6.578A pdb=" N LEU J 527 " --> pdb=" O ARG J 551 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N THR J 553 " --> pdb=" O LEU J 527 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 706 through 707 Processing sheet with id=AE2, first strand: chain 'J' and resid 820 through 822 removed outlier: 4.318A pdb=" N VAL J 880 " --> pdb=" O MET J 822 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 951 through 952 Processing sheet with id=AE4, first strand: chain 'J' and resid 957 through 958 Processing sheet with id=AE5, first strand: chain 'J' and resid 965 through 967 removed outlier: 4.175A pdb=" N VAL J 966 " --> pdb=" O VAL J 974 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VAL J 974 " --> pdb=" O VAL J 966 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU J 973 " --> pdb=" O LEU J1003 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'J' and resid 1033 through 1034 removed outlier: 3.689A pdb=" N GLY J1033 " --> pdb=" O ILE J1115 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 1049 through 1050 Processing sheet with id=AE8, first strand: chain 'J' and resid 1077 through 1079 removed outlier: 3.611A pdb=" N LEU J1078 " --> pdb=" O TYR J1099 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR J1099 " --> pdb=" O LEU J1078 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'J' and resid 1175 through 1177 Processing sheet with id=AF1, first strand: chain 'J' and resid 1279 through 1281 1178 hydrogen bonds defined for protein. 3309 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 158 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 8.40 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10139 1.33 - 1.46: 6818 1.46 - 1.58: 15429 1.58 - 1.71: 172 1.71 - 1.83: 250 Bond restraints: 32808 Sorted by residual: bond pdb=" C19 1N7 L 701 " pdb=" C3 1N7 L 701 " ideal model delta sigma weight residual 1.532 1.832 -0.300 2.00e-02 2.50e+03 2.26e+02 bond pdb=" C19 1N7 J1504 " pdb=" C3 1N7 J1504 " ideal model delta sigma weight residual 1.532 1.828 -0.296 2.00e-02 2.50e+03 2.19e+02 bond pdb=" C19 1N7 N 102 " pdb=" C3 1N7 N 102 " ideal model delta sigma weight residual 1.532 1.826 -0.294 2.00e-02 2.50e+03 2.16e+02 bond pdb=" C19 1N7 I1401 " pdb=" C3 1N7 I1401 " ideal model delta sigma weight residual 1.532 1.819 -0.287 2.00e-02 2.50e+03 2.06e+02 bond pdb=" C3 1N7 N 102 " pdb=" C4 1N7 N 102 " ideal model delta sigma weight residual 1.532 1.729 -0.197 2.00e-02 2.50e+03 9.73e+01 ... (remaining 32803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 44117 3.20 - 6.40: 512 6.40 - 9.60: 30 9.60 - 12.79: 4 12.79 - 15.99: 1 Bond angle restraints: 44664 Sorted by residual: angle pdb=" N GLU I1167 " pdb=" CA GLU I1167 " pdb=" C GLU I1167 " ideal model delta sigma weight residual 110.80 126.79 -15.99 2.13e+00 2.20e-01 5.64e+01 angle pdb=" O4' DT P 36 " pdb=" C4' DT P 36 " pdb=" C3' DT P 36 " ideal model delta sigma weight residual 106.00 102.41 3.59 6.00e-01 2.78e+00 3.58e+01 angle pdb=" N VAL H 14 " pdb=" CA VAL H 14 " pdb=" C VAL H 14 " ideal model delta sigma weight residual 113.20 107.60 5.60 9.60e-01 1.09e+00 3.41e+01 angle pdb=" C ASP I1166 " pdb=" N GLU I1167 " pdb=" CA GLU I1167 " ideal model delta sigma weight residual 121.54 132.50 -10.96 1.91e+00 2.74e-01 3.29e+01 angle pdb=" N ASP I 516 " pdb=" CA ASP I 516 " pdb=" C ASP I 516 " ideal model delta sigma weight residual 108.41 99.75 8.66 1.61e+00 3.86e-01 2.90e+01 ... (remaining 44659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.71: 18857 28.71 - 57.42: 1243 57.42 - 86.14: 141 86.14 - 114.85: 7 114.85 - 143.56: 4 Dihedral angle restraints: 20252 sinusoidal: 9082 harmonic: 11170 Sorted by residual: dihedral pdb=" CA ASP I1166 " pdb=" C ASP I1166 " pdb=" N GLU I1167 " pdb=" CA GLU I1167 " ideal model delta harmonic sigma weight residual -180.00 -51.16 -128.84 0 5.00e+00 4.00e-02 6.64e+02 dihedral pdb=" CA ASP I1240 " pdb=" C ASP I1240 " pdb=" N ASP I1241 " pdb=" CA ASP I1241 " ideal model delta harmonic sigma weight residual 180.00 147.94 32.06 0 5.00e+00 4.00e-02 4.11e+01 dihedral pdb=" CA SER I1165 " pdb=" C SER I1165 " pdb=" N ASP I1166 " pdb=" CA ASP I1166 " ideal model delta harmonic sigma weight residual 180.00 148.27 31.73 0 5.00e+00 4.00e-02 4.03e+01 ... (remaining 20249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4061 0.060 - 0.120: 955 0.120 - 0.180: 95 0.180 - 0.240: 17 0.240 - 0.300: 2 Chirality restraints: 5130 Sorted by residual: chirality pdb=" CA ASP I 516 " pdb=" N ASP I 516 " pdb=" C ASP I 516 " pdb=" CB ASP I 516 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA GLU I1167 " pdb=" N GLU I1167 " pdb=" C GLU I1167 " pdb=" CB GLU I1167 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU J 783 " pdb=" CB LEU J 783 " pdb=" CD1 LEU J 783 " pdb=" CD2 LEU J 783 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 5127 not shown) Planarity restraints: 5537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY J 358 " 0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO J 359 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO J 359 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO J 359 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN J 45 " 0.011 2.00e-02 2.50e+03 2.26e-02 5.09e+00 pdb=" C ASN J 45 " -0.039 2.00e-02 2.50e+03 pdb=" O ASN J 45 " 0.014 2.00e-02 2.50e+03 pdb=" N TYR J 46 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 342 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.98e+00 pdb=" C ASP I 342 " 0.035 2.00e-02 2.50e+03 pdb=" O ASP I 342 " -0.013 2.00e-02 2.50e+03 pdb=" N HIS I 343 " -0.012 2.00e-02 2.50e+03 ... (remaining 5534 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.42: 223 2.42 - 3.04: 22871 3.04 - 3.66: 50424 3.66 - 4.28: 75097 4.28 - 4.90: 119099 Nonbonded interactions: 267714 Sorted by model distance: nonbonded pdb=" O ILE J 937 " pdb=" OD1 ASP J1133 " model vdw 1.805 3.040 nonbonded pdb=" OD2 ASP J 464 " pdb="MG MG J1501 " model vdw 1.954 2.170 nonbonded pdb=" OD1 ASP I 826 " pdb=" OG1 THR I 829 " model vdw 1.962 3.040 nonbonded pdb=" OH TYR J 679 " pdb=" O ILE J 754 " model vdw 2.012 3.040 nonbonded pdb=" OG1 THR I 589 " pdb=" OE1 GLN I 659 " model vdw 2.015 3.040 ... (remaining 267709 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 5 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 158 or resid 171 through 232)) selection = (chain 'H' and (resid 5 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)) } 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 39.590 Find NCS groups from input model: 0.410 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: 43.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 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 : 0.010 0.494 32817 Z= 0.480 Angle : 0.968 22.039 44670 Z= 0.584 Chirality : 0.050 0.300 5130 Planarity : 0.005 0.061 5537 Dihedral : 17.893 143.560 13046 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 47.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.48 % Favored : 87.46 % Rotamer: Outliers : 0.24 % Allowed : 11.16 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -4.34 (0.11), residues: 3845 helix: -2.43 (0.10), residues: 1465 sheet: -3.56 (0.22), residues: 348 loop : -3.16 (0.12), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 259 TYR 0.021 0.003 TYR J 679 PHE 0.033 0.003 PHE N 52 TRP 0.020 0.002 TRP I 807 HIS 0.010 0.002 HIS I1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00926 / 0.46 (32808) covalent geometry : angle 0.95618 / 0.58 (44664) hydrogen bonds : bond 0.22750 / 15.48 ( 1248) hydrogen bonds : angle 8.63683 / 5.91 ( 3467) metal coordination : bond 0.21257 / 12.18 ( 9) metal coordination : angle 13.28995 / 7.34 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 674 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 75 GLN cc_start: 0.8231 (pp30) cc_final: 0.7904 (pp30) REVERT: H 10 LYS cc_start: 0.8647 (mmtp) cc_final: 0.8268 (tppt) REVERT: H 62 ASP cc_start: 0.5509 (m-30) cc_final: 0.5142 (p0) REVERT: H 199 ASP cc_start: 0.6776 (m-30) cc_final: 0.6574 (m-30) REVERT: I 227 LYS cc_start: 0.6450 (mmtt) cc_final: 0.5887 (ptpt) REVERT: I 422 LYS cc_start: 0.8023 (pptt) cc_final: 0.7544 (pttm) REVERT: I 436 ARG cc_start: 0.8080 (tpt90) cc_final: 0.7653 (tpt90) REVERT: I 462 ASN cc_start: 0.7574 (t0) cc_final: 0.7008 (t0) REVERT: I 468 LEU cc_start: 0.7651 (OUTLIER) cc_final: 0.7368 (mt) REVERT: I 644 LEU cc_start: 0.8756 (mm) cc_final: 0.8347 (mp) REVERT: I 699 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8243 (tp) REVERT: I 865 LEU cc_start: 0.8877 (mm) cc_final: 0.8208 (mp) REVERT: I 1025 PHE cc_start: 0.6141 (m-10) cc_final: 0.5851 (m-10) REVERT: I 1174 GLU cc_start: 0.7090 (tp30) cc_final: 0.6864 (tp30) REVERT: I 1232 MET cc_start: 0.7906 (mmm) cc_final: 0.7677 (mmt) REVERT: I 1243 MET cc_start: 0.7402 (tmm) cc_final: 0.7029 (ttp) REVERT: I 1290 MET cc_start: 0.7770 (tpp) cc_final: 0.7363 (tpp) REVERT: J 133 ARG cc_start: 0.5303 (mmt180) cc_final: 0.4974 (mmm160) REVERT: J 180 MET cc_start: 0.6403 (ttm) cc_final: 0.6181 (ttm) REVERT: J 292 VAL cc_start: 0.8024 (m) cc_final: 0.7680 (t) REVERT: J 342 LEU cc_start: 0.8872 (tp) cc_final: 0.8560 (tp) REVERT: J 442 ILE cc_start: 0.8639 (mm) cc_final: 0.8283 (mm) REVERT: J 604 MET cc_start: 0.8412 (ttp) cc_final: 0.8023 (ttp) REVERT: J 679 TYR cc_start: 0.7020 (t80) cc_final: 0.6575 (t80) REVERT: J 936 HIS cc_start: 0.7130 (t70) cc_final: 0.6809 (m-70) REVERT: J 1340 LYS cc_start: 0.7716 (mmtt) cc_final: 0.7496 (tptp) REVERT: J 1352 ILE cc_start: 0.9005 (mm) cc_final: 0.8793 (mt) REVERT: K 35 LYS cc_start: 0.7634 (mptt) cc_final: 0.7426 (mmtp) REVERT: K 49 ILE cc_start: 0.8514 (mt) cc_final: 0.8190 (mt) REVERT: K 59 ILE cc_start: 0.6855 (mt) cc_final: 0.6309 (mt) REVERT: L 96 ASP cc_start: 0.6343 (m-30) cc_final: 0.5759 (m-30) REVERT: L 114 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6274 (pm20) REVERT: L 312 SER cc_start: 0.7217 (m) cc_final: 0.6828 (t) REVERT: L 434 TRP cc_start: 0.7095 (m100) cc_final: 0.6844 (m100) REVERT: L 488 LEU cc_start: 0.7023 (mp) cc_final: 0.6172 (pt) REVERT: L 508 GLU cc_start: 0.7457 (mp0) cc_final: 0.7122 (mp0) REVERT: L 609 SER cc_start: 0.7803 (m) cc_final: 0.7347 (t) outliers start: 8 outliers final: 2 residues processed: 677 average time/residue: 0.2294 time to fit residues: 239.2698 Evaluate side-chains 461 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 457 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 132 HIS H 147 GLN ** H 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 238 GLN I 343 HIS I 406 ASN ** I 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 659 GLN I 856 ASN I 932 GLN I1017 GLN I1116 HIS ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1257 GLN I1268 GLN J 158 GLN J 200 GLN ** J 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 266 ASN J 294 ASN ** J 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 489 ASN J 680 ASN ** J 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1049 GLN J1238 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN L 8 GLN L 128 ASN L 246 GLN L 362 ASN L 409 ASN L 446 GLN ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 579 GLN M 276 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.145619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117487 restraints weight = 61472.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.116967 restraints weight = 81899.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118048 restraints weight = 68088.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117997 restraints weight = 49166.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118116 restraints weight = 44269.812| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 32817 Z= 0.176 Angle : 0.848 53.848 44670 Z= 0.419 Chirality : 0.049 0.366 5130 Planarity : 0.006 0.057 5537 Dihedral : 16.223 141.239 5412 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.26 % Rotamer: Outliers : 2.96 % Allowed : 16.96 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.66 % 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: -3.37 (0.12), residues: 3845 helix: -1.47 (0.12), residues: 1545 sheet: -3.11 (0.24), residues: 334 loop : -2.75 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 976 TYR 0.020 0.002 TYR J 679 PHE 0.021 0.002 PHE N 52 TRP 0.029 0.002 TRP L 315 HIS 0.007 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (32808) covalent geometry : angle 0.79101 / 0.42 (44664) hydrogen bonds : bond 0.05765 / 3.93 ( 1248) hydrogen bonds : angle 6.31943 / 4.36 ( 3467) metal coordination : bond 0.01370 / 0.78 ( 9) metal coordination : angle 26.47413 / 15.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 535 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 6 ASP cc_start: 0.7210 (m-30) cc_final: 0.6866 (m-30) REVERT: N 36 LEU cc_start: 0.6278 (mt) cc_final: 0.6065 (mp) REVERT: H 129 VAL cc_start: 0.8475 (p) cc_final: 0.8157 (t) REVERT: I 227 LYS cc_start: 0.6256 (mmtt) cc_final: 0.5829 (ttpp) REVERT: I 377 THR cc_start: 0.4826 (t) cc_final: 0.4474 (m) REVERT: I 422 LYS cc_start: 0.7761 (pptt) cc_final: 0.7395 (pttm) REVERT: I 435 ILE cc_start: 0.8425 (OUTLIER) cc_final: 0.8219 (tt) REVERT: I 462 ASN cc_start: 0.7356 (t0) cc_final: 0.6887 (t0) REVERT: I 496 LYS cc_start: 0.7694 (tttt) cc_final: 0.7190 (pttt) REVERT: I 644 LEU cc_start: 0.8558 (mm) cc_final: 0.8294 (mp) REVERT: I 653 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.7478 (ttp) REVERT: I 654 ASP cc_start: 0.8014 (m-30) cc_final: 0.7802 (m-30) REVERT: I 699 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8218 (tp) REVERT: I 750 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8116 (pt) REVERT: I 865 LEU cc_start: 0.8727 (mm) cc_final: 0.8195 (mp) REVERT: I 913 VAL cc_start: 0.6985 (OUTLIER) cc_final: 0.6749 (p) REVERT: I 997 TRP cc_start: 0.4713 (m-10) cc_final: 0.4276 (m-10) REVERT: I 1243 MET cc_start: 0.7565 (tmm) cc_final: 0.7145 (ttp) REVERT: I 1290 MET cc_start: 0.8295 (tpp) cc_final: 0.7814 (tpp) REVERT: J 42 GLU cc_start: 0.6574 (mp0) cc_final: 0.6294 (mt-10) REVERT: J 135 ILE cc_start: 0.7442 (mt) cc_final: 0.7054 (mt) REVERT: J 301 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7302 (tm-30) REVERT: J 340 GLN cc_start: 0.5319 (tp40) cc_final: 0.4921 (tp40) REVERT: J 372 MET cc_start: 0.7923 (mtp) cc_final: 0.7586 (ttm) REVERT: J 527 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8772 (mt) REVERT: J 679 TYR cc_start: 0.6956 (t80) cc_final: 0.6334 (t80) REVERT: J 992 LYS cc_start: 0.5362 (mtpt) cc_final: 0.4686 (mmmt) REVERT: J 1244 GLN cc_start: 0.8193 (tp-100) cc_final: 0.7765 (mm-40) REVERT: J 1286 LYS cc_start: 0.7902 (tmtt) cc_final: 0.7699 (tttt) REVERT: K 19 LEU cc_start: 0.6852 (OUTLIER) cc_final: 0.6511 (tp) REVERT: K 42 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6560 (mt-10) REVERT: K 54 ILE cc_start: 0.7225 (mm) cc_final: 0.6994 (mm) REVERT: K 60 ASN cc_start: 0.7313 (p0) cc_final: 0.7009 (p0) REVERT: L 11 LEU cc_start: 0.5971 (tp) cc_final: 0.5752 (tt) REVERT: L 96 ASP cc_start: 0.6175 (m-30) cc_final: 0.5732 (m-30) REVERT: L 117 ILE cc_start: 0.5395 (OUTLIER) cc_final: 0.5116 (mm) REVERT: L 118 ASP cc_start: 0.6651 (m-30) cc_final: 0.6048 (t0) REVERT: L 312 SER cc_start: 0.7269 (m) cc_final: 0.6791 (t) REVERT: L 405 ILE cc_start: 0.8421 (pt) cc_final: 0.8162 (tp) REVERT: L 521 ASP cc_start: 0.6244 (t70) cc_final: 0.5905 (t0) outliers start: 98 outliers final: 47 residues processed: 591 average time/residue: 0.2094 time to fit residues: 199.0369 Evaluate side-chains 477 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 422 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 186 ASN Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 653 MET Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 960 LEU Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 244 VAL Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 567 THR Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 507 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 234 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 chunk 353 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 10 optimal weight: 0.0980 chunk 227 optimal weight: 4.9990 chunk 360 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 71 HIS ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN H 227 GLN I 811 ASN I1268 GLN J 266 ASN ** J 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 335 GLN J 489 ASN J 739 GLN J 762 ASN K 29 GLN L 309 ASN L 362 ASN ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.146694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.118649 restraints weight = 60993.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.118394 restraints weight = 73255.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.118783 restraints weight = 69037.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.119119 restraints weight = 51799.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119207 restraints weight = 45943.572| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32817 Z= 0.145 Angle : 0.761 49.850 44670 Z= 0.374 Chirality : 0.046 0.349 5130 Planarity : 0.005 0.063 5537 Dihedral : 15.867 140.892 5408 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.46 % Rotamer: Outliers : 4.28 % Allowed : 18.56 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % 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: -2.67 (0.13), residues: 3845 helix: -0.95 (0.12), residues: 1563 sheet: -2.57 (0.25), residues: 329 loop : -2.34 (0.13), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 976 TYR 0.019 0.002 TYR I 3 PHE 0.026 0.002 PHE J1325 TRP 0.045 0.002 TRP L 315 HIS 0.006 0.001 HIS I1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 (32808) covalent geometry : angle 0.70530 / 0.37 (44664) hydrogen bonds : bond 0.04725 / 3.20 ( 1248) hydrogen bonds : angle 5.72343 / 3.95 ( 3467) metal coordination : bond 0.00682 / 0.35 ( 9) metal coordination : angle 24.74398 / 14.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 513 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 53 PRO cc_start: 0.7353 (Cg_exo) cc_final: 0.7134 (Cg_endo) REVERT: H 86 LYS cc_start: 0.8460 (ttmm) cc_final: 0.8228 (ttmm) REVERT: H 129 VAL cc_start: 0.8511 (p) cc_final: 0.8156 (t) REVERT: H 196 THR cc_start: 0.5612 (m) cc_final: 0.5238 (m) REVERT: H 227 GLN cc_start: 0.8028 (mm-40) cc_final: 0.7237 (mm-40) REVERT: H 228 LEU cc_start: 0.7997 (mm) cc_final: 0.7705 (mp) REVERT: I 209 ILE cc_start: 0.8181 (mm) cc_final: 0.7965 (mm) REVERT: I 377 THR cc_start: 0.4565 (OUTLIER) cc_final: 0.4177 (m) REVERT: I 422 LYS cc_start: 0.7652 (pptt) cc_final: 0.7311 (pttm) REVERT: I 435 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.8002 (tt) REVERT: I 462 ASN cc_start: 0.7292 (t0) cc_final: 0.6766 (t0) REVERT: I 496 LYS cc_start: 0.7679 (tttt) cc_final: 0.7137 (pttt) REVERT: I 644 LEU cc_start: 0.8684 (mm) cc_final: 0.8413 (mp) REVERT: I 699 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8207 (tp) REVERT: I 704 MET cc_start: 0.7366 (mmm) cc_final: 0.6796 (mmm) REVERT: I 750 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8087 (pt) REVERT: I 865 LEU cc_start: 0.8665 (mm) cc_final: 0.8140 (mp) REVERT: I 913 VAL cc_start: 0.6931 (OUTLIER) cc_final: 0.6712 (p) REVERT: I 1060 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7203 (tt) REVERT: I 1150 ASP cc_start: 0.6307 (p0) cc_final: 0.6003 (p0) REVERT: I 1165 SER cc_start: 0.6200 (OUTLIER) cc_final: 0.5856 (t) REVERT: I 1243 MET cc_start: 0.7573 (tmm) cc_final: 0.7356 (ttp) REVERT: I 1290 MET cc_start: 0.8202 (tpp) cc_final: 0.7634 (tpp) REVERT: J 42 GLU cc_start: 0.6660 (mp0) cc_final: 0.6203 (mt-10) REVERT: J 147 ILE cc_start: 0.6724 (OUTLIER) cc_final: 0.6275 (tp) REVERT: J 342 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8699 (tp) REVERT: J 349 TYR cc_start: 0.8604 (m-80) cc_final: 0.8381 (m-80) REVERT: J 372 MET cc_start: 0.7955 (mtp) cc_final: 0.7545 (ttm) REVERT: J 429 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8056 (mm) REVERT: J 679 TYR cc_start: 0.6931 (t80) cc_final: 0.6474 (t80) REVERT: J 788 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7483 (mp) REVERT: J 833 GLU cc_start: 0.8400 (tp30) cc_final: 0.8172 (tp30) REVERT: J 992 LYS cc_start: 0.5503 (mtpt) cc_final: 0.4833 (mmmt) REVERT: J 1244 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7740 (mm-40) REVERT: K 19 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6452 (tp) REVERT: L 96 ASP cc_start: 0.5933 (m-30) cc_final: 0.5588 (m-30) REVERT: L 117 ILE cc_start: 0.5363 (OUTLIER) cc_final: 0.5154 (mm) REVERT: L 118 ASP cc_start: 0.6468 (m-30) cc_final: 0.6053 (t0) REVERT: L 277 MET cc_start: 0.5268 (tpt) cc_final: 0.4748 (tpt) REVERT: L 344 LEU cc_start: 0.5919 (mt) cc_final: 0.5691 (pp) REVERT: L 510 PRO cc_start: 0.6696 (Cg_endo) cc_final: 0.6484 (Cg_exo) REVERT: L 521 ASP cc_start: 0.6232 (t70) cc_final: 0.5905 (t0) REVERT: L 528 LEU cc_start: 0.8182 (mt) cc_final: 0.7605 (mt) outliers start: 142 outliers final: 67 residues processed: 609 average time/residue: 0.2018 time to fit residues: 199.5329 Evaluate side-chains 491 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 411 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 435 ILE Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 829 THR Chi-restraints excluded: chain I residue 913 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1060 ILE Chi-restraints excluded: chain I residue 1076 ILE Chi-restraints excluded: chain I residue 1165 SER Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 266 ASN Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 489 ASN Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1175 LEU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 387 VAL Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain L residue 591 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 349 optimal weight: 10.0000 chunk 373 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 133 optimal weight: 0.8980 chunk 269 optimal weight: 7.9990 chunk 263 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 75 optimal weight: 0.0670 chunk 205 optimal weight: 3.9990 chunk 337 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 21 ASN ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 GLN J 489 ASN J 739 GLN J 762 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 383 ASN ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 600 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.145097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116215 restraints weight = 61074.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115409 restraints weight = 85399.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116560 restraints weight = 70454.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116680 restraints weight = 51585.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116813 restraints weight = 47030.467| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 32817 Z= 0.187 Angle : 0.737 43.360 44670 Z= 0.367 Chirality : 0.046 0.361 5130 Planarity : 0.005 0.048 5537 Dihedral : 15.815 142.127 5408 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.50 % Favored : 91.47 % Rotamer: Outliers : 4.62 % Allowed : 20.37 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % 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: -2.46 (0.13), residues: 3845 helix: -0.74 (0.12), residues: 1574 sheet: -2.49 (0.25), residues: 341 loop : -2.24 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 436 TYR 0.028 0.002 TYR J 165 PHE 0.023 0.002 PHE J 172 TRP 0.043 0.003 TRP L 315 HIS 0.008 0.001 HIS I 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (32808) covalent geometry : angle 0.69467 / 0.36 (44664) hydrogen bonds : bond 0.04555 / 3.08 ( 1248) hydrogen bonds : angle 5.54345 / 3.84 ( 3467) metal coordination : bond 0.01138 / 0.59 ( 9) metal coordination : angle 21.21427 / 12.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 433 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 53 PRO cc_start: 0.7311 (Cg_exo) cc_final: 0.7101 (Cg_endo) REVERT: G 102 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8350 (mm) REVERT: H 129 VAL cc_start: 0.8485 (p) cc_final: 0.8155 (t) REVERT: H 133 LEU cc_start: 0.4074 (mt) cc_final: 0.3830 (mt) REVERT: H 227 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7385 (mm-40) REVERT: I 209 ILE cc_start: 0.8195 (mm) cc_final: 0.7959 (mm) REVERT: I 377 THR cc_start: 0.4509 (OUTLIER) cc_final: 0.4133 (m) REVERT: I 422 LYS cc_start: 0.7712 (pptt) cc_final: 0.7496 (pttm) REVERT: I 462 ASN cc_start: 0.7508 (t0) cc_final: 0.6945 (t0) REVERT: I 496 LYS cc_start: 0.7648 (tttt) cc_final: 0.7113 (pttt) REVERT: I 644 LEU cc_start: 0.8624 (mm) cc_final: 0.8320 (mp) REVERT: I 699 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8218 (tp) REVERT: I 704 MET cc_start: 0.7349 (mmm) cc_final: 0.6698 (mmm) REVERT: I 750 ILE cc_start: 0.8391 (OUTLIER) cc_final: 0.8129 (pt) REVERT: I 865 LEU cc_start: 0.8681 (mm) cc_final: 0.8130 (mp) REVERT: I 1073 LYS cc_start: 0.7906 (OUTLIER) cc_final: 0.7677 (ptpt) REVERT: I 1150 ASP cc_start: 0.6351 (p0) cc_final: 0.6031 (p0) REVERT: I 1243 MET cc_start: 0.7708 (tmm) cc_final: 0.7209 (ttp) REVERT: I 1290 MET cc_start: 0.8182 (tpp) cc_final: 0.7678 (tpp) REVERT: J 42 GLU cc_start: 0.6715 (mp0) cc_final: 0.6248 (mt-10) REVERT: J 130 MET cc_start: 0.6393 (ttt) cc_final: 0.6055 (tmm) REVERT: J 147 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6325 (tp) REVERT: J 342 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8919 (tp) REVERT: J 361 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.8986 (pp) REVERT: J 413 ASP cc_start: 0.7095 (OUTLIER) cc_final: 0.6881 (m-30) REVERT: J 429 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8083 (mm) REVERT: J 479 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6571 (mt-10) REVERT: J 527 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8914 (mt) REVERT: J 679 TYR cc_start: 0.6947 (t80) cc_final: 0.6594 (t80) REVERT: J 714 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6177 (tt0) REVERT: J 788 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7548 (mp) REVERT: J 833 GLU cc_start: 0.8460 (tp30) cc_final: 0.8215 (tp30) REVERT: J 992 LYS cc_start: 0.5643 (mtpt) cc_final: 0.4863 (mmmt) REVERT: K 19 LEU cc_start: 0.6882 (OUTLIER) cc_final: 0.6540 (tp) REVERT: K 28 ARG cc_start: 0.7534 (tpp80) cc_final: 0.7211 (tpp80) REVERT: L 117 ILE cc_start: 0.5303 (OUTLIER) cc_final: 0.5062 (mm) REVERT: L 277 MET cc_start: 0.5108 (tpt) cc_final: 0.4367 (tpt) REVERT: L 344 LEU cc_start: 0.6112 (mt) cc_final: 0.5788 (pp) REVERT: L 385 ARG cc_start: 0.7834 (mmt90) cc_final: 0.7288 (mmt-90) REVERT: L 510 PRO cc_start: 0.6520 (Cg_endo) cc_final: 0.6311 (Cg_exo) REVERT: L 511 ILE cc_start: 0.5746 (OUTLIER) cc_final: 0.4974 (mp) REVERT: L 521 ASP cc_start: 0.6295 (t70) cc_final: 0.6003 (t0) outliers start: 153 outliers final: 91 residues processed: 534 average time/residue: 0.1889 time to fit residues: 167.8395 Evaluate side-chains 499 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 392 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 241 LEU Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 634 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 752 ASN Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1073 LYS Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1210 ILE Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 413 ASP Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 894 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1260 MET Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 117 ILE Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 307 THR Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 559 LEU Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain L residue 591 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 267 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 326 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 279 optimal weight: 10.0000 chunk 296 optimal weight: 2.9990 chunk 349 optimal weight: 6.9990 chunk 251 optimal weight: 0.5980 chunk 223 optimal weight: 8.9990 chunk 198 optimal weight: 0.6980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN I 659 GLN ** I1136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 489 ASN J 762 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 600 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116652 restraints weight = 61291.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.115539 restraints weight = 85589.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.116555 restraints weight = 75202.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116795 restraints weight = 53848.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116939 restraints weight = 48850.022| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 32817 Z= 0.175 Angle : 0.702 32.688 44670 Z= 0.357 Chirality : 0.045 0.366 5130 Planarity : 0.005 0.046 5537 Dihedral : 15.750 142.217 5408 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.56 % Favored : 91.42 % Rotamer: Outliers : 5.70 % Allowed : 21.00 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % 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: -2.27 (0.13), residues: 3845 helix: -0.60 (0.13), residues: 1578 sheet: -2.31 (0.26), residues: 336 loop : -2.15 (0.14), residues: 1931 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 245 TYR 0.020 0.002 TYR I 123 PHE 0.024 0.002 PHE I 253 TRP 0.042 0.002 TRP L 315 HIS 0.007 0.001 HIS I1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (32808) covalent geometry : angle 0.67954 / 0.36 (44664) hydrogen bonds : bond 0.04377 / 2.94 ( 1248) hydrogen bonds : angle 5.36961 / 3.72 ( 3467) metal coordination : bond 0.00925 / 0.49 ( 9) metal coordination : angle 15.26289 / 9.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 413 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 53 PRO cc_start: 0.7368 (Cg_exo) cc_final: 0.7155 (Cg_endo) REVERT: G 102 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8243 (mm) REVERT: G 143 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6597 (mtp85) REVERT: H 129 VAL cc_start: 0.8465 (p) cc_final: 0.8177 (t) REVERT: I 199 ASP cc_start: 0.6209 (OUTLIER) cc_final: 0.5858 (m-30) REVERT: I 209 ILE cc_start: 0.8152 (mm) cc_final: 0.7915 (mm) REVERT: I 230 PHE cc_start: 0.5424 (m-80) cc_final: 0.4967 (m-80) REVERT: I 321 LEU cc_start: 0.6865 (mt) cc_final: 0.6129 (tp) REVERT: I 377 THR cc_start: 0.4567 (OUTLIER) cc_final: 0.4239 (m) REVERT: I 422 LYS cc_start: 0.7747 (pptt) cc_final: 0.7538 (pttm) REVERT: I 462 ASN cc_start: 0.7471 (t0) cc_final: 0.6947 (t0) REVERT: I 496 LYS cc_start: 0.7684 (tttt) cc_final: 0.7128 (pttt) REVERT: I 644 LEU cc_start: 0.8591 (mm) cc_final: 0.8291 (mp) REVERT: I 699 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8314 (tp) REVERT: I 704 MET cc_start: 0.7354 (mmm) cc_final: 0.6629 (mmm) REVERT: I 733 VAL cc_start: 0.9063 (OUTLIER) cc_final: 0.8790 (m) REVERT: I 750 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8034 (pt) REVERT: I 796 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7664 (mp) REVERT: I 865 LEU cc_start: 0.8670 (mm) cc_final: 0.8127 (mp) REVERT: I 1083 GLU cc_start: 0.7092 (pm20) cc_final: 0.6856 (pm20) REVERT: I 1150 ASP cc_start: 0.6274 (p0) cc_final: 0.5965 (p0) REVERT: I 1243 MET cc_start: 0.7774 (tmm) cc_final: 0.7392 (ttp) REVERT: I 1290 MET cc_start: 0.8198 (tpp) cc_final: 0.7783 (tpp) REVERT: J 42 GLU cc_start: 0.6676 (mp0) cc_final: 0.6394 (mt-10) REVERT: J 92 VAL cc_start: 0.8651 (OUTLIER) cc_final: 0.8444 (p) REVERT: J 130 MET cc_start: 0.6286 (ttt) cc_final: 0.5749 (ttm) REVERT: J 136 GLU cc_start: 0.5755 (OUTLIER) cc_final: 0.5403 (tm-30) REVERT: J 147 ILE cc_start: 0.6825 (OUTLIER) cc_final: 0.6327 (tp) REVERT: J 255 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7023 (tp) REVERT: J 342 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8863 (tp) REVERT: J 349 TYR cc_start: 0.8579 (m-80) cc_final: 0.8376 (m-80) REVERT: J 361 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.8982 (pp) REVERT: J 429 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8124 (mm) REVERT: J 479 GLU cc_start: 0.6928 (mt-10) cc_final: 0.6645 (mt-10) REVERT: J 527 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8914 (mt) REVERT: J 679 TYR cc_start: 0.6833 (t80) cc_final: 0.6550 (t80) REVERT: J 714 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.6298 (tt0) REVERT: J 788 LEU cc_start: 0.7922 (OUTLIER) cc_final: 0.7545 (mp) REVERT: J 871 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7717 (tp) REVERT: J 992 LYS cc_start: 0.5662 (mtpt) cc_final: 0.4871 (mmmt) REVERT: J 1093 THR cc_start: 0.4861 (OUTLIER) cc_final: 0.4616 (m) REVERT: K 19 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6577 (tp) REVERT: K 55 GLU cc_start: 0.6752 (tt0) cc_final: 0.6516 (tt0) REVERT: L 30 HIS cc_start: 0.4491 (OUTLIER) cc_final: 0.4046 (t-170) REVERT: L 288 MET cc_start: 0.2386 (OUTLIER) cc_final: 0.2093 (mtp) REVERT: L 306 PHE cc_start: 0.1703 (t80) cc_final: 0.1167 (t80) REVERT: L 344 LEU cc_start: 0.5915 (mt) cc_final: 0.5705 (pp) REVERT: L 511 ILE cc_start: 0.5821 (OUTLIER) cc_final: 0.5149 (mp) REVERT: L 521 ASP cc_start: 0.6154 (t70) cc_final: 0.5838 (t0) outliers start: 189 outliers final: 108 residues processed: 546 average time/residue: 0.1755 time to fit residues: 160.9022 Evaluate side-chains 519 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 387 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 99 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 478 ARG Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1186 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain I residue 1292 THR Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 136 GLU Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 885 VAL Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 917 VAL Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1017 VAL Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1052 GLU Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1113 VAL Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1204 VAL Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1257 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 30 HIS Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 288 MET Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain L residue 588 ARG Chi-restraints excluded: chain L residue 591 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 298 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 214 optimal weight: 7.9990 chunk 108 optimal weight: 0.6980 chunk 345 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 271 optimal weight: 0.3980 chunk 260 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 147 GLN ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN J1010 GLN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 30 HIS ** L 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 600 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.145870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.116489 restraints weight = 60936.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115571 restraints weight = 83099.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116358 restraints weight = 72727.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116763 restraints weight = 52066.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.116846 restraints weight = 46486.762| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 32817 Z= 0.135 Angle : 0.675 34.961 44670 Z= 0.340 Chirality : 0.044 0.370 5130 Planarity : 0.004 0.048 5537 Dihedral : 15.609 141.649 5408 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.01 % Favored : 91.96 % Rotamer: Outliers : 4.80 % Allowed : 22.33 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 3845 helix: -0.44 (0.13), residues: 1580 sheet: -1.99 (0.27), residues: 323 loop : -2.06 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I1106 TYR 0.018 0.001 TYR I 123 PHE 0.024 0.001 PHE J 172 TRP 0.032 0.002 TRP L 433 HIS 0.038 0.001 HIS L 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (32808) covalent geometry : angle 0.64560 / 0.34 (44664) hydrogen bonds : bond 0.04089 / 2.75 ( 1248) hydrogen bonds : angle 5.18813 / 3.60 ( 3467) metal coordination : bond 0.01091 / 0.56 ( 9) metal coordination : angle 17.08639 / 9.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 429 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 52 PHE cc_start: 0.7234 (m-80) cc_final: 0.6895 (m-80) REVERT: G 102 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8250 (mm) REVERT: G 143 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6622 (mtp85) REVERT: H 129 VAL cc_start: 0.8450 (p) cc_final: 0.8206 (t) REVERT: H 214 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6347 (mp0) REVERT: I 199 ASP cc_start: 0.6332 (OUTLIER) cc_final: 0.5830 (m-30) REVERT: I 321 LEU cc_start: 0.6799 (mt) cc_final: 0.5962 (tp) REVERT: I 377 THR cc_start: 0.4479 (OUTLIER) cc_final: 0.4068 (m) REVERT: I 409 LEU cc_start: 0.8834 (mm) cc_final: 0.8575 (mt) REVERT: I 496 LYS cc_start: 0.7639 (tttt) cc_final: 0.7121 (pttt) REVERT: I 510 GLN cc_start: 0.6173 (OUTLIER) cc_final: 0.5918 (mp-120) REVERT: I 699 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8232 (tp) REVERT: I 704 MET cc_start: 0.7018 (mmm) cc_final: 0.6319 (mmm) REVERT: I 733 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8788 (m) REVERT: I 750 ILE cc_start: 0.8274 (OUTLIER) cc_final: 0.7911 (pt) REVERT: I 796 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7724 (mp) REVERT: I 865 LEU cc_start: 0.8654 (mm) cc_final: 0.8140 (mp) REVERT: I 1150 ASP cc_start: 0.6181 (p0) cc_final: 0.5896 (p0) REVERT: I 1243 MET cc_start: 0.7769 (tmm) cc_final: 0.7372 (ttp) REVERT: I 1290 MET cc_start: 0.8178 (tpp) cc_final: 0.7692 (tpp) REVERT: J 42 GLU cc_start: 0.6678 (mp0) cc_final: 0.6383 (mt-10) REVERT: J 92 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8425 (p) REVERT: J 120 LEU cc_start: 0.5429 (mt) cc_final: 0.5062 (mp) REVERT: J 130 MET cc_start: 0.6267 (ttt) cc_final: 0.5895 (tmm) REVERT: J 147 ILE cc_start: 0.6805 (OUTLIER) cc_final: 0.6336 (tp) REVERT: J 255 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7039 (tp) REVERT: J 342 LEU cc_start: 0.9186 (tp) cc_final: 0.8881 (tp) REVERT: J 361 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8883 (pp) REVERT: J 429 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8033 (mm) REVERT: J 479 GLU cc_start: 0.6770 (mt-10) cc_final: 0.6480 (mt-10) REVERT: J 527 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8883 (mt) REVERT: J 679 TYR cc_start: 0.6843 (t80) cc_final: 0.6607 (t80) REVERT: J 714 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.5976 (tt0) REVERT: J 788 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7411 (mp) REVERT: J 871 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7775 (tp) REVERT: J 992 LYS cc_start: 0.5575 (mtpt) cc_final: 0.4876 (mmmt) REVERT: J 1093 THR cc_start: 0.4839 (OUTLIER) cc_final: 0.4634 (m) REVERT: J 1244 GLN cc_start: 0.8271 (tp-100) cc_final: 0.8006 (mm-40) REVERT: K 19 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6601 (tp) REVERT: L 118 ASP cc_start: 0.6522 (m-30) cc_final: 0.5932 (t0) REVERT: L 306 PHE cc_start: 0.1427 (t80) cc_final: 0.1038 (t80) REVERT: L 344 LEU cc_start: 0.5912 (mt) cc_final: 0.5701 (pp) REVERT: L 385 ARG cc_start: 0.7912 (mmt90) cc_final: 0.7093 (mmt-90) REVERT: L 511 ILE cc_start: 0.5645 (OUTLIER) cc_final: 0.5026 (mp) REVERT: L 513 ASP cc_start: 0.3764 (OUTLIER) cc_final: 0.3143 (t0) REVERT: L 521 ASP cc_start: 0.6092 (t70) cc_final: 0.5779 (t0) REVERT: L 552 THR cc_start: 0.6752 (OUTLIER) cc_final: 0.6443 (p) outliers start: 159 outliers final: 98 residues processed: 544 average time/residue: 0.1907 time to fit residues: 173.9985 Evaluate side-chains 503 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 381 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain H residue 214 GLU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 478 ARG Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 137 ARG Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 271 ARG Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1093 THR Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 333 VAL Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 513 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain L residue 588 ARG Chi-restraints excluded: chain L residue 600 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 227 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 334 optimal weight: 5.9990 chunk 152 optimal weight: 0.9980 chunk 386 optimal weight: 3.9990 chunk 318 optimal weight: 9.9990 chunk 166 optimal weight: 9.9990 chunk 254 optimal weight: 7.9990 chunk 370 optimal weight: 0.0870 chunk 287 optimal weight: 10.0000 chunk 280 optimal weight: 10.0000 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 600 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.144453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115331 restraints weight = 61144.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114477 restraints weight = 86424.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.115318 restraints weight = 73427.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.115574 restraints weight = 55729.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115748 restraints weight = 49009.870| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 32817 Z= 0.189 Angle : 0.700 32.908 44670 Z= 0.354 Chirality : 0.045 0.375 5130 Planarity : 0.004 0.046 5537 Dihedral : 15.617 142.838 5408 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.40 % Favored : 91.57 % Rotamer: Outliers : 4.98 % Allowed : 22.66 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % 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: -2.00 (0.13), residues: 3845 helix: -0.37 (0.13), residues: 1566 sheet: -1.89 (0.26), residues: 356 loop : -2.04 (0.14), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J1304 TYR 0.020 0.002 TYR I 810 PHE 0.022 0.002 PHE I 253 TRP 0.025 0.002 TRP L 433 HIS 0.013 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.19 (32808) covalent geometry : angle 0.67620 / 0.35 (44664) hydrogen bonds : bond 0.04226 / 2.83 ( 1248) hydrogen bonds : angle 5.19705 / 3.60 ( 3467) metal coordination : bond 0.00886 / 0.48 ( 9) metal coordination : angle 15.77146 / 9.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 389 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8265 (mm) REVERT: G 143 ARG cc_start: 0.7395 (OUTLIER) cc_final: 0.6572 (mtp85) REVERT: H 129 VAL cc_start: 0.8510 (p) cc_final: 0.8275 (t) REVERT: H 191 ARG cc_start: 0.6846 (ptm-80) cc_final: 0.6517 (ptm-80) REVERT: I 199 ASP cc_start: 0.6172 (OUTLIER) cc_final: 0.5665 (m-30) REVERT: I 321 LEU cc_start: 0.6830 (mt) cc_final: 0.6049 (tp) REVERT: I 377 THR cc_start: 0.4365 (OUTLIER) cc_final: 0.4114 (m) REVERT: I 409 LEU cc_start: 0.8855 (mm) cc_final: 0.8581 (mt) REVERT: I 496 LYS cc_start: 0.7678 (tttt) cc_final: 0.7147 (pttt) REVERT: I 510 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.6009 (mp-120) REVERT: I 733 VAL cc_start: 0.9062 (OUTLIER) cc_final: 0.8808 (m) REVERT: I 750 ILE cc_start: 0.8316 (OUTLIER) cc_final: 0.7956 (pt) REVERT: I 796 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7804 (mp) REVERT: I 865 LEU cc_start: 0.8695 (mm) cc_final: 0.8187 (mp) REVERT: I 1150 ASP cc_start: 0.6250 (p0) cc_final: 0.5957 (p0) REVERT: I 1243 MET cc_start: 0.7702 (tmm) cc_final: 0.7326 (ttp) REVERT: I 1290 MET cc_start: 0.8173 (tpp) cc_final: 0.7775 (tpp) REVERT: J 42 GLU cc_start: 0.6467 (mp0) cc_final: 0.6004 (mt-10) REVERT: J 92 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8451 (p) REVERT: J 130 MET cc_start: 0.6294 (ttt) cc_final: 0.5902 (tmm) REVERT: J 147 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6333 (tp) REVERT: J 255 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7029 (tp) REVERT: J 293 ARG cc_start: 0.7139 (ptm160) cc_final: 0.6760 (ptt90) REVERT: J 342 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8867 (tp) REVERT: J 361 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8930 (pp) REVERT: J 429 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8097 (mm) REVERT: J 527 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8854 (mt) REVERT: J 679 TYR cc_start: 0.7050 (t80) cc_final: 0.6677 (t80) REVERT: J 714 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6093 (tt0) REVERT: J 788 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7410 (mp) REVERT: J 871 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7760 (tp) REVERT: J 992 LYS cc_start: 0.5661 (mtpt) cc_final: 0.4897 (mmmt) REVERT: K 19 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6660 (tp) REVERT: L 11 LEU cc_start: 0.6117 (tt) cc_final: 0.5033 (mt) REVERT: L 118 ASP cc_start: 0.6537 (m-30) cc_final: 0.5791 (t0) REVERT: L 288 MET cc_start: 0.1308 (mtp) cc_final: 0.0952 (mtp) REVERT: L 511 ILE cc_start: 0.5792 (OUTLIER) cc_final: 0.5103 (mp) REVERT: L 552 THR cc_start: 0.6807 (OUTLIER) cc_final: 0.6602 (p) outliers start: 165 outliers final: 118 residues processed: 505 average time/residue: 0.1948 time to fit residues: 164.0070 Evaluate side-chains 509 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 370 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 124 MET Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 226 GLU Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 478 ARG Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 271 ARG Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 871 LEU Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1052 GLU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain L residue 588 ARG Chi-restraints excluded: chain M residue 288 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 192 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 342 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 270 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 287 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 66 HIS ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I1268 GLN ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 600 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.144217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.115594 restraints weight = 61455.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.114944 restraints weight = 80290.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.115661 restraints weight = 73116.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.115882 restraints weight = 54215.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.116026 restraints weight = 48009.476| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 32817 Z= 0.203 Angle : 0.713 31.056 44670 Z= 0.361 Chirality : 0.046 0.377 5130 Planarity : 0.005 0.046 5537 Dihedral : 15.634 143.516 5408 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.71 % Favored : 91.26 % Rotamer: Outliers : 5.16 % Allowed : 22.72 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % 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: -2.03 (0.13), residues: 3845 helix: -0.43 (0.13), residues: 1575 sheet: -1.87 (0.26), residues: 361 loop : -2.04 (0.14), residues: 1909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 385 TYR 0.020 0.002 TYR I 810 PHE 0.026 0.002 PHE J 172 TRP 0.019 0.002 TRP I 997 HIS 0.006 0.001 HIS I1070 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (32808) covalent geometry : angle 0.69216 / 0.36 (44664) hydrogen bonds : bond 0.04313 / 2.89 ( 1248) hydrogen bonds : angle 5.20304 / 3.60 ( 3467) metal coordination : bond 0.00982 / 0.52 ( 9) metal coordination : angle 14.77525 / 8.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 383 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8435 (mm) REVERT: G 143 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6597 (mtp85) REVERT: H 129 VAL cc_start: 0.8487 (p) cc_final: 0.8281 (t) REVERT: H 191 ARG cc_start: 0.6814 (ptm-80) cc_final: 0.6519 (ptm-80) REVERT: I 199 ASP cc_start: 0.6143 (OUTLIER) cc_final: 0.5633 (m-30) REVERT: I 321 LEU cc_start: 0.6967 (mt) cc_final: 0.6015 (tp) REVERT: I 377 THR cc_start: 0.4363 (OUTLIER) cc_final: 0.4136 (m) REVERT: I 409 LEU cc_start: 0.8856 (mm) cc_final: 0.8584 (mt) REVERT: I 496 LYS cc_start: 0.7734 (tttt) cc_final: 0.7153 (pttt) REVERT: I 510 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.6015 (mp-120) REVERT: I 733 VAL cc_start: 0.9078 (OUTLIER) cc_final: 0.8835 (m) REVERT: I 750 ILE cc_start: 0.8297 (OUTLIER) cc_final: 0.7942 (pt) REVERT: I 796 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7661 (mp) REVERT: I 865 LEU cc_start: 0.8711 (mm) cc_final: 0.8247 (mp) REVERT: I 979 LEU cc_start: 0.5030 (OUTLIER) cc_final: 0.4551 (mm) REVERT: I 1150 ASP cc_start: 0.6300 (p0) cc_final: 0.5999 (p0) REVERT: I 1243 MET cc_start: 0.7743 (tmm) cc_final: 0.7325 (ttp) REVERT: I 1290 MET cc_start: 0.8189 (tpp) cc_final: 0.7820 (tpp) REVERT: J 42 GLU cc_start: 0.6429 (mp0) cc_final: 0.6023 (mt-10) REVERT: J 92 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8461 (p) REVERT: J 130 MET cc_start: 0.6298 (ttt) cc_final: 0.5837 (ttm) REVERT: J 147 ILE cc_start: 0.6785 (OUTLIER) cc_final: 0.6338 (tp) REVERT: J 255 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7011 (tp) REVERT: J 342 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8903 (tp) REVERT: J 361 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.8954 (pp) REVERT: J 429 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8083 (mm) REVERT: J 527 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8834 (mt) REVERT: J 679 TYR cc_start: 0.7032 (t80) cc_final: 0.6687 (t80) REVERT: J 714 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6069 (tt0) REVERT: J 788 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7452 (mp) REVERT: J 992 LYS cc_start: 0.5695 (mtpt) cc_final: 0.4873 (mmmt) REVERT: K 12 LYS cc_start: 0.6748 (mmtm) cc_final: 0.6525 (mmtm) REVERT: L 11 LEU cc_start: 0.6157 (tt) cc_final: 0.5024 (mt) REVERT: L 118 ASP cc_start: 0.6290 (m-30) cc_final: 0.5659 (t0) REVERT: L 306 PHE cc_start: 0.1999 (t80) cc_final: 0.0596 (t80) REVERT: L 511 ILE cc_start: 0.5854 (OUTLIER) cc_final: 0.5210 (mp) outliers start: 171 outliers final: 123 residues processed: 508 average time/residue: 0.1923 time to fit residues: 163.8715 Evaluate side-chains 511 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 369 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 16 THR Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 127 ILE Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 164 THR Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 426 ILE Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 453 ILE Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 478 ARG Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 533 LEU Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 635 THR Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 802 VAL Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 882 ILE Chi-restraints excluded: chain I residue 920 VAL Chi-restraints excluded: chain I residue 966 ILE Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1050 VAL Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1240 ASP Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 92 VAL Chi-restraints excluded: chain J residue 95 THR Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 238 ILE Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 271 ARG Chi-restraints excluded: chain J residue 291 ILE Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 552 ILE Chi-restraints excluded: chain J residue 617 THR Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 847 ASP Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 908 ILE Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1052 GLU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1266 ILE Chi-restraints excluded: chain J residue 1285 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 39 VAL Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 505 ILE Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 572 THR Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain L residue 588 ARG Chi-restraints excluded: chain L residue 600 HIS Chi-restraints excluded: chain M residue 288 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 301 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 144 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 240 optimal weight: 2.9990 chunk 239 optimal weight: 4.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 66 HIS ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 343 HIS ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 762 ASN ** K 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.116884 restraints weight = 61152.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.116095 restraints weight = 83928.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.116830 restraints weight = 74438.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117257 restraints weight = 53493.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117395 restraints weight = 46226.607| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 32817 Z= 0.136 Angle : 0.670 27.653 44670 Z= 0.341 Chirality : 0.044 0.371 5130 Planarity : 0.004 0.068 5537 Dihedral : 15.519 142.411 5408 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.93 % Favored : 92.04 % Rotamer: Outliers : 4.16 % Allowed : 23.63 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.13), residues: 3845 helix: -0.27 (0.13), residues: 1570 sheet: -1.80 (0.27), residues: 362 loop : -1.97 (0.14), residues: 1913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 293 TYR 0.022 0.002 TYR J 349 PHE 0.029 0.001 PHE I 253 TRP 0.015 0.001 TRP I 997 HIS 0.018 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (32808) covalent geometry : angle 0.65225 / 0.34 (44664) hydrogen bonds : bond 0.03999 / 2.67 ( 1248) hydrogen bonds : angle 5.06012 / 3.50 ( 3467) metal coordination : bond 0.00840 / 0.44 ( 9) metal coordination : angle 13.18499 / 7.65 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 393 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 102 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8385 (mm) REVERT: G 143 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.6552 (mtp85) REVERT: I 199 ASP cc_start: 0.6124 (OUTLIER) cc_final: 0.5597 (m-30) REVERT: I 284 LEU cc_start: 0.5944 (tp) cc_final: 0.5466 (tt) REVERT: I 321 LEU cc_start: 0.6812 (mt) cc_final: 0.6049 (tp) REVERT: I 409 LEU cc_start: 0.8881 (mm) cc_final: 0.8637 (mt) REVERT: I 496 LYS cc_start: 0.7672 (tttt) cc_final: 0.7122 (pttt) REVERT: I 510 GLN cc_start: 0.6208 (OUTLIER) cc_final: 0.5947 (mp-120) REVERT: I 704 MET cc_start: 0.7225 (mmm) cc_final: 0.6540 (mmm) REVERT: I 733 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8807 (m) REVERT: I 750 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7820 (pt) REVERT: I 796 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7693 (mp) REVERT: I 865 LEU cc_start: 0.8647 (mm) cc_final: 0.8139 (mp) REVERT: I 979 LEU cc_start: 0.5053 (OUTLIER) cc_final: 0.4565 (mm) REVERT: I 1150 ASP cc_start: 0.6350 (p0) cc_final: 0.6018 (p0) REVERT: I 1243 MET cc_start: 0.7734 (tmm) cc_final: 0.7350 (ttp) REVERT: I 1290 MET cc_start: 0.8121 (tpp) cc_final: 0.7717 (tpp) REVERT: J 42 GLU cc_start: 0.6468 (mp0) cc_final: 0.6021 (mt-10) REVERT: J 130 MET cc_start: 0.6190 (ttt) cc_final: 0.5840 (tmm) REVERT: J 147 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6318 (tp) REVERT: J 255 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.6979 (tp) REVERT: J 342 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8926 (tp) REVERT: J 361 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8897 (pp) REVERT: J 429 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8072 (mm) REVERT: J 527 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8892 (mt) REVERT: J 679 TYR cc_start: 0.6977 (t80) cc_final: 0.6572 (t80) REVERT: J 714 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6145 (tt0) REVERT: J 770 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8189 (tp) REVERT: J 788 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7239 (mp) REVERT: J 992 LYS cc_start: 0.5650 (mtpt) cc_final: 0.4924 (mmmt) REVERT: K 19 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6672 (tp) REVERT: L 11 LEU cc_start: 0.6108 (tt) cc_final: 0.4977 (mt) REVERT: L 118 ASP cc_start: 0.6348 (m-30) cc_final: 0.5742 (t0) REVERT: L 215 GLU cc_start: -0.0007 (OUTLIER) cc_final: -0.0633 (tp30) REVERT: L 511 ILE cc_start: 0.5761 (OUTLIER) cc_final: 0.5174 (mp) REVERT: L 513 ASP cc_start: 0.3874 (OUTLIER) cc_final: 0.3084 (t0) REVERT: L 552 THR cc_start: 0.6714 (OUTLIER) cc_final: 0.6500 (p) outliers start: 138 outliers final: 96 residues processed: 491 average time/residue: 0.1968 time to fit residues: 161.5039 Evaluate side-chains 491 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 373 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 140 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 129 LEU Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 229 ILE Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 468 LEU Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 478 ARG Chi-restraints excluded: chain I residue 485 ASP Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 510 GLN Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 750 ILE Chi-restraints excluded: chain I residue 773 LEU Chi-restraints excluded: chain I residue 796 LEU Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 271 ARG Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 304 ASP Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 342 LEU Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 932 MET Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1052 GLU Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 471 LEU Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 513 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 552 THR Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 582 VAL Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain L residue 588 ARG Chi-restraints excluded: chain M residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 342 optimal weight: 0.9990 chunk 328 optimal weight: 6.9990 chunk 275 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 186 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 43 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 190 optimal weight: 0.0870 chunk 108 optimal weight: 0.9980 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 66 HIS ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 618 GLN ** I1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 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 = 0.3916 r_free = 0.3916 target = 0.147132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118378 restraints weight = 61593.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.117671 restraints weight = 82738.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118552 restraints weight = 70017.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.118711 restraints weight = 53476.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118849 restraints weight = 47851.812| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32817 Z= 0.127 Angle : 0.663 24.412 44670 Z= 0.337 Chirality : 0.044 0.356 5130 Planarity : 0.004 0.048 5537 Dihedral : 15.404 143.013 5408 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.52 % Favored : 92.46 % Rotamer: Outliers : 3.71 % Allowed : 24.32 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.13), residues: 3845 helix: -0.16 (0.13), residues: 1573 sheet: -1.67 (0.27), residues: 369 loop : -1.92 (0.14), residues: 1903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG H 191 TYR 0.021 0.001 TYR J 349 PHE 0.030 0.001 PHE I 253 TRP 0.016 0.001 TRP I 997 HIS 0.012 0.001 HIS L 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (32808) covalent geometry : angle 0.64862 / 0.34 (44664) hydrogen bonds : bond 0.03847 / 2.57 ( 1248) hydrogen bonds : angle 4.94318 / 3.43 ( 3467) metal coordination : bond 0.00832 / 0.43 ( 9) metal coordination : angle 11.89583 / 6.86 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 407 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 76 GLU cc_start: 0.8058 (mp0) cc_final: 0.7703 (mp0) REVERT: G 102 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8338 (mm) REVERT: G 143 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6478 (mtp85) REVERT: I 199 ASP cc_start: 0.5990 (OUTLIER) cc_final: 0.5447 (m-30) REVERT: I 284 LEU cc_start: 0.5810 (tp) cc_final: 0.5293 (tt) REVERT: I 321 LEU cc_start: 0.6830 (mt) cc_final: 0.6047 (tp) REVERT: I 409 LEU cc_start: 0.8866 (mm) cc_final: 0.8660 (mt) REVERT: I 496 LYS cc_start: 0.7453 (tttt) cc_final: 0.7048 (pttt) REVERT: I 733 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8787 (m) REVERT: I 865 LEU cc_start: 0.8546 (mm) cc_final: 0.8009 (mp) REVERT: I 979 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4676 (mm) REVERT: I 1150 ASP cc_start: 0.6347 (p0) cc_final: 0.5972 (p0) REVERT: I 1243 MET cc_start: 0.7718 (tmm) cc_final: 0.7330 (ttp) REVERT: I 1290 MET cc_start: 0.8081 (tpp) cc_final: 0.7685 (tpp) REVERT: J 42 GLU cc_start: 0.6536 (mp0) cc_final: 0.6061 (mt-10) REVERT: J 130 MET cc_start: 0.6173 (ttt) cc_final: 0.5774 (tmm) REVERT: J 147 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6500 (tp) REVERT: J 255 LEU cc_start: 0.7489 (OUTLIER) cc_final: 0.6977 (tp) REVERT: J 361 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8926 (pp) REVERT: J 429 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8005 (mm) REVERT: J 527 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8742 (mt) REVERT: J 679 TYR cc_start: 0.6906 (t80) cc_final: 0.6514 (t80) REVERT: J 714 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.6137 (tt0) REVERT: J 770 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8101 (tp) REVERT: J 788 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7239 (mp) REVERT: J 867 GLN cc_start: 0.6288 (mp10) cc_final: 0.5824 (tm-30) REVERT: J 992 LYS cc_start: 0.5695 (mtpt) cc_final: 0.4965 (mmmt) REVERT: K 19 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6529 (tp) REVERT: L 11 LEU cc_start: 0.6089 (tt) cc_final: 0.5025 (mt) REVERT: L 56 MET cc_start: 0.1402 (mmp) cc_final: 0.0961 (tpt) REVERT: L 118 ASP cc_start: 0.5840 (m-30) cc_final: 0.5424 (t0) REVERT: L 215 GLU cc_start: -0.0008 (OUTLIER) cc_final: -0.0611 (tp30) REVERT: L 511 ILE cc_start: 0.5654 (OUTLIER) cc_final: 0.5081 (mp) REVERT: L 513 ASP cc_start: 0.3629 (OUTLIER) cc_final: 0.3089 (t0) outliers start: 123 outliers final: 84 residues processed: 493 average time/residue: 0.1941 time to fit residues: 160.3888 Evaluate side-chains 471 residues out of total 3324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 370 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 44 ILE Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 74 VAL Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 124 VAL Chi-restraints excluded: chain G residue 143 ARG Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain H residue 16 ILE Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain H residue 172 LEU Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 202 VAL Chi-restraints excluded: chain H residue 203 ILE Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 173 ASN Chi-restraints excluded: chain I residue 199 ASP Chi-restraints excluded: chain I residue 216 THR Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 250 THR Chi-restraints excluded: chain I residue 263 VAL Chi-restraints excluded: chain I residue 289 VAL Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 434 ASP Chi-restraints excluded: chain I residue 442 VAL Chi-restraints excluded: chain I residue 469 VAL Chi-restraints excluded: chain I residue 478 ARG Chi-restraints excluded: chain I residue 492 MET Chi-restraints excluded: chain I residue 502 VAL Chi-restraints excluded: chain I residue 550 VAL Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 699 LEU Chi-restraints excluded: chain I residue 733 VAL Chi-restraints excluded: chain I residue 818 VAL Chi-restraints excluded: chain I residue 979 LEU Chi-restraints excluded: chain I residue 1029 LEU Chi-restraints excluded: chain I residue 1049 ILE Chi-restraints excluded: chain I residue 1169 VAL Chi-restraints excluded: chain I residue 1225 VAL Chi-restraints excluded: chain I residue 1238 LEU Chi-restraints excluded: chain I residue 1244 HIS Chi-restraints excluded: chain J residue 44 ILE Chi-restraints excluded: chain J residue 46 TYR Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 120 LEU Chi-restraints excluded: chain J residue 145 VAL Chi-restraints excluded: chain J residue 147 ILE Chi-restraints excluded: chain J residue 160 LEU Chi-restraints excluded: chain J residue 171 GLU Chi-restraints excluded: chain J residue 252 LEU Chi-restraints excluded: chain J residue 253 VAL Chi-restraints excluded: chain J residue 255 LEU Chi-restraints excluded: chain J residue 267 ASP Chi-restraints excluded: chain J residue 271 ARG Chi-restraints excluded: chain J residue 327 LEU Chi-restraints excluded: chain J residue 338 PHE Chi-restraints excluded: chain J residue 361 LEU Chi-restraints excluded: chain J residue 429 LEU Chi-restraints excluded: chain J residue 526 VAL Chi-restraints excluded: chain J residue 527 LEU Chi-restraints excluded: chain J residue 654 ILE Chi-restraints excluded: chain J residue 706 VAL Chi-restraints excluded: chain J residue 714 GLU Chi-restraints excluded: chain J residue 717 VAL Chi-restraints excluded: chain J residue 769 VAL Chi-restraints excluded: chain J residue 770 LEU Chi-restraints excluded: chain J residue 788 LEU Chi-restraints excluded: chain J residue 807 LEU Chi-restraints excluded: chain J residue 858 VAL Chi-restraints excluded: chain J residue 870 ASP Chi-restraints excluded: chain J residue 895 CYS Chi-restraints excluded: chain J residue 918 ILE Chi-restraints excluded: chain J residue 923 ILE Chi-restraints excluded: chain J residue 1031 VAL Chi-restraints excluded: chain J residue 1196 LEU Chi-restraints excluded: chain J residue 1209 VAL Chi-restraints excluded: chain J residue 1237 VAL Chi-restraints excluded: chain J residue 1289 ASN Chi-restraints excluded: chain J residue 1316 THR Chi-restraints excluded: chain J residue 1370 MET Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 19 LEU Chi-restraints excluded: chain K residue 46 THR Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 212 ILE Chi-restraints excluded: chain L residue 215 GLU Chi-restraints excluded: chain L residue 452 ILE Chi-restraints excluded: chain L residue 458 GLU Chi-restraints excluded: chain L residue 463 LEU Chi-restraints excluded: chain L residue 507 MET Chi-restraints excluded: chain L residue 511 ILE Chi-restraints excluded: chain L residue 513 ASP Chi-restraints excluded: chain L residue 526 THR Chi-restraints excluded: chain L residue 567 MET Chi-restraints excluded: chain L residue 583 THR Chi-restraints excluded: chain L residue 588 ARG Chi-restraints excluded: chain M residue 288 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 90 optimal weight: 8.9990 chunk 334 optimal weight: 5.9990 chunk 139 optimal weight: 0.7980 chunk 221 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 322 optimal weight: 8.9990 chunk 223 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 164 optimal weight: 0.0060 chunk 154 optimal weight: 0.4980 chunk 162 optimal weight: 4.9990 overall best weight: 1.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 66 HIS ** I 339 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 200 GLN ** J 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 409 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 = 0.3906 r_free = 0.3906 target = 0.146300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.117194 restraints weight = 61476.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.116276 restraints weight = 90176.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.117380 restraints weight = 76103.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.117400 restraints weight = 58763.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117654 restraints weight = 49522.685| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 32817 Z= 0.148 Angle : 0.674 21.446 44670 Z= 0.344 Chirality : 0.044 0.346 5130 Planarity : 0.004 0.048 5537 Dihedral : 15.380 143.695 5408 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.72 % Favored : 92.25 % Rotamer: Outliers : 3.53 % Allowed : 24.80 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.32 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.13), residues: 3845 helix: -0.13 (0.13), residues: 1567 sheet: -1.70 (0.26), residues: 388 loop : -1.88 (0.14), residues: 1890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 293 TYR 0.022 0.002 TYR J 349 PHE 0.027 0.001 PHE I 253 TRP 0.018 0.002 TRP L 315 HIS 0.005 0.001 HIS I 673 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (32808) covalent geometry : angle 0.66232 / 0.34 (44664) hydrogen bonds : bond 0.03926 / 2.63 ( 1248) hydrogen bonds : angle 4.91399 / 3.40 ( 3467) metal coordination : bond 0.01015 / 0.53 ( 9) metal coordination : angle 10.77858 / 6.13 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5095.88 seconds wall clock time: 89 minutes 23.09 seconds (5363.09 seconds total)